From bef5ca67b0a8f2581bced50abf64ece3ff593cda Mon Sep 17 00:00:00 2001 From: leandrohw Date: Tue, 28 Feb 2017 14:38:28 -0700 Subject: [PATCH] Added license header to source code files --- .gitignore | 1 + bin/ATACSGUI.bat | 13 +++++++++++++ bin/LEMA.bat | 13 +++++++++++++ bin/apply_post_filter.pl | 13 +++++++++++++ bin/checkHpn.pl | 13 +++++++++++++ bin/check_dot.pl | 13 +++++++++++++ bin/detect-java.sh | 13 +++++++++++++ bin/gcm2sbml.pl | 13 +++++++++++++ bin/genBackgroundGCM.pl | 13 +++++++++++++ bin/gen_GeneNet_report.pl | 13 +++++++++++++ bin/iBioSim.bat | 13 +++++++++++++ bin/remote.sh | 13 +++++++++++++ bin/remoteATACS.sh | 13 +++++++++++++ bin/remoteTangATACS.sh | 13 +++++++++++++ bin/remoteTangSim.sh | 13 +++++++++++++ makeATACS.sh | 13 +++++++++++++ makeATACS64.sh | 13 +++++++++++++ makeLEMA.sh | 13 +++++++++++++ makeLEMA64.sh | 13 +++++++++++++ makedmg.sh | 13 +++++++++++++ makedmg64.sh | 13 +++++++++++++ .../analysis/dynamicsim/DynamicSimulation.java | 13 +++++++++++++ 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src/frontend/biomodel/gui/comp/GridPanel.java | 13 +++++++++++++ src/frontend/biomodel/gui/fba/FBAObjective.java | 13 +++++++++++++ src/frontend/biomodel/gui/gcm/InfluencePanel.java | 13 +++++++++++++ src/frontend/biomodel/gui/gcm/PromoterPanel.java | 13 +++++++++++++ .../biomodel/gui/movie/MovieAppearance.java | 13 +++++++++++++ src/frontend/biomodel/gui/movie/MovieContainer.java | 13 +++++++++++++ src/frontend/biomodel/gui/movie/MovieScheme.java | 13 +++++++++++++ .../biomodel/gui/movie/SchemeChooserPanel.java | 13 +++++++++++++ .../biomodel/gui/movie/SerializableScheme.java | 13 +++++++++++++ .../biomodel/gui/sbmlcore/Compartments.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbmlcore/Constraints.java | 13 +++++++++++++ .../biomodel/gui/sbmlcore/ElementsPanel.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbmlcore/Events.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbmlcore/Functions.java | 13 +++++++++++++ .../biomodel/gui/sbmlcore/InitialAssignments.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbmlcore/ModelPanel.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbmlcore/MySpecies.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbmlcore/Parameters.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbmlcore/Reactions.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbmlcore/Rules.java | 13 +++++++++++++ .../biomodel/gui/sbmlcore/SpeciesPanel.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbmlcore/Units.java | 13 +++++++++++++ .../biomodel/gui/sbol/SBOLAssociationPanel2.java | 13 +++++++++++++ .../biomodel/gui/sbol/SBOLDescriptorPanel2.java | 13 +++++++++++++ src/frontend/biomodel/gui/sbol/SBOLField2.java | 13 +++++++++++++ src/frontend/biomodel/gui/schematic/BioGraph.java | 13 +++++++++++++ .../biomodel/gui/schematic/EditorPopupMenu.java | 13 +++++++++++++ src/frontend/biomodel/gui/schematic/Layouting.java | 13 +++++++++++++ .../biomodel/gui/schematic/ListChooser.java | 13 +++++++++++++ .../biomodel/gui/schematic/ModelEditor.java | 13 +++++++++++++ .../biomodel/gui/schematic/ModelToolBar.java | 13 +++++++++++++ src/frontend/biomodel/gui/schematic/Schematic.java | 13 +++++++++++++ .../biomodel/gui/schematic/TreeChooser.java | 13 +++++++++++++ src/frontend/biomodel/gui/schematic/Utils.java | 13 +++++++++++++ .../gui/util/AbstractRunnableNamedButton.java | 13 +++++++++++++ src/frontend/biomodel/gui/util/ComponentAction.java | 13 +++++++++++++ src/frontend/biomodel/gui/util/EnableElement.java | 13 +++++++++++++ src/frontend/biomodel/gui/util/FieldPanel.java | 13 +++++++++++++ src/frontend/biomodel/gui/util/NamedObject.java | 13 +++++++++++++ src/frontend/biomodel/gui/util/PropertyField.java | 13 +++++++++++++ src/frontend/biomodel/gui/util/PropertyList.java | 13 +++++++++++++ .../biomodel/gui/util/PropertyProvider.java | 13 +++++++++++++ src/frontend/biomodel/gui/util/Runnable.java | 13 +++++++++++++ src/frontend/biomodel/gui/util/StateElement.java | 13 +++++++++++++ src/frontend/biomodel/util/UndoManager.java | 13 +++++++++++++ src/frontend/graph/Graph.java | 13 +++++++++++++ src/frontend/learn/AMSModel/LearnLPN.java | 13 +++++++++++++ src/frontend/learn/GCM/LearnGCM.java | 13 +++++++++++++ src/frontend/learn/datamanager/DataManager.java | 13 +++++++++++++ .../parameterestimator/ParamEstimatorPanel.java | 13 +++++++++++++ src/frontend/lpn/gui/AssignmentPanel.java | 13 +++++++++++++ src/frontend/lpn/gui/ControlFlowPanel.java | 13 +++++++++++++ src/frontend/lpn/gui/LHPNEditor.java | 13 +++++++++++++ src/frontend/lpn/gui/PlacePanel.java | 13 +++++++++++++ src/frontend/lpn/gui/PropertyField.java | 13 +++++++++++++ src/frontend/lpn/gui/PropertyPanel.java | 13 +++++++++++++ src/frontend/lpn/gui/TransitionsPanel.java | 13 +++++++++++++ src/frontend/lpn/gui/VariablesPanel.java | 13 +++++++++++++ src/frontend/main/Gui.java | 13 +++++++++++++ src/frontend/main/Log.java | 13 +++++++++++++ src/frontend/main/util/EditPreferences.java | 13 +++++++++++++ src/frontend/main/util/ExampleFileFilter.java | 2 +- src/frontend/main/util/FileTree.java | 13 +++++++++++++ src/frontend/main/util/SpringUtilities.java | 2 +- src/frontend/main/util/Utility.java | 13 +++++++++++++ .../main/util/tabs/CloseAndMaxTabbedPane.java | 13 +++++++++++++ src/frontend/main/util/tabs/CloseListener.java | 13 +++++++++++++ .../main/util/tabs/CloseTabPaneEnhancedUI.java | 13 +++++++++++++ src/frontend/main/util/tabs/CloseTabPaneUI.java | 2 +- .../main/util/tabs/DoubleClickListener.java | 13 +++++++++++++ src/frontend/main/util/tabs/MaxListener.java | 13 +++++++++++++ .../main/util/tabs/PopupOutsideListener.java | 13 +++++++++++++ .../sbol/browser/CollectionBrowserPanel2.java | 13 +++++++++++++ .../browser/ComponentDefinitionBrowserPanel.java | 13 +++++++++++++ src/frontend/sbol/browser/SBOLBrowser2.java | 13 +++++++++++++ src/frontend/synthesis/async/Synthesis.java | 13 +++++++++++++ src/frontend/synthesis/genetic/SynthesisView.java | 13 +++++++++++++ src/frontend/verification/AbstPane.java | 13 +++++++++++++ src/frontend/verification/ParamEditor.java | 13 +++++++++++++ src/frontend/verification/Verification.java | 13 +++++++++++++ src/test/conversion/ConversionAbstractTests.java | 13 +++++++++++++ src/test/conversion/RoundtripTest.java | 13 +++++++++++++ src/test/gcm2sbml/FieldPanelTest.java | 13 +++++++++++++ src/test/gcm2sbml/GCM2SBMLEditorTest.java | 13 +++++++++++++ src/test/gcm2sbml/GCMFileTest.java | 13 +++++++++++++ src/test/gcm2sbml/GCMParserTest.java | 13 +++++++++++++ src/test/gcm2sbml/GCMScriptTest.java | 13 +++++++++++++ src/test/gcm2sbml/SBMLTest.java | 13 +++++++++++++ src/test/gcm2sbml/ScriptTest.java | 13 +++++++++++++ src/test/gcm2sbml/SpeciesThresholdTesterTest.java | 13 +++++++++++++ src/test/gcm2sbml/UtilityTest.java | 13 +++++++++++++ src/test/scripts/AbstractTester.java | 13 +++++++++++++ src/test/scripts/GCMScript.java | 13 +++++++++++++ src/test/scripts/ProbabilityScript.java | 13 +++++++++++++ src/test/scripts/SpeciesThresholdTester.java | 13 +++++++++++++ src/test/scripts/TesterInterface.java | 13 +++++++++++++ src/test/scripts/TimingScript.java | 13 +++++++++++++ 470 files changed, 6062 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 2a23974b8..f30d2cf03 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ /dist/ /target/ jsbml.log +/bin/ diff --git a/bin/ATACSGUI.bat b/bin/ATACSGUI.bat index 2da83683a..a172bf25e 100755 --- a/bin/ATACSGUI.bat +++ b/bin/ATACSGUI.bat @@ -1,3 +1,16 @@ +@rem *************************************************************************** +@rem +@rem This file is part of iBioSim. Please visit +@rem for the latest version of iBioSim. +@rem +@rem Copyright (C) 2017 University of Utah +@rem +@rem This library is free software; you can redistribute it and/or modify it +@rem under the terms of the Apache License. A copy of the license agreement is provided +@rem in the file named "LICENSE.txt" included with this software distribution +@rem and also available online at . +@rem +@rem *************************************************************************** setlocal ENABLEDELAYEDEXPANSION set CLASSPATH="%ATACSGUI%\gui\dist\classes" for /f %%a IN ('dir /b "%ATACSGUI%\gui\lib\*.jar"') do call set CLASSPATH=!CLASSPATH!;"%ATACSGUI%\gui\lib\%%a" diff --git a/bin/LEMA.bat b/bin/LEMA.bat index fb7acd071..4b1d1e4d0 100644 --- a/bin/LEMA.bat +++ b/bin/LEMA.bat @@ -1,3 +1,16 @@ +@rem *************************************************************************** +@rem +@rem This file is part of iBioSim. Please visit +@rem for the latest version of iBioSim. +@rem +@rem Copyright (C) 2017 University of Utah +@rem +@rem This library is free software; you can redistribute it and/or modify it +@rem under the terms of the Apache License. A copy of the license agreement is provided +@rem in the file named "LICENSE.txt" included with this software distribution +@rem and also available online at . +@rem +@rem *************************************************************************** setlocal ENABLEDELAYEDEXPANSION set CLASSPATH="%LEMA%\gui\dist\classes" for /f %%a IN ('dir /b "%LEMA%\gui\lib\*.jar"') do call set CLASSPATH=!CLASSPATH!;"%LEMA%\gui\lib\%%a" diff --git a/bin/apply_post_filter.pl b/bin/apply_post_filter.pl index 92fac5f7d..6dcb118f6 100755 --- a/bin/apply_post_filter.pl +++ b/bin/apply_post_filter.pl @@ -1,4 +1,17 @@ #!/usr/bin/perl +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* if ($#ARGV != 3){ print "Usage: ./recheck_results.pl cutoff file_method_dot file_correct.dot file_output\n"; diff --git a/bin/checkHpn.pl b/bin/checkHpn.pl index 1f6ac682c..5256f98db 100755 --- a/bin/checkHpn.pl +++ b/bin/checkHpn.pl @@ -1,4 +1,17 @@ #!/usr/bin/perl +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* ############################################################################### ## diff --git a/bin/check_dot.pl b/bin/check_dot.pl index 759452d74..75b80e4a2 100755 --- a/bin/check_dot.pl +++ b/bin/check_dot.pl @@ -1,4 +1,17 @@ #!/usr/bin/perl +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* #This file writes the checked dot file. diff --git a/bin/detect-java.sh b/bin/detect-java.sh index 02fe2ae76..00ec19ee2 100755 --- a/bin/detect-java.sh +++ b/bin/detect-java.sh @@ -1,4 +1,17 @@ #!/bin/bash +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* # This script attempts to find an existing installation of Java that meets a minimum version # requirement on a Linux machine. If it is successful, it will export a JAVA_HOME environment # variable that can be used by another calling script. diff --git a/bin/gcm2sbml.pl b/bin/gcm2sbml.pl index 53d45420f..faa2db0c5 100755 --- a/bin/gcm2sbml.pl +++ b/bin/gcm2sbml.pl @@ -1,4 +1,17 @@ #!/usr/bin/perl -w +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* use Getopt::Std; diff --git a/bin/genBackgroundGCM.pl b/bin/genBackgroundGCM.pl index 37ce89695..9a9b2f1fe 100755 --- a/bin/genBackgroundGCM.pl +++ b/bin/genBackgroundGCM.pl @@ -1,4 +1,17 @@ #!/usr/bin/perl +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* open (IN, "run-1.tsd"); @in = ; diff --git a/bin/gen_GeneNet_report.pl b/bin/gen_GeneNet_report.pl index 41bf0669f..a77c56954 100755 --- a/bin/gen_GeneNet_report.pl +++ b/bin/gen_GeneNet_report.pl @@ -1,4 +1,17 @@ #!/usr/bin/perl +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* $genenet_dir = $ARGV[0]; diff --git a/bin/iBioSim.bat b/bin/iBioSim.bat index 6d93154d8..ffcfa2498 100755 --- a/bin/iBioSim.bat +++ b/bin/iBioSim.bat @@ -1,3 +1,16 @@ +@rem *************************************************************************** +@rem +@rem This file is part of iBioSim. Please visit +@rem for the latest version of iBioSim. +@rem +@rem Copyright (C) 2017 University of Utah +@rem +@rem This library is free software; you can redistribute it and/or modify it +@rem under the terms of the Apache License. A copy of the license agreement is provided +@rem in the file named "LICENSE.txt" included with this software distribution +@rem and also available online at . +@rem +@rem *************************************************************************** setlocal ENABLEDELAYEDEXPANSION set CLASSPATH="%BIOSIM%\gui\dist\classes" for /f %%a IN ('dir /b "%BIOSIM%\gui\lib\*.jar"') do call set CLASSPATH=!CLASSPATH!;"%BIOSIM%\gui\lib\%%a" diff --git a/bin/remote.sh b/bin/remote.sh index 2631a0942..25681dccc 100755 --- a/bin/remote.sh +++ b/bin/remote.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* scp $2.xml $1:/tmp/. scp $2.properties $1:/tmp/. ssh $1 "reb2sac --target.encoding=$3 /tmp/$2.xml" diff --git a/bin/remoteATACS.sh b/bin/remoteATACS.sh index 61727562d..42bb6a896 100755 --- a/bin/remoteATACS.sh +++ b/bin/remoteATACS.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* scp $3.lpn $1:/tmp/. ssh $1 "atacs $2 /tmp/$3.lpn" scp $1:"atacs.log" . diff --git a/bin/remoteTangATACS.sh b/bin/remoteTangATACS.sh index dcd47428f..1cf6a85d3 100755 --- a/bin/remoteTangATACS.sh +++ b/bin/remoteTangATACS.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* scp $2.lpn tang.ece.utah.edu:/tmp/. ssh tang.ece.utah.edu "/home/tang/myers/BioSim/bin/atacs $1 /tmp/$2.lpn" scp tang.ece.utah.edu:"atacs.log" . diff --git a/bin/remoteTangSim.sh b/bin/remoteTangSim.sh index aeac42e96..294340f01 100755 --- a/bin/remoteTangSim.sh +++ b/bin/remoteTangSim.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* scp $1.xml tang.ece.utah.edu:/tmp/. scp $1.properties tang.ece.utah.edu:/tmp/. ssh tang.ece.utah.edu "setenv LD_LIBRARY_PATH /home/tang/myers/BioSim/lib64;/home/tang/myers/BioSim/bin/reb2sac --target.encoding=$2 /tmp/$1.xml" diff --git a/makeATACS.sh b/makeATACS.sh index b95429db2..c903e976f 100755 --- a/makeATACS.sh +++ b/makeATACS.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* cp bin/*.py /Applications/ATACS.app/Contents/Resources/bin/. cp bin/*.pyc /Applications/ATACS.app/Contents/Resources/bin/. cp bin/atacs /Applications/ATACS.app/Contents/Resources/bin/. diff --git a/makeATACS64.sh b/makeATACS64.sh index 7a873a1db..667cb426c 100755 --- a/makeATACS64.sh +++ b/makeATACS64.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* cp bin/*.py /Applications/ATACS.app/Contents/Resources/bin/. cp bin/*.pyc /Applications/ATACS.app/Contents/Resources/bin/. cp bin/atacs /Applications/ATACS.app/Contents/Resources/bin/. diff --git a/makeLEMA.sh b/makeLEMA.sh index 105fb8b4d..ab0034ce4 100755 --- a/makeLEMA.sh +++ b/makeLEMA.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* cp bin/*.py /Applications/LEMA.app/Contents/Resources/bin/. cp bin/*.pyc /Applications/LEMA.app/Contents/Resources/bin/. cp bin/atacs /Applications/LEMA.app/Contents/Resources/bin/. diff --git a/makeLEMA64.sh b/makeLEMA64.sh index 742e5ef6c..e4720df8b 100755 --- a/makeLEMA64.sh +++ b/makeLEMA64.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* cp bin/*.py /Applications/LEMA.app/Contents/Resources/bin/. cp bin/*.pyc /Applications/LEMA.app/Contents/Resources/bin/. cp bin/reb2sac.mac64 /Applications/iBioSim.app/Contents/Resources/bin/reb2sac diff --git a/makedmg.sh b/makedmg.sh index d3002d502..a81d27f85 100755 --- a/makedmg.sh +++ b/makedmg.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* cp bin/*.pl /Applications/iBioSim.app/Contents/Resources/bin/. cp bin/reb2sac /Applications/iBioSim.app/Contents/Resources/bin/. cp bin/GeneNet /Applications/iBioSim.app/Contents/Resources/bin/. diff --git a/makedmg64.sh b/makedmg64.sh index 4c809ff61..555e60e15 100755 --- a/makedmg64.sh +++ b/makedmg64.sh @@ -1,4 +1,17 @@ #!/bin/sh +#******************************************************************************* +# +# This file is part of iBioSim. Please visit +# for the latest version of iBioSim. +# +# Copyright (C) 2017 University of Utah +# +# This library is free software; you can redistribute it and/or modify it +# under the terms of the Apache License. A copy of the license agreement is provided +# in the file named "LICENSE.txt" included with this software distribution +# and also available online at . +# +#******************************************************************************* cp bin/*.pl /Applications/iBioSim.app/Contents/Resources/bin/. cp bin/reb2sac.mac64 /Applications/iBioSim.app/Contents/Resources/bin/reb2sac cp bin/GeneNet.mac64 /Applications/iBioSim.app/Contents/Resources/bin/GeneNet diff --git a/src/backend/analysis/dynamicsim/DynamicSimulation.java b/src/backend/analysis/dynamicsim/DynamicSimulation.java index b6ac5f477..6d7f3b0de 100644 --- a/src/backend/analysis/dynamicsim/DynamicSimulation.java +++ b/src/backend/analysis/dynamicsim/DynamicSimulation.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim; import java.awt.Dimension; diff --git a/src/backend/analysis/dynamicsim/ParentSimulator.java b/src/backend/analysis/dynamicsim/ParentSimulator.java index 61fdb2e6a..3f535b380 100644 --- a/src/backend/analysis/dynamicsim/ParentSimulator.java +++ b/src/backend/analysis/dynamicsim/ParentSimulator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim; import java.io.IOException; diff --git a/src/backend/analysis/dynamicsim/flattened/DynSim.java b/src/backend/analysis/dynamicsim/flattened/DynSim.java index 97201677f..d1abce325 100644 --- a/src/backend/analysis/dynamicsim/flattened/DynSim.java +++ b/src/backend/analysis/dynamicsim/flattened/DynSim.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.flattened; import java.io.File; diff --git a/src/backend/analysis/dynamicsim/flattened/Simulator.java b/src/backend/analysis/dynamicsim/flattened/Simulator.java index 9c17c8c1b..cc492c162 100644 --- a/src/backend/analysis/dynamicsim/flattened/Simulator.java +++ b/src/backend/analysis/dynamicsim/flattened/Simulator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.flattened; import flanagan.math.Fmath; diff --git a/src/backend/analysis/dynamicsim/flattened/SimulatorODERK.java b/src/backend/analysis/dynamicsim/flattened/SimulatorODERK.java index 846ecbdea..505977ae3 100644 --- a/src/backend/analysis/dynamicsim/flattened/SimulatorODERK.java +++ b/src/backend/analysis/dynamicsim/flattened/SimulatorODERK.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.flattened; import java.io.IOException; diff --git a/src/backend/analysis/dynamicsim/flattened/SimulatorSSACR.java b/src/backend/analysis/dynamicsim/flattened/SimulatorSSACR.java index db8d3c233..1f07ae897 100644 --- a/src/backend/analysis/dynamicsim/flattened/SimulatorSSACR.java +++ b/src/backend/analysis/dynamicsim/flattened/SimulatorSSACR.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.flattened; import gnu.trove.map.hash.TIntDoubleHashMap; diff --git a/src/backend/analysis/dynamicsim/flattened/SimulatorSSADirect.java b/src/backend/analysis/dynamicsim/flattened/SimulatorSSADirect.java index fb54715ab..de5a0ee68 100644 --- a/src/backend/analysis/dynamicsim/flattened/SimulatorSSADirect.java +++ b/src/backend/analysis/dynamicsim/flattened/SimulatorSSADirect.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.flattened; import java.io.IOException; diff --git a/src/backend/analysis/dynamicsim/flattened/SpeciesDimensions.java b/src/backend/analysis/dynamicsim/flattened/SpeciesDimensions.java index 31fba7c3e..67b60b181 100644 --- a/src/backend/analysis/dynamicsim/flattened/SpeciesDimensions.java +++ b/src/backend/analysis/dynamicsim/flattened/SpeciesDimensions.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.flattened; public class SpeciesDimensions { diff --git a/src/backend/analysis/dynamicsim/flattened/XORShiftRandom.java b/src/backend/analysis/dynamicsim/flattened/XORShiftRandom.java index c9b3378b4..0e67a98e6 100644 --- a/src/backend/analysis/dynamicsim/flattened/XORShiftRandom.java +++ b/src/backend/analysis/dynamicsim/flattened/XORShiftRandom.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.flattened; /* diff --git a/src/backend/analysis/dynamicsim/hierarchical/HierarchicalSimulation.java b/src/backend/analysis/dynamicsim/hierarchical/HierarchicalSimulation.java index d5aa869eb..6e541bc40 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/HierarchicalSimulation.java +++ b/src/backend/analysis/dynamicsim/hierarchical/HierarchicalSimulation.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical; import java.io.BufferedWriter; diff --git a/src/backend/analysis/dynamicsim/hierarchical/io/HierarchicalWriter.java b/src/backend/analysis/dynamicsim/hierarchical/io/HierarchicalWriter.java index 1e60c3051..d8a21f2d8 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/io/HierarchicalWriter.java +++ b/src/backend/analysis/dynamicsim/hierarchical/io/HierarchicalWriter.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.io; import java.io.BufferedWriter; diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/AbstractHierarchicalNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/AbstractHierarchicalNode.java index 7b1f697cd..6c57b3a2b 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/AbstractHierarchicalNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/AbstractHierarchicalNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; public abstract class AbstractHierarchicalNode diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/ArrayDimensionNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/ArrayDimensionNode.java index dcfd5d521..a9967c30d 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/ArrayDimensionNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/ArrayDimensionNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; public class ArrayDimensionNode extends VariableNode diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/ArrayNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/ArrayNode.java index e6b3d0617..73a50cc5b 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/ArrayNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/ArrayNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; import java.util.ArrayList; diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/ConstraintNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/ConstraintNode.java index 5e7b90ba1..7aad5162f 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/ConstraintNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/ConstraintNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; public class ConstraintNode extends HierarchicalNode diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/Evaluator.java b/src/backend/analysis/dynamicsim/hierarchical/math/Evaluator.java index 23b831473..4acf85faf 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/Evaluator.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/Evaluator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; import odk.lang.FastMath; diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/EventNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/EventNode.java index d0916de10..b9a119aa9 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/EventNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/EventNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; import java.util.ArrayList; diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/FunctionNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/FunctionNode.java index b6f0278a4..265eee915 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/FunctionNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/FunctionNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; import java.util.ArrayList; diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/HierarchicalNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/HierarchicalNode.java index eb8de0537..482d800b1 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/HierarchicalNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/HierarchicalNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; import java.util.ArrayList; diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/ReactionNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/ReactionNode.java index 8ab69a8f1..eb261eb7a 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/ReactionNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/ReactionNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; import java.util.ArrayList; diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/SpeciesNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/SpeciesNode.java index b44a42922..b47e47d87 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/SpeciesNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/SpeciesNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; import java.util.ArrayList; diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/SpeciesReferenceNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/SpeciesReferenceNode.java index 945ef442d..28388b571 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/SpeciesReferenceNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/SpeciesReferenceNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; public class SpeciesReferenceNode extends VariableNode diff --git a/src/backend/analysis/dynamicsim/hierarchical/math/VariableNode.java b/src/backend/analysis/dynamicsim/hierarchical/math/VariableNode.java index f41189afb..3d663e22a 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/math/VariableNode.java +++ b/src/backend/analysis/dynamicsim/hierarchical/math/VariableNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.math; import java.util.ArrayList; diff --git a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalFBASimulator.java b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalFBASimulator.java index 07c55fd8d..0707c1516 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalFBASimulator.java +++ b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalFBASimulator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.methods; import java.io.IOException; diff --git a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalHybridSimulator.java b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalHybridSimulator.java index aba684960..aaa8c1a52 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalHybridSimulator.java +++ b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalHybridSimulator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.methods; diff --git a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalMixedSimulator.java b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalMixedSimulator.java index 5f0180910..f2c8a7789 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalMixedSimulator.java +++ b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalMixedSimulator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.methods; import java.io.IOException; diff --git a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalODERKSimulator.java b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalODERKSimulator.java index f7f4996f5..9f4f73657 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalODERKSimulator.java +++ b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalODERKSimulator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.methods; import java.io.IOException; diff --git a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalSSADirectSimulator.java b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalSSADirectSimulator.java index 56a21ad38..905f130c0 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalSSADirectSimulator.java +++ b/src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalSSADirectSimulator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.methods; import java.io.IOException; diff --git a/src/backend/analysis/dynamicsim/hierarchical/model/HierarchicalModel.java b/src/backend/analysis/dynamicsim/hierarchical/model/HierarchicalModel.java index 1e4adc1a3..8aa8a96be 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/model/HierarchicalModel.java +++ b/src/backend/analysis/dynamicsim/hierarchical/model/HierarchicalModel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.model; import java.util.ArrayList; diff --git a/src/backend/analysis/dynamicsim/hierarchical/states/DenseState.java b/src/backend/analysis/dynamicsim/hierarchical/states/DenseState.java index 6b17e67df..72f9cfc1e 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/states/DenseState.java +++ b/src/backend/analysis/dynamicsim/hierarchical/states/DenseState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.states; diff --git a/src/backend/analysis/dynamicsim/hierarchical/states/HierarchicalState.java b/src/backend/analysis/dynamicsim/hierarchical/states/HierarchicalState.java index 851d3cf3a..58a5d4389 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/states/HierarchicalState.java +++ b/src/backend/analysis/dynamicsim/hierarchical/states/HierarchicalState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.states; diff --git a/src/backend/analysis/dynamicsim/hierarchical/states/SparseState.java b/src/backend/analysis/dynamicsim/hierarchical/states/SparseState.java index d82208e79..e9dd20cd0 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/states/SparseState.java +++ b/src/backend/analysis/dynamicsim/hierarchical/states/SparseState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.states; diff --git a/src/backend/analysis/dynamicsim/hierarchical/states/TreeState.java b/src/backend/analysis/dynamicsim/hierarchical/states/TreeState.java index ea94d8020..bd158e096 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/states/TreeState.java +++ b/src/backend/analysis/dynamicsim/hierarchical/states/TreeState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.states; diff --git a/src/backend/analysis/dynamicsim/hierarchical/states/ValueState.java b/src/backend/analysis/dynamicsim/hierarchical/states/ValueState.java index 7cd607335..32bd6a255 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/states/ValueState.java +++ b/src/backend/analysis/dynamicsim/hierarchical/states/ValueState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.states; diff --git a/src/backend/analysis/dynamicsim/hierarchical/states/VectorState.java b/src/backend/analysis/dynamicsim/hierarchical/states/VectorState.java index 4cefd49cf..62f57361b 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/states/VectorState.java +++ b/src/backend/analysis/dynamicsim/hierarchical/states/VectorState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.states; public class VectorState extends HierarchicalState{ diff --git a/src/backend/analysis/dynamicsim/hierarchical/states/VectorWrapper.java b/src/backend/analysis/dynamicsim/hierarchical/states/VectorWrapper.java index 4044d9b0a..f8bd135c6 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/states/VectorWrapper.java +++ b/src/backend/analysis/dynamicsim/hierarchical/states/VectorWrapper.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.states; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/HierarchicalUtilities.java b/src/backend/analysis/dynamicsim/hierarchical/util/HierarchicalUtilities.java index fe2a7acfd..08eaf3306 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/HierarchicalUtilities.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/HierarchicalUtilities.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util; import java.io.File; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/comp/HierarchicalEventComparator.java b/src/backend/analysis/dynamicsim/hierarchical/util/comp/HierarchicalEventComparator.java index 5878767e6..24b77178d 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/comp/HierarchicalEventComparator.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/comp/HierarchicalEventComparator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.comp; import java.util.Comparator; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/comp/ReplacementHandler.java b/src/backend/analysis/dynamicsim/hierarchical/util/comp/ReplacementHandler.java index 9be4299f2..e7f81fd88 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/comp/ReplacementHandler.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/comp/ReplacementHandler.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.comp; import backend.analysis.dynamicsim.hierarchical.model.HierarchicalModel; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/interpreter/MathInterpreter.java b/src/backend/analysis/dynamicsim/hierarchical/util/interpreter/MathInterpreter.java index 4a8229cdd..f83a82bc7 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/interpreter/MathInterpreter.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/interpreter/MathInterpreter.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.interpreter; import java.util.Map; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/interpreter/RateSplitterInterpreter.java b/src/backend/analysis/dynamicsim/hierarchical/util/interpreter/RateSplitterInterpreter.java index bd2d4442a..b5179eb6e 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/interpreter/RateSplitterInterpreter.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/interpreter/RateSplitterInterpreter.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.interpreter; import java.util.ArrayList; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/scripts/HierarchicalSimulatorRunner.java b/src/backend/analysis/dynamicsim/hierarchical/util/scripts/HierarchicalSimulatorRunner.java index 655a3e32d..024c896ad 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/scripts/HierarchicalSimulatorRunner.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/scripts/HierarchicalSimulatorRunner.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.scripts; import java.io.File; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ArraysSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ArraysSetup.java index 45dab8272..5d2988821 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ArraysSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ArraysSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import org.sbml.jsbml.ASTNode; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/CompartmentSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/CompartmentSetup.java index 684c908b8..bff601712 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/CompartmentSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/CompartmentSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ConstraintSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ConstraintSetup.java index 4694538ad..74b17defc 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ConstraintSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ConstraintSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import org.sbml.jsbml.ASTNode; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/CoreSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/CoreSetup.java index 79eb1884e..5ced21e31 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/CoreSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/CoreSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import java.io.IOException; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/EventSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/EventSetup.java index d4f82e77b..e04d321e2 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/EventSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/EventSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import java.util.Map; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/InitAssignmentSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/InitAssignmentSetup.java index 237ea51e3..2ecefdbbd 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/InitAssignmentSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/InitAssignmentSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import org.sbml.jsbml.ASTNode; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ModelSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ModelSetup.java index c2d8c97a0..ab80096ca 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ModelSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ModelSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ParameterSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ParameterSetup.java index 2f2af3c80..490ed738c 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ParameterSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ParameterSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import org.sbml.jsbml.KineticLaw; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ReactionSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ReactionSetup.java index 95cb92606..816640b30 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ReactionSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ReactionSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import org.sbml.jsbml.ASTNode; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ReplacementSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ReplacementSetup.java index e4403d38e..db9daac03 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/ReplacementSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/ReplacementSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import java.util.List; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/RuleSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/RuleSetup.java index bb6e53858..afbb33971 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/RuleSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/RuleSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import java.util.Map; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesReferenceSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesReferenceSetup.java index 60908e326..0d7aa3178 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesReferenceSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesReferenceSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import org.sbml.jsbml.SpeciesReference; diff --git a/src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesSetup.java b/src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesSetup.java index aa43f1827..ea0aff6ed 100644 --- a/src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesSetup.java +++ b/src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesSetup.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.dynamicsim.hierarchical.util.setup; import java.io.IOException; diff --git a/src/backend/analysis/fba/FluxBalanceAnalysis.java b/src/backend/analysis/fba/FluxBalanceAnalysis.java index 839da1572..1db793f2e 100644 --- a/src/backend/analysis/fba/FluxBalanceAnalysis.java +++ b/src/backend/analysis/fba/FluxBalanceAnalysis.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.fba; import java.io.BufferedWriter; diff --git a/src/backend/analysis/markov/BuildStateGraphThread.java b/src/backend/analysis/markov/BuildStateGraphThread.java index 06ec47fab..d509c8f91 100644 --- a/src/backend/analysis/markov/BuildStateGraphThread.java +++ b/src/backend/analysis/markov/BuildStateGraphThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.markov; import javax.swing.JProgressBar; diff --git a/src/backend/analysis/markov/PerfromSteadyStateMarkovAnalysisThread.java b/src/backend/analysis/markov/PerfromSteadyStateMarkovAnalysisThread.java index 25cbc8e4f..a36a590fb 100644 --- a/src/backend/analysis/markov/PerfromSteadyStateMarkovAnalysisThread.java +++ b/src/backend/analysis/markov/PerfromSteadyStateMarkovAnalysisThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.markov; import java.util.ArrayList; diff --git a/src/backend/analysis/markov/PerfromTransientMarkovAnalysisThread.java b/src/backend/analysis/markov/PerfromTransientMarkovAnalysisThread.java index 811da15af..28603fd34 100644 --- a/src/backend/analysis/markov/PerfromTransientMarkovAnalysisThread.java +++ b/src/backend/analysis/markov/PerfromTransientMarkovAnalysisThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.markov; import javax.swing.JProgressBar; diff --git a/src/backend/analysis/markov/StateGraph.java b/src/backend/analysis/markov/StateGraph.java index 34dda08a6..07362addf 100644 --- a/src/backend/analysis/markov/StateGraph.java +++ b/src/backend/analysis/markov/StateGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.markov; import java.io.BufferedWriter; diff --git a/src/backend/analysis/markov/TransientMarkovMatrixMultiplyThread.java b/src/backend/analysis/markov/TransientMarkovMatrixMultiplyThread.java index 2bb212c5e..87cd300b0 100644 --- a/src/backend/analysis/markov/TransientMarkovMatrixMultiplyThread.java +++ b/src/backend/analysis/markov/TransientMarkovMatrixMultiplyThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.markov; public class TransientMarkovMatrixMultiplyThread extends Thread { diff --git a/src/backend/analysis/util/SEDMLutilities.java b/src/backend/analysis/util/SEDMLutilities.java index a14558b06..4b5ccf7c6 100644 --- a/src/backend/analysis/util/SEDMLutilities.java +++ b/src/backend/analysis/util/SEDMLutilities.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.analysis.util; import java.util.ArrayList; diff --git a/src/backend/learn/AMSModel/DMVCrun.java b/src/backend/learn/AMSModel/DMVCrun.java index a268d832a..892999ef6 100644 --- a/src/backend/learn/AMSModel/DMVCrun.java +++ b/src/backend/learn/AMSModel/DMVCrun.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.AMSModel; import java.util.*; diff --git a/src/backend/learn/AMSModel/LearnModel.java b/src/backend/learn/AMSModel/LearnModel.java index 0ce884837..63d2bfb23 100644 --- a/src/backend/learn/AMSModel/LearnModel.java +++ b/src/backend/learn/AMSModel/LearnModel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.AMSModel; import java.io.*; diff --git a/src/backend/learn/AMSModel/Variable.java b/src/backend/learn/AMSModel/Variable.java index 6db17fb0f..250e33e07 100644 --- a/src/backend/learn/AMSModel/Variable.java +++ b/src/backend/learn/AMSModel/Variable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.AMSModel; diff --git a/src/backend/learn/genenet/Connection.java b/src/backend/learn/genenet/Connection.java index 4eb2d0e5a..6e3860a1d 100644 --- a/src/backend/learn/genenet/Connection.java +++ b/src/backend/learn/genenet/Connection.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.genenet; import java.util.ArrayList; diff --git a/src/backend/learn/genenet/Encodings.java b/src/backend/learn/genenet/Encodings.java index 5d03f029d..6c44f3fcd 100644 --- a/src/backend/learn/genenet/Encodings.java +++ b/src/backend/learn/genenet/Encodings.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.genenet; import java.util.ArrayList; diff --git a/src/backend/learn/genenet/Experiments.java b/src/backend/learn/genenet/Experiments.java index f6c312506..ce6c22877 100644 --- a/src/backend/learn/genenet/Experiments.java +++ b/src/backend/learn/genenet/Experiments.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.genenet; import java.util.ArrayList; diff --git a/src/backend/learn/genenet/Learn.java b/src/backend/learn/genenet/Learn.java index 6475af949..d275a094d 100644 --- a/src/backend/learn/genenet/Learn.java +++ b/src/backend/learn/genenet/Learn.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.genenet; import java.io.File; diff --git a/src/backend/learn/genenet/NetCon.java b/src/backend/learn/genenet/NetCon.java index d5627099b..2e2e1848c 100644 --- a/src/backend/learn/genenet/NetCon.java +++ b/src/backend/learn/genenet/NetCon.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.genenet; import java.util.ArrayList; diff --git a/src/backend/learn/genenet/Run.java b/src/backend/learn/genenet/Run.java index e4d29743e..22e70e104 100644 --- a/src/backend/learn/genenet/Run.java +++ b/src/backend/learn/genenet/Run.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.genenet; import java.io.File; diff --git a/src/backend/learn/genenet/SpeciesCollection.java b/src/backend/learn/genenet/SpeciesCollection.java index 926a2da01..edc55b674 100644 --- a/src/backend/learn/genenet/SpeciesCollection.java +++ b/src/backend/learn/genenet/SpeciesCollection.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.genenet; import java.util.ArrayList; diff --git a/src/backend/learn/genenet/Thresholds.java b/src/backend/learn/genenet/Thresholds.java index b3c3e5bae..c851508f1 100644 --- a/src/backend/learn/genenet/Thresholds.java +++ b/src/backend/learn/genenet/Thresholds.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.genenet; public class Thresholds diff --git a/src/backend/learn/parameterestimator/ParameterEstimator.java b/src/backend/learn/parameterestimator/ParameterEstimator.java index 0ee8740cc..6541ae999 100644 --- a/src/backend/learn/parameterestimator/ParameterEstimator.java +++ b/src/backend/learn/parameterestimator/ParameterEstimator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.parameterestimator; import java.io.IOException; diff --git a/src/backend/learn/parameterestimator/methods/AbstractEstimator.java b/src/backend/learn/parameterestimator/methods/AbstractEstimator.java index c0b23e813..57cd886af 100644 --- a/src/backend/learn/parameterestimator/methods/AbstractEstimator.java +++ b/src/backend/learn/parameterestimator/methods/AbstractEstimator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.parameterestimator.methods; public interface AbstractEstimator diff --git a/src/backend/learn/parameterestimator/methods/pedi/GeneProduct.java b/src/backend/learn/parameterestimator/methods/pedi/GeneProduct.java index 1374b3ced..5a2329b1b 100644 --- a/src/backend/learn/parameterestimator/methods/pedi/GeneProduct.java +++ b/src/backend/learn/parameterestimator/methods/pedi/GeneProduct.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.parameterestimator.methods.pedi; public class GeneProduct diff --git a/src/backend/learn/parameterestimator/methods/pedi/PEDIBridge.java b/src/backend/learn/parameterestimator/methods/pedi/PEDIBridge.java index da9dff2b0..b06110f3f 100644 --- a/src/backend/learn/parameterestimator/methods/pedi/PEDIBridge.java +++ b/src/backend/learn/parameterestimator/methods/pedi/PEDIBridge.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.parameterestimator.methods.pedi; public interface PEDIBridge diff --git a/src/backend/learn/parameterestimator/methods/sres/EvolutionMethodSetting.java b/src/backend/learn/parameterestimator/methods/sres/EvolutionMethodSetting.java index 75fe3f204..c85171c54 100644 --- a/src/backend/learn/parameterestimator/methods/sres/EvolutionMethodSetting.java +++ b/src/backend/learn/parameterestimator/methods/sres/EvolutionMethodSetting.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.parameterestimator.methods.sres; public class EvolutionMethodSetting diff --git a/src/backend/learn/parameterestimator/methods/sres/Modelsettings.java b/src/backend/learn/parameterestimator/methods/sres/Modelsettings.java index 7fe2b0266..f9d363f7f 100644 --- a/src/backend/learn/parameterestimator/methods/sres/Modelsettings.java +++ b/src/backend/learn/parameterestimator/methods/sres/Modelsettings.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.parameterestimator.methods.sres; import java.io.BufferedReader; diff --git a/src/backend/learn/parameterestimator/methods/sres/Objective.java b/src/backend/learn/parameterestimator/methods/sres/Objective.java index 5e8c06d37..7907988e5 100644 --- a/src/backend/learn/parameterestimator/methods/sres/Objective.java +++ b/src/backend/learn/parameterestimator/methods/sres/Objective.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.parameterestimator.methods.sres; import java.util.Arrays; diff --git a/src/backend/learn/parameterestimator/methods/sres/ObjectiveSqureError.java b/src/backend/learn/parameterestimator/methods/sres/ObjectiveSqureError.java index d8b6d40cc..08da6db3c 100644 --- a/src/backend/learn/parameterestimator/methods/sres/ObjectiveSqureError.java +++ b/src/backend/learn/parameterestimator/methods/sres/ObjectiveSqureError.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.parameterestimator.methods.sres; import static java.lang.Math.abs; diff --git a/src/backend/learn/parameterestimator/methods/sres/SRES.java b/src/backend/learn/parameterestimator/methods/sres/SRES.java index c8f58ca72..39fabad7e 100644 --- a/src/backend/learn/parameterestimator/methods/sres/SRES.java +++ b/src/backend/learn/parameterestimator/methods/sres/SRES.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.learn.parameterestimator.methods.sres; import java.util.Arrays; diff --git a/src/backend/sbol/assembly/Assembler2.java b/src/backend/sbol/assembly/Assembler2.java index ef3ca9ec2..aff3dae5d 100644 --- a/src/backend/sbol/assembly/Assembler2.java +++ b/src/backend/sbol/assembly/Assembler2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.assembly; import org.sbolstandard.core2.ComponentDefinition; diff --git a/src/backend/sbol/assembly/AssemblyGraph2.java b/src/backend/sbol/assembly/AssemblyGraph2.java index b9060c77b..38a04d371 100644 --- a/src/backend/sbol/assembly/AssemblyGraph2.java +++ b/src/backend/sbol/assembly/AssemblyGraph2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.assembly; import java.io.IOException; diff --git a/src/backend/sbol/assembly/AssemblyNode2.java b/src/backend/sbol/assembly/AssemblyNode2.java index 981a76773..690d427a4 100644 --- a/src/backend/sbol/assembly/AssemblyNode2.java +++ b/src/backend/sbol/assembly/AssemblyNode2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.assembly; import java.net.URI; diff --git a/src/backend/sbol/assembly/SequenceTypeValidator.java b/src/backend/sbol/assembly/SequenceTypeValidator.java index c18a860ff..7a3bf973e 100644 --- a/src/backend/sbol/assembly/SequenceTypeValidator.java +++ b/src/backend/sbol/assembly/SequenceTypeValidator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.assembly; import java.util.HashMap; diff --git a/src/backend/sbol/util/ChEBI.java b/src/backend/sbol/util/ChEBI.java index a78788ad5..c0536392d 100644 --- a/src/backend/sbol/util/ChEBI.java +++ b/src/backend/sbol/util/ChEBI.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.util; import java.net.URI; diff --git a/src/backend/sbol/util/MyersOntology.java b/src/backend/sbol/util/MyersOntology.java index 16cd4c135..a9034ba42 100644 --- a/src/backend/sbol/util/MyersOntology.java +++ b/src/backend/sbol/util/MyersOntology.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.util; import java.net.URI; diff --git a/src/backend/sbol/util/SBO.java b/src/backend/sbol/util/SBO.java index 4118bbd45..4a1268b76 100644 --- a/src/backend/sbol/util/SBO.java +++ b/src/backend/sbol/util/SBO.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.util; import java.net.URI; diff --git a/src/backend/sbol/util/SBOLFileManager2.java b/src/backend/sbol/util/SBOLFileManager2.java index 3eca8ad8e..949a1d4fc 100644 --- a/src/backend/sbol/util/SBOLFileManager2.java +++ b/src/backend/sbol/util/SBOLFileManager2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.util; import java.io.File; diff --git a/src/backend/sbol/util/SBOLIdentityManager2.java b/src/backend/sbol/util/SBOLIdentityManager2.java index 4e37f7090..19294c036 100644 --- a/src/backend/sbol/util/SBOLIdentityManager2.java +++ b/src/backend/sbol/util/SBOLIdentityManager2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.util; import java.net.URI; diff --git a/src/backend/sbol/util/SBOLOntology.java b/src/backend/sbol/util/SBOLOntology.java index 4a02c9040..a02a06416 100644 --- a/src/backend/sbol/util/SBOLOntology.java +++ b/src/backend/sbol/util/SBOLOntology.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.util; import java.net.URI; diff --git a/src/backend/sbol/util/SBOLTestFactory.java b/src/backend/sbol/util/SBOLTestFactory.java index 34e8dcd6f..8d40f308e 100644 --- a/src/backend/sbol/util/SBOLTestFactory.java +++ b/src/backend/sbol/util/SBOLTestFactory.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.util; import java.io.File; diff --git a/src/backend/sbol/util/SBOLUtility2.java b/src/backend/sbol/util/SBOLUtility2.java index 457b40306..a54a6d648 100644 --- a/src/backend/sbol/util/SBOLUtility2.java +++ b/src/backend/sbol/util/SBOLUtility2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.sbol.util; import java.io.File; diff --git a/src/backend/synthesis/genetic/SynthesisGraph.java b/src/backend/synthesis/genetic/SynthesisGraph.java index bf8aa83b5..16b5b8dd8 100644 --- a/src/backend/synthesis/genetic/SynthesisGraph.java +++ b/src/backend/synthesis/genetic/SynthesisGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.genetic; import java.net.URI; diff --git a/src/backend/synthesis/genetic/SynthesisMatcher.java b/src/backend/synthesis/genetic/SynthesisMatcher.java index e56316371..1cba21979 100644 --- a/src/backend/synthesis/genetic/SynthesisMatcher.java +++ b/src/backend/synthesis/genetic/SynthesisMatcher.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.genetic; import java.util.HashMap; diff --git a/src/backend/synthesis/genetic/SynthesisNode.java b/src/backend/synthesis/genetic/SynthesisNode.java index 633fa6492..380a8fb3b 100644 --- a/src/backend/synthesis/genetic/SynthesisNode.java +++ b/src/backend/synthesis/genetic/SynthesisNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.genetic; import java.net.URI; diff --git a/src/backend/synthesis/genetic/SynthesisThread.java b/src/backend/synthesis/genetic/SynthesisThread.java index 3234f05a9..f1daf79da 100644 --- a/src/backend/synthesis/genetic/SynthesisThread.java +++ b/src/backend/synthesis/genetic/SynthesisThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.genetic; public class SynthesisThread { diff --git a/src/backend/synthesis/genetic/Synthesizer.java b/src/backend/synthesis/genetic/Synthesizer.java index b2c5adc30..5dd5bf27b 100644 --- a/src/backend/synthesis/genetic/Synthesizer.java +++ b/src/backend/synthesis/genetic/Synthesizer.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.genetic; import java.io.IOException; diff --git a/src/backend/synthesis/mapTechnology/SBOLGraph.java b/src/backend/synthesis/mapTechnology/SBOLGraph.java index 93909893c..dda421a52 100644 --- a/src/backend/synthesis/mapTechnology/SBOLGraph.java +++ b/src/backend/synthesis/mapTechnology/SBOLGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.mapTechnology; import java.io.BufferedWriter; diff --git a/src/backend/synthesis/mapTechnology/StringGraph.java b/src/backend/synthesis/mapTechnology/StringGraph.java index 9bf3f118b..217555cbd 100644 --- a/src/backend/synthesis/mapTechnology/StringGraph.java +++ b/src/backend/synthesis/mapTechnology/StringGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.mapTechnology; import java.util.HashMap; diff --git a/src/backend/synthesis/mapTechnology/StringNode.java b/src/backend/synthesis/mapTechnology/StringNode.java index bf01bc854..c1534fc81 100644 --- a/src/backend/synthesis/mapTechnology/StringNode.java +++ b/src/backend/synthesis/mapTechnology/StringNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.mapTechnology; import java.util.ArrayList; diff --git a/src/backend/synthesis/mapTechnology/Synthesis.java b/src/backend/synthesis/mapTechnology/Synthesis.java index ae8bee303..c618a7e2a 100644 --- a/src/backend/synthesis/mapTechnology/Synthesis.java +++ b/src/backend/synthesis/mapTechnology/Synthesis.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.mapTechnology; import java.io.File; diff --git a/src/backend/synthesis/mapTechnology/SynthesisNode.java b/src/backend/synthesis/mapTechnology/SynthesisNode.java index 1a2c84b4c..7b35b55a7 100644 --- a/src/backend/synthesis/mapTechnology/SynthesisNode.java +++ b/src/backend/synthesis/mapTechnology/SynthesisNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.mapTechnology; import java.net.URI; diff --git a/src/backend/synthesis/mapTechnology/TempSynthesisRunner.java b/src/backend/synthesis/mapTechnology/TempSynthesisRunner.java index 6dce8470a..43a77b592 100644 --- a/src/backend/synthesis/mapTechnology/TempSynthesisRunner.java +++ b/src/backend/synthesis/mapTechnology/TempSynthesisRunner.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.mapTechnology; import java.io.File; diff --git a/src/backend/synthesis/mapTechnology/WeightedGraph.java b/src/backend/synthesis/mapTechnology/WeightedGraph.java index 2aff579a8..778580a9e 100644 --- a/src/backend/synthesis/mapTechnology/WeightedGraph.java +++ b/src/backend/synthesis/mapTechnology/WeightedGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.synthesis.mapTechnology; public class WeightedGraph diff --git a/src/backend/verification/FileExtentionFilter.java b/src/backend/verification/FileExtentionFilter.java index a89831226..ab6e27e3e 100644 --- a/src/backend/verification/FileExtentionFilter.java +++ b/src/backend/verification/FileExtentionFilter.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification; import java.io.File; diff --git a/src/backend/verification/VerificationCommandLine.java b/src/backend/verification/VerificationCommandLine.java index 7a968fcbc..edc5e3a68 100644 --- a/src/backend/verification/VerificationCommandLine.java +++ b/src/backend/verification/VerificationCommandLine.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification; import java.io.File; diff --git a/src/backend/verification/platu/BinaryTree/BinaryTree.java b/src/backend/verification/platu/BinaryTree/BinaryTree.java index e6d9c55a4..b2bde6d87 100644 --- a/src/backend/verification/platu/BinaryTree/BinaryTree.java +++ b/src/backend/verification/platu/BinaryTree/BinaryTree.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.BinaryTree; import java.util.*; diff --git a/src/backend/verification/platu/BinaryTree/Node.java b/src/backend/verification/platu/BinaryTree/Node.java index 5eb371bf5..9aa6ce122 100644 --- a/src/backend/verification/platu/BinaryTree/Node.java +++ b/src/backend/verification/platu/BinaryTree/Node.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.BinaryTree; import java.util.*; diff --git a/src/backend/verification/platu/MDD/MDT.java b/src/backend/verification/platu/MDD/MDT.java index 9cabf38e0..76132baa5 100644 --- a/src/backend/verification/platu/MDD/MDT.java +++ b/src/backend/verification/platu/MDD/MDT.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.MDD; import java.util.*; diff --git a/src/backend/verification/platu/MDD/Mdd.java b/src/backend/verification/platu/MDD/Mdd.java index ef707a4fd..964e61685 100644 --- a/src/backend/verification/platu/MDD/Mdd.java +++ b/src/backend/verification/platu/MDD/Mdd.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.MDD; import java.util.*; diff --git a/src/backend/verification/platu/MDD/mddNode.java b/src/backend/verification/platu/MDD/mddNode.java index 63a226984..618671409 100644 --- a/src/backend/verification/platu/MDD/mddNode.java +++ b/src/backend/verification/platu/MDD/mddNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.MDD; import java.util.*; diff --git a/src/backend/verification/platu/MDD/mdtNode.java b/src/backend/verification/platu/MDD/mdtNode.java index 6ed2b11af..536a7253b 100644 --- a/src/backend/verification/platu/MDD/mdtNode.java +++ b/src/backend/verification/platu/MDD/mdtNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.MDD; import java.util.*; diff --git a/src/backend/verification/platu/TimingAnalysis/DBM.java b/src/backend/verification/platu/TimingAnalysis/DBM.java index e87cfa48e..183595d38 100644 --- a/src/backend/verification/platu/TimingAnalysis/DBM.java +++ b/src/backend/verification/platu/TimingAnalysis/DBM.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.TimingAnalysis; import java.util.*; diff --git a/src/backend/verification/platu/TimingAnalysis/Poset.java b/src/backend/verification/platu/TimingAnalysis/Poset.java index f67cdf66e..14073742e 100644 --- a/src/backend/verification/platu/TimingAnalysis/Poset.java +++ b/src/backend/verification/platu/TimingAnalysis/Poset.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.TimingAnalysis; import java.util.*; diff --git a/src/backend/verification/platu/TimingAnalysis/PrjStateZone.java b/src/backend/verification/platu/TimingAnalysis/PrjStateZone.java index e9adb92f3..f5bd37160 100644 --- a/src/backend/verification/platu/TimingAnalysis/PrjStateZone.java +++ b/src/backend/verification/platu/TimingAnalysis/PrjStateZone.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.TimingAnalysis; import java.util.Arrays; diff --git a/src/backend/verification/platu/TimingAnalysis/TimingAnalysis.java b/src/backend/verification/platu/TimingAnalysis/TimingAnalysis.java index a3d35483d..6f8f74e98 100644 --- a/src/backend/verification/platu/TimingAnalysis/TimingAnalysis.java +++ b/src/backend/verification/platu/TimingAnalysis/TimingAnalysis.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.TimingAnalysis; import java.util.*; diff --git a/src/backend/verification/platu/TimingAnalysis/TimingState.java b/src/backend/verification/platu/TimingAnalysis/TimingState.java index a499a83ee..157b0807d 100644 --- a/src/backend/verification/platu/TimingAnalysis/TimingState.java +++ b/src/backend/verification/platu/TimingAnalysis/TimingState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.TimingAnalysis; import backend.verification.platu.stategraph.State; diff --git a/src/backend/verification/platu/TimingAnalysis/Zone1.java b/src/backend/verification/platu/TimingAnalysis/Zone1.java index dbcd4468a..eb438cc76 100644 --- a/src/backend/verification/platu/TimingAnalysis/Zone1.java +++ b/src/backend/verification/platu/TimingAnalysis/Zone1.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.TimingAnalysis; import java.util.*; diff --git a/src/backend/verification/platu/TimingAnalysis/mdtNode.java b/src/backend/verification/platu/TimingAnalysis/mdtNode.java index 00c754ad6..1a7c82bd3 100644 --- a/src/backend/verification/platu/TimingAnalysis/mdtNode.java +++ b/src/backend/verification/platu/TimingAnalysis/mdtNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.TimingAnalysis; import java.util.*; diff --git a/src/backend/verification/platu/common/BinTreeTable.java b/src/backend/verification/platu/common/BinTreeTable.java index 4907a2312..523db3439 100644 --- a/src/backend/verification/platu/common/BinTreeTable.java +++ b/src/backend/verification/platu/common/BinTreeTable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.common; diff --git a/src/backend/verification/platu/common/Common.java b/src/backend/verification/platu/common/Common.java index 3687069ff..5c0ef5a9f 100644 --- a/src/backend/verification/platu/common/Common.java +++ b/src/backend/verification/platu/common/Common.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.common; import java.io.Console; diff --git a/src/backend/verification/platu/common/HashTable.java b/src/backend/verification/platu/common/HashTable.java index ef1bfd496..14ea583e6 100644 --- a/src/backend/verification/platu/common/HashTable.java +++ b/src/backend/verification/platu/common/HashTable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.common; import java.util.*; diff --git a/src/backend/verification/platu/common/IndexObjMap.java b/src/backend/verification/platu/common/IndexObjMap.java index de52af8c2..1986c78cf 100644 --- a/src/backend/verification/platu/common/IndexObjMap.java +++ b/src/backend/verification/platu/common/IndexObjMap.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.common; import java.util.HashMap; diff --git a/src/backend/verification/platu/common/IntArrayObj.java b/src/backend/verification/platu/common/IntArrayObj.java index f9df43573..fc18ead5d 100644 --- a/src/backend/verification/platu/common/IntArrayObj.java +++ b/src/backend/verification/platu/common/IntArrayObj.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.common; diff --git a/src/backend/verification/platu/common/MddTable.java b/src/backend/verification/platu/common/MddTable.java index ee595478a..5b9864b86 100644 --- a/src/backend/verification/platu/common/MddTable.java +++ b/src/backend/verification/platu/common/MddTable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.common; diff --git a/src/backend/verification/platu/common/Pair.java b/src/backend/verification/platu/common/Pair.java index 08f8092d7..9fc05d3d2 100644 --- a/src/backend/verification/platu/common/Pair.java +++ b/src/backend/verification/platu/common/Pair.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.common; public class Pair { diff --git a/src/backend/verification/platu/common/PlatuObj.java b/src/backend/verification/platu/common/PlatuObj.java index e7c9b87f2..0b570e41d 100644 --- a/src/backend/verification/platu/common/PlatuObj.java +++ b/src/backend/verification/platu/common/PlatuObj.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.common; abstract public class PlatuObj { diff --git a/src/backend/verification/platu/common/SetIntTuple.java b/src/backend/verification/platu/common/SetIntTuple.java index 4265210fd..a83c3742d 100644 --- a/src/backend/verification/platu/common/SetIntTuple.java +++ b/src/backend/verification/platu/common/SetIntTuple.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.common; public abstract class SetIntTuple { diff --git a/src/backend/verification/platu/expression/AddNode.java b/src/backend/verification/platu/expression/AddNode.java index 71493e10e..089db6339 100644 --- a/src/backend/verification/platu/expression/AddNode.java +++ b/src/backend/verification/platu/expression/AddNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/AndNode.java b/src/backend/verification/platu/expression/AndNode.java index d70323f41..508a1b5e2 100644 --- a/src/backend/verification/platu/expression/AndNode.java +++ b/src/backend/verification/platu/expression/AndNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/ArrayElement.java b/src/backend/verification/platu/expression/ArrayElement.java index 4eb4d6694..9023b3876 100644 --- a/src/backend/verification/platu/expression/ArrayElement.java +++ b/src/backend/verification/platu/expression/ArrayElement.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.ArrayList; diff --git a/src/backend/verification/platu/expression/ArrayNode.java b/src/backend/verification/platu/expression/ArrayNode.java index 8c1b53294..f7db71e6f 100644 --- a/src/backend/verification/platu/expression/ArrayNode.java +++ b/src/backend/verification/platu/expression/ArrayNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.ArrayList; diff --git a/src/backend/verification/platu/expression/BitAndNode.java b/src/backend/verification/platu/expression/BitAndNode.java index cf9decb3b..e5854382d 100644 --- a/src/backend/verification/platu/expression/BitAndNode.java +++ b/src/backend/verification/platu/expression/BitAndNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/BitNegNode.java b/src/backend/verification/platu/expression/BitNegNode.java index 7fed0c059..9bf51f6db 100644 --- a/src/backend/verification/platu/expression/BitNegNode.java +++ b/src/backend/verification/platu/expression/BitNegNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/BitOrNode.java b/src/backend/verification/platu/expression/BitOrNode.java index 950a3248b..dc9a6c95b 100644 --- a/src/backend/verification/platu/expression/BitOrNode.java +++ b/src/backend/verification/platu/expression/BitOrNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/BitXorNode.java b/src/backend/verification/platu/expression/BitXorNode.java index c02a7ed0b..df73955cc 100644 --- a/src/backend/verification/platu/expression/BitXorNode.java +++ b/src/backend/verification/platu/expression/BitXorNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/ConstNode.java b/src/backend/verification/platu/expression/ConstNode.java index 8d15632d0..9c9a98a76 100644 --- a/src/backend/verification/platu/expression/ConstNode.java +++ b/src/backend/verification/platu/expression/ConstNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/DivNode.java b/src/backend/verification/platu/expression/DivNode.java index ec79b6cf9..be5c9431c 100644 --- a/src/backend/verification/platu/expression/DivNode.java +++ b/src/backend/verification/platu/expression/DivNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/EquivNode.java b/src/backend/verification/platu/expression/EquivNode.java index 225369a60..c0054cb21 100644 --- a/src/backend/verification/platu/expression/EquivNode.java +++ b/src/backend/verification/platu/expression/EquivNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/Expression.java b/src/backend/verification/platu/expression/Expression.java index ec8c0ed3e..ce05929ec 100644 --- a/src/backend/verification/platu/expression/Expression.java +++ b/src/backend/verification/platu/expression/Expression.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/ExpressionNode.java b/src/backend/verification/platu/expression/ExpressionNode.java index e46cea6d7..5d571fada 100644 --- a/src/backend/verification/platu/expression/ExpressionNode.java +++ b/src/backend/verification/platu/expression/ExpressionNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/GreatEqualNode.java b/src/backend/verification/platu/expression/GreatEqualNode.java index d6f6fc92d..176e57bde 100644 --- a/src/backend/verification/platu/expression/GreatEqualNode.java +++ b/src/backend/verification/platu/expression/GreatEqualNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/GreatNode.java b/src/backend/verification/platu/expression/GreatNode.java index fdc07f269..e392d2645 100644 --- a/src/backend/verification/platu/expression/GreatNode.java +++ b/src/backend/verification/platu/expression/GreatNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/ImplicationNode.java b/src/backend/verification/platu/expression/ImplicationNode.java index e2558d806..3509e3404 100644 --- a/src/backend/verification/platu/expression/ImplicationNode.java +++ b/src/backend/verification/platu/expression/ImplicationNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/LeftShiftNode.java b/src/backend/verification/platu/expression/LeftShiftNode.java index 7330c23e7..709a59040 100644 --- a/src/backend/verification/platu/expression/LeftShiftNode.java +++ b/src/backend/verification/platu/expression/LeftShiftNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/LessEqualNode.java b/src/backend/verification/platu/expression/LessEqualNode.java index d1075935f..c9cf91b2a 100644 --- a/src/backend/verification/platu/expression/LessEqualNode.java +++ b/src/backend/verification/platu/expression/LessEqualNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/LessNode.java b/src/backend/verification/platu/expression/LessNode.java index 85c1bd73e..e58758a3f 100644 --- a/src/backend/verification/platu/expression/LessNode.java +++ b/src/backend/verification/platu/expression/LessNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/MinNode.java b/src/backend/verification/platu/expression/MinNode.java index 48355a911..fb7cfb3e5 100644 --- a/src/backend/verification/platu/expression/MinNode.java +++ b/src/backend/verification/platu/expression/MinNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/ModNode.java b/src/backend/verification/platu/expression/ModNode.java index cac6c91fc..f3a685de9 100644 --- a/src/backend/verification/platu/expression/ModNode.java +++ b/src/backend/verification/platu/expression/ModNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/MultNode.java b/src/backend/verification/platu/expression/MultNode.java index ee8f37060..3bf6f9b0e 100644 --- a/src/backend/verification/platu/expression/MultNode.java +++ b/src/backend/verification/platu/expression/MultNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/NegNode.java b/src/backend/verification/platu/expression/NegNode.java index 8c77d11a2..298acbe74 100644 --- a/src/backend/verification/platu/expression/NegNode.java +++ b/src/backend/verification/platu/expression/NegNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/NotEquivNode.java b/src/backend/verification/platu/expression/NotEquivNode.java index c9abbb456..a175e51a4 100644 --- a/src/backend/verification/platu/expression/NotEquivNode.java +++ b/src/backend/verification/platu/expression/NotEquivNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/OrNode.java b/src/backend/verification/platu/expression/OrNode.java index 4b8965ade..6d83bc934 100644 --- a/src/backend/verification/platu/expression/OrNode.java +++ b/src/backend/verification/platu/expression/OrNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/RightShiftNode.java b/src/backend/verification/platu/expression/RightShiftNode.java index 3003ccb96..1db999dd9 100644 --- a/src/backend/verification/platu/expression/RightShiftNode.java +++ b/src/backend/verification/platu/expression/RightShiftNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/SubNode.java b/src/backend/verification/platu/expression/SubNode.java index 36c99419e..38e73dc61 100644 --- a/src/backend/verification/platu/expression/SubNode.java +++ b/src/backend/verification/platu/expression/SubNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/TernaryNode.java b/src/backend/verification/platu/expression/TernaryNode.java index 64ede8936..2c8013d7d 100644 --- a/src/backend/verification/platu/expression/TernaryNode.java +++ b/src/backend/verification/platu/expression/TernaryNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/expression/VarNode.java b/src/backend/verification/platu/expression/VarNode.java index 74dca07cc..a8c500c3d 100644 --- a/src/backend/verification/platu/expression/VarNode.java +++ b/src/backend/verification/platu/expression/VarNode.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.expression; import java.util.HashMap; diff --git a/src/backend/verification/platu/gui/Graph.java b/src/backend/verification/platu/gui/Graph.java index a9554cca7..edcabac72 100644 --- a/src/backend/verification/platu/gui/Graph.java +++ b/src/backend/verification/platu/gui/Graph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/gui/GraphFrame.java b/src/backend/verification/platu/gui/GraphFrame.java index ce166b902..82663df6f 100644 --- a/src/backend/verification/platu/gui/GraphFrame.java +++ b/src/backend/verification/platu/gui/GraphFrame.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/gui/MemoryChart.java b/src/backend/verification/platu/gui/MemoryChart.java index e40bddb07..23a0ba64b 100644 --- a/src/backend/verification/platu/gui/MemoryChart.java +++ b/src/backend/verification/platu/gui/MemoryChart.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/gui/MemoryWindow.java b/src/backend/verification/platu/gui/MemoryWindow.java index 021747c61..dc80fafed 100644 --- a/src/backend/verification/platu/gui/MemoryWindow.java +++ b/src/backend/verification/platu/gui/MemoryWindow.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/gui/PrintTable.java b/src/backend/verification/platu/gui/PrintTable.java index def2f3b0b..0a9902bb2 100644 --- a/src/backend/verification/platu/gui/PrintTable.java +++ b/src/backend/verification/platu/gui/PrintTable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/gui/StackWindow.java b/src/backend/verification/platu/gui/StackWindow.java index 797c6b207..023ae45cf 100644 --- a/src/backend/verification/platu/gui/StackWindow.java +++ b/src/backend/verification/platu/gui/StackWindow.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/gui/StateChart.java b/src/backend/verification/platu/gui/StateChart.java index 8368ec190..0fddb31ef 100644 --- a/src/backend/verification/platu/gui/StateChart.java +++ b/src/backend/verification/platu/gui/StateChart.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/logicAnalysis/Analysis.java b/src/backend/verification/platu/logicAnalysis/Analysis.java index 82bb3b0b5..762e76cda 100644 --- a/src/backend/verification/platu/logicAnalysis/Analysis.java +++ b/src/backend/verification/platu/logicAnalysis/Analysis.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import java.io.BufferedWriter; diff --git a/src/backend/verification/platu/logicAnalysis/CompositeState.java b/src/backend/verification/platu/logicAnalysis/CompositeState.java index 4472130e2..ffad7cb62 100644 --- a/src/backend/verification/platu/logicAnalysis/CompositeState.java +++ b/src/backend/verification/platu/logicAnalysis/CompositeState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import java.util.Arrays; diff --git a/src/backend/verification/platu/logicAnalysis/CompositeStateGraph.java b/src/backend/verification/platu/logicAnalysis/CompositeStateGraph.java index dface8ba4..791dcf6e6 100644 --- a/src/backend/verification/platu/logicAnalysis/CompositeStateGraph.java +++ b/src/backend/verification/platu/logicAnalysis/CompositeStateGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import java.io.FileNotFoundException; diff --git a/src/backend/verification/platu/logicAnalysis/CompositeStateTran.java b/src/backend/verification/platu/logicAnalysis/CompositeStateTran.java index 105bb0a87..71c8d35ca 100644 --- a/src/backend/verification/platu/logicAnalysis/CompositeStateTran.java +++ b/src/backend/verification/platu/logicAnalysis/CompositeStateTran.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import dataModels.lpn.parser.Transition; diff --git a/src/backend/verification/platu/logicAnalysis/CompositionalAnalysis.java b/src/backend/verification/platu/logicAnalysis/CompositionalAnalysis.java index cd42226ed..317b95141 100644 --- a/src/backend/verification/platu/logicAnalysis/CompositionalAnalysis.java +++ b/src/backend/verification/platu/logicAnalysis/CompositionalAnalysis.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import java.util.ArrayList; diff --git a/src/backend/verification/platu/logicAnalysis/CompositionalThread.java b/src/backend/verification/platu/logicAnalysis/CompositionalThread.java index 7295b5a26..22acc6558 100644 --- a/src/backend/verification/platu/logicAnalysis/CompositionalThread.java +++ b/src/backend/verification/platu/logicAnalysis/CompositionalThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import java.util.ArrayList; diff --git a/src/backend/verification/platu/logicAnalysis/Constraint.java b/src/backend/verification/platu/logicAnalysis/Constraint.java index 3e44f7d4a..1b7ff8663 100644 --- a/src/backend/verification/platu/logicAnalysis/Constraint.java +++ b/src/backend/verification/platu/logicAnalysis/Constraint.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import java.util.ArrayList; diff --git a/src/backend/verification/platu/logicAnalysis/HashSetWrapper.java b/src/backend/verification/platu/logicAnalysis/HashSetWrapper.java index 8fb4b7733..967daa468 100644 --- a/src/backend/verification/platu/logicAnalysis/HashSetWrapper.java +++ b/src/backend/verification/platu/logicAnalysis/HashSetWrapper.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import java.util.HashSet; diff --git a/src/backend/verification/platu/logicAnalysis/LpnState.java b/src/backend/verification/platu/logicAnalysis/LpnState.java index 0d4066ffe..07ce7bd38 100644 --- a/src/backend/verification/platu/logicAnalysis/LpnState.java +++ b/src/backend/verification/platu/logicAnalysis/LpnState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; diff --git a/src/backend/verification/platu/logicAnalysis/PrjLpnState.java b/src/backend/verification/platu/logicAnalysis/PrjLpnState.java index a244f0361..76698a3c9 100644 --- a/src/backend/verification/platu/logicAnalysis/PrjLpnState.java +++ b/src/backend/verification/platu/logicAnalysis/PrjLpnState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import java.util.*; diff --git a/src/backend/verification/platu/logicAnalysis/StateSetInterface.java b/src/backend/verification/platu/logicAnalysis/StateSetInterface.java index 7e1babc33..bf60b7e1d 100644 --- a/src/backend/verification/platu/logicAnalysis/StateSetInterface.java +++ b/src/backend/verification/platu/logicAnalysis/StateSetInterface.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.logicAnalysis; import backend.verification.platu.project.PrjState; diff --git a/src/backend/verification/platu/main/Interpretor.java b/src/backend/verification/platu/main/Interpretor.java index aa18bbf86..5a66efd31 100644 --- a/src/backend/verification/platu/main/Interpretor.java +++ b/src/backend/verification/platu/main/Interpretor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/main/Main.java b/src/backend/verification/platu/main/Main.java index d5fe31311..a202b919c 100644 --- a/src/backend/verification/platu/main/Main.java +++ b/src/backend/verification/platu/main/Main.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.main; import java.util.concurrent.Executors; diff --git a/src/backend/verification/platu/main/Options.java b/src/backend/verification/platu/main/Options.java index 446358666..73f5c3a37 100644 --- a/src/backend/verification/platu/main/Options.java +++ b/src/backend/verification/platu/main/Options.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.main; public class Options { diff --git a/src/backend/verification/platu/markovianAnalysis/MarkovianAnalysis.java b/src/backend/verification/platu/markovianAnalysis/MarkovianAnalysis.java index 611ca813e..789bbf11f 100644 --- a/src/backend/verification/platu/markovianAnalysis/MarkovianAnalysis.java +++ b/src/backend/verification/platu/markovianAnalysis/MarkovianAnalysis.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.markovianAnalysis; import java.util.ArrayList; diff --git a/src/backend/verification/platu/markovianAnalysis/PerfromTransientMarkovAnalysisThread.java b/src/backend/verification/platu/markovianAnalysis/PerfromTransientMarkovAnalysisThread.java index dba56aa90..ffc564d9f 100644 --- a/src/backend/verification/platu/markovianAnalysis/PerfromTransientMarkovAnalysisThread.java +++ b/src/backend/verification/platu/markovianAnalysis/PerfromTransientMarkovAnalysisThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.markovianAnalysis; import javax.swing.JProgressBar; diff --git a/src/backend/verification/platu/markovianAnalysis/ProbGlobalState.java b/src/backend/verification/platu/markovianAnalysis/ProbGlobalState.java index c09bc0ce9..7fac3376e 100644 --- a/src/backend/verification/platu/markovianAnalysis/ProbGlobalState.java +++ b/src/backend/verification/platu/markovianAnalysis/ProbGlobalState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.markovianAnalysis; import java.util.HashMap; diff --git a/src/backend/verification/platu/markovianAnalysis/ProbGlobalStateSet.java b/src/backend/verification/platu/markovianAnalysis/ProbGlobalStateSet.java index b6ad437d1..e04ad760c 100644 --- a/src/backend/verification/platu/markovianAnalysis/ProbGlobalStateSet.java +++ b/src/backend/verification/platu/markovianAnalysis/ProbGlobalStateSet.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.markovianAnalysis; import java.util.HashMap; diff --git a/src/backend/verification/platu/markovianAnalysis/ProbLocalState.java b/src/backend/verification/platu/markovianAnalysis/ProbLocalState.java index 3ce76fde4..afb7c8f18 100644 --- a/src/backend/verification/platu/markovianAnalysis/ProbLocalState.java +++ b/src/backend/verification/platu/markovianAnalysis/ProbLocalState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.markovianAnalysis; import java.util.HashMap; diff --git a/src/backend/verification/platu/markovianAnalysis/ProbLocalStateGraph.java b/src/backend/verification/platu/markovianAnalysis/ProbLocalStateGraph.java index c1d60cdcf..ef9e379e4 100644 --- a/src/backend/verification/platu/markovianAnalysis/ProbLocalStateGraph.java +++ b/src/backend/verification/platu/markovianAnalysis/ProbLocalStateGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.markovianAnalysis; import java.io.BufferedWriter; diff --git a/src/backend/verification/platu/markovianAnalysis/Property.java b/src/backend/verification/platu/markovianAnalysis/Property.java index 0ff0e0d6d..cb83d52da 100644 --- a/src/backend/verification/platu/markovianAnalysis/Property.java +++ b/src/backend/verification/platu/markovianAnalysis/Property.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.markovianAnalysis; public class Property { diff --git a/src/backend/verification/platu/markovianAnalysis/TransientMarkovMatrixMultiplyThread.java b/src/backend/verification/platu/markovianAnalysis/TransientMarkovMatrixMultiplyThread.java index 813c243d7..c7e19dbff 100644 --- a/src/backend/verification/platu/markovianAnalysis/TransientMarkovMatrixMultiplyThread.java +++ b/src/backend/verification/platu/markovianAnalysis/TransientMarkovMatrixMultiplyThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.markovianAnalysis; public class TransientMarkovMatrixMultiplyThread extends Thread { diff --git a/src/backend/verification/platu/partialOrders/DependentSet.java b/src/backend/verification/platu/partialOrders/DependentSet.java index d6f725299..52998284d 100644 --- a/src/backend/verification/platu/partialOrders/DependentSet.java +++ b/src/backend/verification/platu/partialOrders/DependentSet.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.partialOrders; import java.util.HashSet; diff --git a/src/backend/verification/platu/partialOrders/DependentSetComparator.java b/src/backend/verification/platu/partialOrders/DependentSetComparator.java index 68e869911..179373f7d 100644 --- a/src/backend/verification/platu/partialOrders/DependentSetComparator.java +++ b/src/backend/verification/platu/partialOrders/DependentSetComparator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.partialOrders; import java.util.Comparator; diff --git a/src/backend/verification/platu/partialOrders/ProbStaticDependencySets.java b/src/backend/verification/platu/partialOrders/ProbStaticDependencySets.java index c165f8242..79f88e409 100644 --- a/src/backend/verification/platu/partialOrders/ProbStaticDependencySets.java +++ b/src/backend/verification/platu/partialOrders/ProbStaticDependencySets.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.partialOrders; import java.util.ArrayList; diff --git a/src/backend/verification/platu/partialOrders/StaticDependencySets.java b/src/backend/verification/platu/partialOrders/StaticDependencySets.java index 14b1ba34a..072ba34f0 100644 --- a/src/backend/verification/platu/partialOrders/StaticDependencySets.java +++ b/src/backend/verification/platu/partialOrders/StaticDependencySets.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.partialOrders; import java.io.BufferedWriter; diff --git a/src/backend/verification/platu/platuLpn/DualHashMap.java b/src/backend/verification/platu/platuLpn/DualHashMap.java index 632525838..75fe4dc87 100644 --- a/src/backend/verification/platu/platuLpn/DualHashMap.java +++ b/src/backend/verification/platu/platuLpn/DualHashMap.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.platuLpn; import java.util.HashMap; diff --git a/src/backend/verification/platu/platuLpn/LPNTran.java b/src/backend/verification/platu/platuLpn/LPNTran.java index eccf45857..571205735 100644 --- a/src/backend/verification/platu/platuLpn/LPNTran.java +++ b/src/backend/verification/platu/platuLpn/LPNTran.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.platuLpn; import java.util.ArrayList; diff --git a/src/backend/verification/platu/platuLpn/LPNTranRelation.java b/src/backend/verification/platu/platuLpn/LPNTranRelation.java index 93e74bea6..b6d391d8e 100644 --- a/src/backend/verification/platu/platuLpn/LPNTranRelation.java +++ b/src/backend/verification/platu/platuLpn/LPNTranRelation.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.platuLpn; import java.util.HashMap; diff --git a/src/backend/verification/platu/platuLpn/LpnTranList.java b/src/backend/verification/platu/platuLpn/LpnTranList.java index d31b2ca5a..d57882ffc 100644 --- a/src/backend/verification/platu/platuLpn/LpnTranList.java +++ b/src/backend/verification/platu/platuLpn/LpnTranList.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.platuLpn; import java.util.Collection; diff --git a/src/backend/verification/platu/platuLpn/PlatuLPN.java b/src/backend/verification/platu/platuLpn/PlatuLPN.java index 550f6f725..e3dca52c2 100644 --- a/src/backend/verification/platu/platuLpn/PlatuLPN.java +++ b/src/backend/verification/platu/platuLpn/PlatuLPN.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.platuLpn; import java.util.ArrayList; diff --git a/src/backend/verification/platu/platuLpn/VarExpr.java b/src/backend/verification/platu/platuLpn/VarExpr.java index fc1c961c3..5e1f70d6a 100644 --- a/src/backend/verification/platu/platuLpn/VarExpr.java +++ b/src/backend/verification/platu/platuLpn/VarExpr.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.platuLpn; import java.util.HashMap; diff --git a/src/backend/verification/platu/platuLpn/VarExprList.java b/src/backend/verification/platu/platuLpn/VarExprList.java index c77689a94..bad4a40f8 100644 --- a/src/backend/verification/platu/platuLpn/VarExprList.java +++ b/src/backend/verification/platu/platuLpn/VarExprList.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/platuLpn/VarSet.java b/src/backend/verification/platu/platuLpn/VarSet.java index 2b1b80e91..a7a95849f 100644 --- a/src/backend/verification/platu/platuLpn/VarSet.java +++ b/src/backend/verification/platu/platuLpn/VarSet.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/platuLpn/VarType.java b/src/backend/verification/platu/platuLpn/VarType.java index 38f71b602..9e0ada1fd 100644 --- a/src/backend/verification/platu/platuLpn/VarType.java +++ b/src/backend/verification/platu/platuLpn/VarType.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.platuLpn; public enum VarType { diff --git a/src/backend/verification/platu/platuLpn/VarVal.java b/src/backend/verification/platu/platuLpn/VarVal.java index 862b5c584..2603238f4 100644 --- a/src/backend/verification/platu/platuLpn/VarVal.java +++ b/src/backend/verification/platu/platuLpn/VarVal.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/platuLpn/VarValSet.java b/src/backend/verification/platu/platuLpn/VarValSet.java index b0393e0ab..638e9b1de 100644 --- a/src/backend/verification/platu/platuLpn/VarValSet.java +++ b/src/backend/verification/platu/platuLpn/VarValSet.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/platuLpn/io/Instance.java b/src/backend/verification/platu/platuLpn/io/Instance.java index 1face092e..0bc3cef3c 100644 --- a/src/backend/verification/platu/platuLpn/io/Instance.java +++ b/src/backend/verification/platu/platuLpn/io/Instance.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.platuLpn.io; import java.util.List; diff --git a/src/backend/verification/platu/platuLpn/io/PlatuGrammarLexer.java b/src/backend/verification/platu/platuLpn/io/PlatuGrammarLexer.java index 76a833340..7330d224f 100644 --- a/src/backend/verification/platu/platuLpn/io/PlatuGrammarLexer.java +++ b/src/backend/verification/platu/platuLpn/io/PlatuGrammarLexer.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ // $ANTLR 3.4 /Users/zhangz/myBioSim/BioSim/gui/src/verification/platu/lpn/io/PlatuGrammar.g 2013-06-26 17:00:36 package backend.verification.platu.platuLpn.io; diff --git a/src/backend/verification/platu/platuLpn/io/PlatuGrammarParser.java b/src/backend/verification/platu/platuLpn/io/PlatuGrammarParser.java index 8385e72ac..0909c9286 100644 --- a/src/backend/verification/platu/platuLpn/io/PlatuGrammarParser.java +++ b/src/backend/verification/platu/platuLpn/io/PlatuGrammarParser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ // $ANTLR 3.4 /Users/zhangz/myBioSim/BioSim/gui/src/verification/platu/lpn/io/PlatuGrammar.g 2013-06-26 17:00:34 package backend.verification.platu.platuLpn.io; diff --git a/src/backend/verification/platu/platuLpn/io/PlatuInstLexer.java b/src/backend/verification/platu/platuLpn/io/PlatuInstLexer.java index 1b40c77a0..a1ff5933d 100644 --- a/src/backend/verification/platu/platuLpn/io/PlatuInstLexer.java +++ b/src/backend/verification/platu/platuLpn/io/PlatuInstLexer.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ // $ANTLR 3.3 Nov 30, 2010 12:50:56 /Users/erodrig9/workspace/platu/src/platu/lpn/io/PlatuInst.g 2011-09-05 15:36:31 package backend.verification.platu.platuLpn.io; diff --git a/src/backend/verification/platu/platuLpn/io/PlatuInstParser.java b/src/backend/verification/platu/platuLpn/io/PlatuInstParser.java index 3cf183392..aac6c2ea5 100644 --- a/src/backend/verification/platu/platuLpn/io/PlatuInstParser.java +++ b/src/backend/verification/platu/platuLpn/io/PlatuInstParser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ // $ANTLR 3.3 Nov 30, 2010 12:50:56 /Users/erodrig9/workspace/platu/src/platu/lpn/io/PlatuInst.g 2011-09-05 15:36:30 package backend.verification.platu.platuLpn.io; diff --git a/src/backend/verification/platu/platuLpn/io/WriteLPN.java b/src/backend/verification/platu/platuLpn/io/WriteLPN.java index 8dd79c45f..80a227863 100644 --- a/src/backend/verification/platu/platuLpn/io/WriteLPN.java +++ b/src/backend/verification/platu/platuLpn/io/WriteLPN.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.platuLpn.io; diff --git a/src/backend/verification/platu/por1/AmpleSet.java b/src/backend/verification/platu/por1/AmpleSet.java index 766e313f2..aca70e261 100644 --- a/src/backend/verification/platu/por1/AmpleSet.java +++ b/src/backend/verification/platu/por1/AmpleSet.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.por1; import java.util.HashMap; diff --git a/src/backend/verification/platu/por1/AmpleSubset.java b/src/backend/verification/platu/por1/AmpleSubset.java index 7a53ab1f7..53b2da064 100644 --- a/src/backend/verification/platu/por1/AmpleSubset.java +++ b/src/backend/verification/platu/por1/AmpleSubset.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.por1; import java.util.HashMap; diff --git a/src/backend/verification/platu/por1/SearchDepFromLPN.java b/src/backend/verification/platu/por1/SearchDepFromLPN.java index 350cf5027..b3601f568 100644 --- a/src/backend/verification/platu/por1/SearchDepFromLPN.java +++ b/src/backend/verification/platu/por1/SearchDepFromLPN.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.por1; import java.util.HashMap; diff --git a/src/backend/verification/platu/por1/SearchDepFromState.java b/src/backend/verification/platu/por1/SearchDepFromState.java index e726f511f..c49fee246 100644 --- a/src/backend/verification/platu/por1/SearchDepFromState.java +++ b/src/backend/verification/platu/por1/SearchDepFromState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.por1; import java.util.HashMap; diff --git a/src/backend/verification/platu/project/DesignUnit.java b/src/backend/verification/platu/project/DesignUnit.java index b06367d27..a444dad8d 100644 --- a/src/backend/verification/platu/project/DesignUnit.java +++ b/src/backend/verification/platu/project/DesignUnit.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.project; ///* // * To change this template, choose Tools | Templates diff --git a/src/backend/verification/platu/project/IDGenerator.java b/src/backend/verification/platu/project/IDGenerator.java index c3f1d1213..bad85bc37 100644 --- a/src/backend/verification/platu/project/IDGenerator.java +++ b/src/backend/verification/platu/project/IDGenerator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/project/PrintStackTrace.java b/src/backend/verification/platu/project/PrintStackTrace.java index 24ae9a031..4acc4965f 100644 --- a/src/backend/verification/platu/project/PrintStackTrace.java +++ b/src/backend/verification/platu/project/PrintStackTrace.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/project/PrjState.java b/src/backend/verification/platu/project/PrjState.java index 6dafd19ad..0dd092170 100644 --- a/src/backend/verification/platu/project/PrjState.java +++ b/src/backend/verification/platu/project/PrjState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.project; import java.util.Arrays; diff --git a/src/backend/verification/platu/project/Project.java b/src/backend/verification/platu/project/Project.java index 0acb08fcd..7da756006 100644 --- a/src/backend/verification/platu/project/Project.java +++ b/src/backend/verification/platu/project/Project.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.project; import java.io.BufferedWriter; diff --git a/src/backend/verification/platu/project/prjStateTimed.java b/src/backend/verification/platu/project/prjStateTimed.java index 9befc6138..37da1d58f 100644 --- a/src/backend/verification/platu/project/prjStateTimed.java +++ b/src/backend/verification/platu/project/prjStateTimed.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.project; import java.util.Arrays; diff --git a/src/backend/verification/platu/stategraph/State.java b/src/backend/verification/platu/stategraph/State.java index 3f4142704..5563d1cb2 100644 --- a/src/backend/verification/platu/stategraph/State.java +++ b/src/backend/verification/platu/stategraph/State.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.stategraph; import java.io.File; diff --git a/src/backend/verification/platu/stategraph/StateGraph.java b/src/backend/verification/platu/stategraph/StateGraph.java index 9a45bf731..5925d1dc1 100644 --- a/src/backend/verification/platu/stategraph/StateGraph.java +++ b/src/backend/verification/platu/stategraph/StateGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.platu.stategraph; import java.io.BufferedWriter; diff --git a/src/backend/verification/platu/stategraph/StateTran.java b/src/backend/verification/platu/stategraph/StateTran.java index 5b60fd966..2603b7a1e 100644 --- a/src/backend/verification/platu/stategraph/StateTran.java +++ b/src/backend/verification/platu/stategraph/StateTran.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/platu/stategraph/UpdateTimer.java b/src/backend/verification/platu/stategraph/UpdateTimer.java index 34315167c..0f55f4474 100644 --- a/src/backend/verification/platu/stategraph/UpdateTimer.java +++ b/src/backend/verification/platu/stategraph/UpdateTimer.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * To change this template, choose Tools | Templates * and open the template in the editor. diff --git a/src/backend/verification/timed_state_exploration/archive/Interval.java b/src/backend/verification/timed_state_exploration/archive/Interval.java index f494503ef..22553e3c7 100644 --- a/src/backend/verification/timed_state_exploration/archive/Interval.java +++ b/src/backend/verification/timed_state_exploration/archive/Interval.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.archive; diff --git a/src/backend/verification/timed_state_exploration/archive/OctMember.java b/src/backend/verification/timed_state_exploration/archive/OctMember.java index 5d63513cf..e6fab5bc3 100644 --- a/src/backend/verification/timed_state_exploration/archive/OctMember.java +++ b/src/backend/verification/timed_state_exploration/archive/OctMember.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.archive; import dataModels.lpn.parser.LPN; diff --git a/src/backend/verification/timed_state_exploration/archive/PreContinuous.java b/src/backend/verification/timed_state_exploration/archive/PreContinuous.java index 4a06a0b98..79f107c91 100644 --- a/src/backend/verification/timed_state_exploration/archive/PreContinuous.java +++ b/src/backend/verification/timed_state_exploration/archive/PreContinuous.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.archive; public abstract class PreContinuous extends OctMember { diff --git a/src/backend/verification/timed_state_exploration/archive/RateNonZero.java b/src/backend/verification/timed_state_exploration/archive/RateNonZero.java index 916e54e31..f71ce7692 100644 --- a/src/backend/verification/timed_state_exploration/archive/RateNonZero.java +++ b/src/backend/verification/timed_state_exploration/archive/RateNonZero.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.archive; diff --git a/src/backend/verification/timed_state_exploration/archive/RateZero.java b/src/backend/verification/timed_state_exploration/archive/RateZero.java index 6339173b1..981d1de09 100644 --- a/src/backend/verification/timed_state_exploration/archive/RateZero.java +++ b/src/backend/verification/timed_state_exploration/archive/RateZero.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.archive; diff --git a/src/backend/verification/timed_state_exploration/archive/Timer.java b/src/backend/verification/timed_state_exploration/archive/Timer.java index 0549cd142..91866ee8d 100644 --- a/src/backend/verification/timed_state_exploration/archive/Timer.java +++ b/src/backend/verification/timed_state_exploration/archive/Timer.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.archive; diff --git a/src/backend/verification/timed_state_exploration/dbm2/DBMLL.java b/src/backend/verification/timed_state_exploration/dbm2/DBMLL.java index 6742e14fa..d6a6d9def 100644 --- a/src/backend/verification/timed_state_exploration/dbm2/DBMLL.java +++ b/src/backend/verification/timed_state_exploration/dbm2/DBMLL.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.dbm2; import java.util.ArrayList; diff --git a/src/backend/verification/timed_state_exploration/dbm2/IDBM.java b/src/backend/verification/timed_state_exploration/dbm2/IDBM.java index 0fe84ee16..f01495f1a 100644 --- a/src/backend/verification/timed_state_exploration/dbm2/IDBM.java +++ b/src/backend/verification/timed_state_exploration/dbm2/IDBM.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.dbm2; /** diff --git a/src/backend/verification/timed_state_exploration/dbm2/LPNState.java b/src/backend/verification/timed_state_exploration/dbm2/LPNState.java index 7c821caf6..d4adfa6fe 100644 --- a/src/backend/verification/timed_state_exploration/dbm2/LPNState.java +++ b/src/backend/verification/timed_state_exploration/dbm2/LPNState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.dbm2; import java.util.*; diff --git a/src/backend/verification/timed_state_exploration/dbm2/LPNTransitionState.java b/src/backend/verification/timed_state_exploration/dbm2/LPNTransitionState.java index 84ef0e3fa..47a896d53 100644 --- a/src/backend/verification/timed_state_exploration/dbm2/LPNTransitionState.java +++ b/src/backend/verification/timed_state_exploration/dbm2/LPNTransitionState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.dbm2; import java.util.*; diff --git a/src/backend/verification/timed_state_exploration/dbm2/LPNTranslator.java b/src/backend/verification/timed_state_exploration/dbm2/LPNTranslator.java index f1c15f4bf..9cfbc294d 100644 --- a/src/backend/verification/timed_state_exploration/dbm2/LPNTranslator.java +++ b/src/backend/verification/timed_state_exploration/dbm2/LPNTranslator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.dbm2; import java.util.HashMap; import java.util.HashSet; diff --git a/src/backend/verification/timed_state_exploration/dbm2/StateExploration.java b/src/backend/verification/timed_state_exploration/dbm2/StateExploration.java index e3de467e2..b860178fe 100644 --- a/src/backend/verification/timed_state_exploration/dbm2/StateExploration.java +++ b/src/backend/verification/timed_state_exploration/dbm2/StateExploration.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.dbm2; import java.io.File; diff --git a/src/backend/verification/timed_state_exploration/octagon/Equivalence.java b/src/backend/verification/timed_state_exploration/octagon/Equivalence.java index 355b9cefb..5cba41aa4 100644 --- a/src/backend/verification/timed_state_exploration/octagon/Equivalence.java +++ b/src/backend/verification/timed_state_exploration/octagon/Equivalence.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.octagon; import java.util.Collection; diff --git a/src/backend/verification/timed_state_exploration/octagon/Octagon.java b/src/backend/verification/timed_state_exploration/octagon/Octagon.java index e2319c147..6bfcfa1f4 100644 --- a/src/backend/verification/timed_state_exploration/octagon/Octagon.java +++ b/src/backend/verification/timed_state_exploration/octagon/Octagon.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.octagon; import java.io.BufferedWriter; diff --git a/src/backend/verification/timed_state_exploration/zone/Analysis_Timed.java b/src/backend/verification/timed_state_exploration/zone/Analysis_Timed.java index 1bfd92957..220a218e6 100644 --- a/src/backend/verification/timed_state_exploration/zone/Analysis_Timed.java +++ b/src/backend/verification/timed_state_exploration/zone/Analysis_Timed.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import java.util.HashSet; diff --git a/src/backend/verification/timed_state_exploration/zone/Project_Timed.java b/src/backend/verification/timed_state_exploration/zone/Project_Timed.java index 586ec6538..dfe05cb04 100644 --- a/src/backend/verification/timed_state_exploration/zone/Project_Timed.java +++ b/src/backend/verification/timed_state_exploration/zone/Project_Timed.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import java.util.ArrayList; diff --git a/src/backend/verification/timed_state_exploration/zone/StateGraph_timed.java b/src/backend/verification/timed_state_exploration/zone/StateGraph_timed.java index f75175919..c4171591b 100644 --- a/src/backend/verification/timed_state_exploration/zone/StateGraph_timed.java +++ b/src/backend/verification/timed_state_exploration/zone/StateGraph_timed.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import java.io.BufferedWriter; diff --git a/src/backend/verification/timed_state_exploration/zone/TimedPrjState.java b/src/backend/verification/timed_state_exploration/zone/TimedPrjState.java index d21e9d2d7..58019a8e8 100644 --- a/src/backend/verification/timed_state_exploration/zone/TimedPrjState.java +++ b/src/backend/verification/timed_state_exploration/zone/TimedPrjState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import java.util.Arrays; diff --git a/src/backend/verification/timed_state_exploration/zone/TimedState.java b/src/backend/verification/timed_state_exploration/zone/TimedState.java index ff9deac3d..305c647a3 100644 --- a/src/backend/verification/timed_state_exploration/zone/TimedState.java +++ b/src/backend/verification/timed_state_exploration/zone/TimedState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import java.io.File; diff --git a/src/backend/verification/timed_state_exploration/zone/Zone.java b/src/backend/verification/timed_state_exploration/zone/Zone.java index ddac1a0f2..3a5b4bc53 100644 --- a/src/backend/verification/timed_state_exploration/zone/Zone.java +++ b/src/backend/verification/timed_state_exploration/zone/Zone.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import java.io.PrintStream; diff --git a/src/backend/verification/timed_state_exploration/zone/ZoneGraph.java b/src/backend/verification/timed_state_exploration/zone/ZoneGraph.java index 659adf011..c6efadeb3 100644 --- a/src/backend/verification/timed_state_exploration/zone/ZoneGraph.java +++ b/src/backend/verification/timed_state_exploration/zone/ZoneGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import java.io.PrintStream; diff --git a/src/backend/verification/timed_state_exploration/zone/ZoneGraphTest.java b/src/backend/verification/timed_state_exploration/zone/ZoneGraphTest.java index 12683ac7b..82882c2c7 100644 --- a/src/backend/verification/timed_state_exploration/zone/ZoneGraphTest.java +++ b/src/backend/verification/timed_state_exploration/zone/ZoneGraphTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import static org.junit.Assert.*; diff --git a/src/backend/verification/timed_state_exploration/zone/ZoneTest.java b/src/backend/verification/timed_state_exploration/zone/ZoneTest.java index d394ae33a..d8125aca2 100644 --- a/src/backend/verification/timed_state_exploration/zone/ZoneTest.java +++ b/src/backend/verification/timed_state_exploration/zone/ZoneTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import static org.junit.Assert.*; diff --git a/src/backend/verification/timed_state_exploration/zone/ZoneType.java b/src/backend/verification/timed_state_exploration/zone/ZoneType.java index 2126d4dae..7a3520f79 100644 --- a/src/backend/verification/timed_state_exploration/zone/ZoneType.java +++ b/src/backend/verification/timed_state_exploration/zone/ZoneType.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zone; import java.util.HashMap; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/Conolse7_26_2012.java b/src/backend/verification/timed_state_exploration/zoneProject/Conolse7_26_2012.java index 9c70821fc..b30ed931e 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/Conolse7_26_2012.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/Conolse7_26_2012.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import java.io.File; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/ContinuousRecordSet.java b/src/backend/verification/timed_state_exploration/zoneProject/ContinuousRecordSet.java index 00d736a03..43639369f 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/ContinuousRecordSet.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/ContinuousRecordSet.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import java.util.HashMap; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/ContinuousUtilities.java b/src/backend/verification/timed_state_exploration/zoneProject/ContinuousUtilities.java index bf2d64fbb..a7c8bd94f 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/ContinuousUtilities.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/ContinuousUtilities.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import java.util.ArrayList; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/Event.java b/src/backend/verification/timed_state_exploration/zoneProject/Event.java index 4d4ce339f..461ed3bde 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/Event.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/Event.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import dataModels.lpn.parser.Transition; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/EventSet.java b/src/backend/verification/timed_state_exploration/zoneProject/EventSet.java index 0f6fe3790..db720e4fd 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/EventSet.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/EventSet.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import java.util.ArrayList; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/InequalityVariable.java b/src/backend/verification/timed_state_exploration/zoneProject/InequalityVariable.java index 16987736e..5dc9b5a9b 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/InequalityVariable.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/InequalityVariable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import java.util.ArrayList; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/IntervalPair.java b/src/backend/verification/timed_state_exploration/zoneProject/IntervalPair.java index 2c2210aa6..65beebcd2 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/IntervalPair.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/IntervalPair.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/LPNContAndRate.java b/src/backend/verification/timed_state_exploration/zoneProject/LPNContAndRate.java index 97ef0c3fd..3cfc4850a 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/LPNContAndRate.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/LPNContAndRate.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; /** diff --git a/src/backend/verification/timed_state_exploration/zoneProject/LPNContinuousPair.java b/src/backend/verification/timed_state_exploration/zoneProject/LPNContinuousPair.java index 3d9aca55d..76f65e3b0 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/LPNContinuousPair.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/LPNContinuousPair.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; /** diff --git a/src/backend/verification/timed_state_exploration/zoneProject/LPNTransitionPair.java b/src/backend/verification/timed_state_exploration/zoneProject/LPNTransitionPair.java index a9ea38090..cdbc29d54 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/LPNTransitionPair.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/LPNTransitionPair.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; /** diff --git a/src/backend/verification/timed_state_exploration/zoneProject/RangeAndPairing.java b/src/backend/verification/timed_state_exploration/zoneProject/RangeAndPairing.java index 7008c2bb7..674d003e5 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/RangeAndPairing.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/RangeAndPairing.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; public class RangeAndPairing { diff --git a/src/backend/verification/timed_state_exploration/zoneProject/StateSet.java b/src/backend/verification/timed_state_exploration/zoneProject/StateSet.java index 4f05804d5..b0f4ff3cd 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/StateSet.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/StateSet.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import java.util.HashMap; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/TimedPrjState.java b/src/backend/verification/timed_state_exploration/zoneProject/TimedPrjState.java index caf8ab99e..61deefdb0 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/TimedPrjState.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/TimedPrjState.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import java.util.Arrays; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/TimedStateSet.java b/src/backend/verification/timed_state_exploration/zoneProject/TimedStateSet.java index 132559554..1510049c4 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/TimedStateSet.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/TimedStateSet.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import java.util.HashMap; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/UpdateContinuous.java b/src/backend/verification/timed_state_exploration/zoneProject/UpdateContinuous.java index 588ffb5e2..3ff82700b 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/UpdateContinuous.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/UpdateContinuous.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; /** diff --git a/src/backend/verification/timed_state_exploration/zoneProject/VariableRangePair.java b/src/backend/verification/timed_state_exploration/zoneProject/VariableRangePair.java index 1390b7fdb..c28cfa2bd 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/VariableRangePair.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/VariableRangePair.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import dataModels.lpn.parser.Variable; diff --git a/src/backend/verification/timed_state_exploration/zoneProject/Zone.java b/src/backend/verification/timed_state_exploration/zoneProject/Zone.java index f5fe5af66..5ab03611f 100644 --- a/src/backend/verification/timed_state_exploration/zoneProject/Zone.java +++ b/src/backend/verification/timed_state_exploration/zoneProject/Zone.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package backend.verification.timed_state_exploration.zoneProject; import java.io.BufferedWriter; diff --git a/src/conversion/SBML2SBOL.java b/src/conversion/SBML2SBOL.java index 763426705..4e3cde78f 100644 --- a/src/conversion/SBML2SBOL.java +++ b/src/conversion/SBML2SBOL.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package conversion; import java.io.File; diff --git a/src/conversion/SBOL2SBML.java b/src/conversion/SBOL2SBML.java index 8e056e978..f8d0547f6 100644 --- a/src/conversion/SBOL2SBML.java +++ b/src/conversion/SBOL2SBML.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package conversion; import java.io.File; diff --git a/src/conversion/SBOLValidate.java b/src/conversion/SBOLValidate.java index 5aa339c0a..0c1d8e27a 100644 --- a/src/conversion/SBOLValidate.java +++ b/src/conversion/SBOLValidate.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package conversion; import java.io.File; diff --git a/src/dataModels/biomodel/annotation/AnnotationAttribute.java b/src/dataModels/biomodel/annotation/AnnotationAttribute.java index 40d251cda..24c88dc6c 100644 --- a/src/dataModels/biomodel/annotation/AnnotationAttribute.java +++ b/src/dataModels/biomodel/annotation/AnnotationAttribute.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.annotation; public class AnnotationAttribute { diff --git a/src/dataModels/biomodel/annotation/AnnotationElement.java b/src/dataModels/biomodel/annotation/AnnotationElement.java index 28f027fe6..a6db90770 100644 --- a/src/dataModels/biomodel/annotation/AnnotationElement.java +++ b/src/dataModels/biomodel/annotation/AnnotationElement.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.annotation; import java.util.LinkedList; diff --git a/src/dataModels/biomodel/annotation/AnnotationNamespace.java b/src/dataModels/biomodel/annotation/AnnotationNamespace.java index f12f4e8a1..b7c8b05b5 100644 --- a/src/dataModels/biomodel/annotation/AnnotationNamespace.java +++ b/src/dataModels/biomodel/annotation/AnnotationNamespace.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.annotation; public class AnnotationNamespace { diff --git a/src/dataModels/biomodel/annotation/AnnotationUtility.java b/src/dataModels/biomodel/annotation/AnnotationUtility.java index 7e8578c30..ac9ce51d4 100644 --- a/src/dataModels/biomodel/annotation/AnnotationUtility.java +++ b/src/dataModels/biomodel/annotation/AnnotationUtility.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.annotation; import java.net.URI; diff --git a/src/dataModels/biomodel/annotation/SBOLAnnotation.java b/src/dataModels/biomodel/annotation/SBOLAnnotation.java index 1b5bf3748..95cf5b9ce 100644 --- a/src/dataModels/biomodel/annotation/SBOLAnnotation.java +++ b/src/dataModels/biomodel/annotation/SBOLAnnotation.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.annotation; import java.net.URI; diff --git a/src/dataModels/biomodel/network/AbstractSpecies.java b/src/dataModels/biomodel/network/AbstractSpecies.java index 418c7b484..060bfa0a0 100644 --- a/src/dataModels/biomodel/network/AbstractSpecies.java +++ b/src/dataModels/biomodel/network/AbstractSpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; /** diff --git a/src/dataModels/biomodel/network/AbstractionEngine.java b/src/dataModels/biomodel/network/AbstractionEngine.java index af542144e..82fc2f949 100644 --- a/src/dataModels/biomodel/network/AbstractionEngine.java +++ b/src/dataModels/biomodel/network/AbstractionEngine.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; diff --git a/src/dataModels/biomodel/network/BaseSpecies.java b/src/dataModels/biomodel/network/BaseSpecies.java index 060c4879a..716d50749 100644 --- a/src/dataModels/biomodel/network/BaseSpecies.java +++ b/src/dataModels/biomodel/network/BaseSpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; diff --git a/src/dataModels/biomodel/network/ComplexSpecies.java b/src/dataModels/biomodel/network/ComplexSpecies.java index 6d90d87c0..e2222f38e 100644 --- a/src/dataModels/biomodel/network/ComplexSpecies.java +++ b/src/dataModels/biomodel/network/ComplexSpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; diff --git a/src/dataModels/biomodel/network/ConstantSpecies.java b/src/dataModels/biomodel/network/ConstantSpecies.java index 85f992658..c850e00d4 100644 --- a/src/dataModels/biomodel/network/ConstantSpecies.java +++ b/src/dataModels/biomodel/network/ConstantSpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; diff --git a/src/dataModels/biomodel/network/DiffusibleConstitutiveSpecies.java b/src/dataModels/biomodel/network/DiffusibleConstitutiveSpecies.java index 61dded42e..703485e29 100644 --- a/src/dataModels/biomodel/network/DiffusibleConstitutiveSpecies.java +++ b/src/dataModels/biomodel/network/DiffusibleConstitutiveSpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; import dataModels.biomodel.visitor.SpeciesVisitor; diff --git a/src/dataModels/biomodel/network/DiffusibleSpecies.java b/src/dataModels/biomodel/network/DiffusibleSpecies.java index dfdc64357..ecb7b251d 100644 --- a/src/dataModels/biomodel/network/DiffusibleSpecies.java +++ b/src/dataModels/biomodel/network/DiffusibleSpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; import dataModels.biomodel.visitor.SpeciesVisitor; diff --git a/src/dataModels/biomodel/network/GeneticNetwork.java b/src/dataModels/biomodel/network/GeneticNetwork.java index 93084287b..e1f9a27c1 100644 --- a/src/dataModels/biomodel/network/GeneticNetwork.java +++ b/src/dataModels/biomodel/network/GeneticNetwork.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; import java.io.File; diff --git a/src/dataModels/biomodel/network/Influence.java b/src/dataModels/biomodel/network/Influence.java index 5dd0262e6..8735359d3 100644 --- a/src/dataModels/biomodel/network/Influence.java +++ b/src/dataModels/biomodel/network/Influence.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; diff --git a/src/dataModels/biomodel/network/NullSpecies.java b/src/dataModels/biomodel/network/NullSpecies.java index a75f50ec8..b0100cd9e 100644 --- a/src/dataModels/biomodel/network/NullSpecies.java +++ b/src/dataModels/biomodel/network/NullSpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; import dataModels.biomodel.visitor.SpeciesVisitor; diff --git a/src/dataModels/biomodel/network/Promoter.java b/src/dataModels/biomodel/network/Promoter.java index 634325779..50ccebf10 100644 --- a/src/dataModels/biomodel/network/Promoter.java +++ b/src/dataModels/biomodel/network/Promoter.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; diff --git a/src/dataModels/biomodel/network/SpasticSpecies.java b/src/dataModels/biomodel/network/SpasticSpecies.java index 592c14528..5aae994be 100644 --- a/src/dataModels/biomodel/network/SpasticSpecies.java +++ b/src/dataModels/biomodel/network/SpasticSpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; diff --git a/src/dataModels/biomodel/network/SpeciesInterface.java b/src/dataModels/biomodel/network/SpeciesInterface.java index c8ee2e352..30e55514c 100644 --- a/src/dataModels/biomodel/network/SpeciesInterface.java +++ b/src/dataModels/biomodel/network/SpeciesInterface.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.network; import dataModels.biomodel.visitor.VisitableSpecies; diff --git a/src/dataModels/biomodel/parser/BioModel.java b/src/dataModels/biomodel/parser/BioModel.java index b84b17775..fef5ec69f 100644 --- a/src/dataModels/biomodel/parser/BioModel.java +++ b/src/dataModels/biomodel/parser/BioModel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.parser; diff --git a/src/dataModels/biomodel/parser/CompatibilityFixer.java b/src/dataModels/biomodel/parser/CompatibilityFixer.java index 796ee1285..0cd59bf1f 100644 --- a/src/dataModels/biomodel/parser/CompatibilityFixer.java +++ b/src/dataModels/biomodel/parser/CompatibilityFixer.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.parser; diff --git a/src/dataModels/biomodel/parser/GCM2SBML.java b/src/dataModels/biomodel/parser/GCM2SBML.java index 97b939c39..68c0dc224 100644 --- a/src/dataModels/biomodel/parser/GCM2SBML.java +++ b/src/dataModels/biomodel/parser/GCM2SBML.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.parser; diff --git a/src/dataModels/biomodel/parser/GCMParser.java b/src/dataModels/biomodel/parser/GCMParser.java index 8de6f1d21..ba73d635a 100644 --- a/src/dataModels/biomodel/parser/GCMParser.java +++ b/src/dataModels/biomodel/parser/GCMParser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.parser; diff --git a/src/dataModels/biomodel/parser/GridTable.java b/src/dataModels/biomodel/parser/GridTable.java index f576df34b..b990cc9ad 100644 --- a/src/dataModels/biomodel/parser/GridTable.java +++ b/src/dataModels/biomodel/parser/GridTable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.parser; diff --git a/src/dataModels/biomodel/util/ExperimentResult.java b/src/dataModels/biomodel/util/ExperimentResult.java index 139e76440..1373c6cd5 100644 --- a/src/dataModels/biomodel/util/ExperimentResult.java +++ b/src/dataModels/biomodel/util/ExperimentResult.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /** * This class contains eperimental results. */ diff --git a/src/dataModels/biomodel/util/SBMLutilities.java b/src/dataModels/biomodel/util/SBMLutilities.java index f67c67c78..59ef28894 100644 --- a/src/dataModels/biomodel/util/SBMLutilities.java +++ b/src/dataModels/biomodel/util/SBMLutilities.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.util; import java.io.File; diff --git a/src/dataModels/biomodel/util/Utility.java b/src/dataModels/biomodel/util/Utility.java index cb4f67835..e8fb92e58 100644 --- a/src/dataModels/biomodel/util/Utility.java +++ b/src/dataModels/biomodel/util/Utility.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.util; import java.awt.BorderLayout; diff --git a/src/dataModels/biomodel/util/Validation.java b/src/dataModels/biomodel/util/Validation.java index 0f6279a18..d2e9c47ad 100644 --- a/src/dataModels/biomodel/util/Validation.java +++ b/src/dataModels/biomodel/util/Validation.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.util; import org.sbml.jsbml.SBMLDocument; diff --git a/src/dataModels/biomodel/visitor/AbstractPrintVisitor.java b/src/dataModels/biomodel/visitor/AbstractPrintVisitor.java index 224f5531b..730604268 100644 --- a/src/dataModels/biomodel/visitor/AbstractPrintVisitor.java +++ b/src/dataModels/biomodel/visitor/AbstractPrintVisitor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /** * diff --git a/src/dataModels/biomodel/visitor/PrintActivatedBindingVisitor.java b/src/dataModels/biomodel/visitor/PrintActivatedBindingVisitor.java index f496ee94b..e5222e1e6 100644 --- a/src/dataModels/biomodel/visitor/PrintActivatedBindingVisitor.java +++ b/src/dataModels/biomodel/visitor/PrintActivatedBindingVisitor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.visitor; import java.util.ArrayList; diff --git a/src/dataModels/biomodel/visitor/PrintActivatedProductionVisitor.java b/src/dataModels/biomodel/visitor/PrintActivatedProductionVisitor.java index 00046416f..58670d789 100644 --- a/src/dataModels/biomodel/visitor/PrintActivatedProductionVisitor.java +++ b/src/dataModels/biomodel/visitor/PrintActivatedProductionVisitor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.visitor; import org.sbml.jsbml.SBMLDocument; diff --git a/src/dataModels/biomodel/visitor/PrintComplexVisitor.java b/src/dataModels/biomodel/visitor/PrintComplexVisitor.java index bb973df66..7ef3324d0 100644 --- a/src/dataModels/biomodel/visitor/PrintComplexVisitor.java +++ b/src/dataModels/biomodel/visitor/PrintComplexVisitor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.visitor; import java.util.ArrayList; diff --git a/src/dataModels/biomodel/visitor/PrintDecaySpeciesVisitor.java b/src/dataModels/biomodel/visitor/PrintDecaySpeciesVisitor.java index fe344dcf8..7385abef7 100644 --- a/src/dataModels/biomodel/visitor/PrintDecaySpeciesVisitor.java +++ b/src/dataModels/biomodel/visitor/PrintDecaySpeciesVisitor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.visitor; diff --git a/src/dataModels/biomodel/visitor/PrintRepressionBindingVisitor.java b/src/dataModels/biomodel/visitor/PrintRepressionBindingVisitor.java index aa0ca3ca5..23f65d3ea 100644 --- a/src/dataModels/biomodel/visitor/PrintRepressionBindingVisitor.java +++ b/src/dataModels/biomodel/visitor/PrintRepressionBindingVisitor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.visitor; import java.util.ArrayList; diff --git a/src/dataModels/biomodel/visitor/PrintSpeciesVisitor.java b/src/dataModels/biomodel/visitor/PrintSpeciesVisitor.java index 5cf0acbbf..ec6394e94 100644 --- a/src/dataModels/biomodel/visitor/PrintSpeciesVisitor.java +++ b/src/dataModels/biomodel/visitor/PrintSpeciesVisitor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.visitor; import java.util.HashMap; diff --git a/src/dataModels/biomodel/visitor/SpeciesVisitor.java b/src/dataModels/biomodel/visitor/SpeciesVisitor.java index e3ea5c044..49f4c120c 100644 --- a/src/dataModels/biomodel/visitor/SpeciesVisitor.java +++ b/src/dataModels/biomodel/visitor/SpeciesVisitor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.visitor; import dataModels.biomodel.network.BaseSpecies; diff --git a/src/dataModels/biomodel/visitor/VisitableSpecies.java b/src/dataModels/biomodel/visitor/VisitableSpecies.java index f34a37899..bc7a8e79c 100644 --- a/src/dataModels/biomodel/visitor/VisitableSpecies.java +++ b/src/dataModels/biomodel/visitor/VisitableSpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.biomodel.visitor; /** * Describes a species that can be visited diff --git a/src/dataModels/lpn/parser/Abstraction.java b/src/dataModels/lpn/parser/Abstraction.java index 04e6bb842..cfafe5c4c 100644 --- a/src/dataModels/lpn/parser/Abstraction.java +++ b/src/dataModels/lpn/parser/Abstraction.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser; diff --git a/src/dataModels/lpn/parser/ExprTree.java b/src/dataModels/lpn/parser/ExprTree.java index 16418907a..5c032288c 100644 --- a/src/dataModels/lpn/parser/ExprTree.java +++ b/src/dataModels/lpn/parser/ExprTree.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser; import java.util.ArrayList; diff --git a/src/dataModels/lpn/parser/JavaCharStream.java b/src/dataModels/lpn/parser/JavaCharStream.java index d2cb772f3..a9260de12 100644 --- a/src/dataModels/lpn/parser/JavaCharStream.java +++ b/src/dataModels/lpn/parser/JavaCharStream.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* Generated By:JavaCC: Do not edit this line. JavaCharStream.java Version 5.0 */ /* JavaCCOptions:STATIC=false,SUPPORT_CLASS_VISIBILITY_PUBLIC=true */ package dataModels.lpn.parser; diff --git a/src/dataModels/lpn/parser/LPN.java b/src/dataModels/lpn/parser/LPN.java index 044a8ab04..23b0108a4 100644 --- a/src/dataModels/lpn/parser/LPN.java +++ b/src/dataModels/lpn/parser/LPN.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser; diff --git a/src/dataModels/lpn/parser/Lpn2verilog.java b/src/dataModels/lpn/parser/Lpn2verilog.java index 096a049a0..7001a3616 100644 --- a/src/dataModels/lpn/parser/Lpn2verilog.java +++ b/src/dataModels/lpn/parser/Lpn2verilog.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser; import java.io.*; diff --git a/src/dataModels/lpn/parser/LpnDecomposition/Component.java b/src/dataModels/lpn/parser/LpnDecomposition/Component.java index e0c9028c0..93594f052 100644 --- a/src/dataModels/lpn/parser/LpnDecomposition/Component.java +++ b/src/dataModels/lpn/parser/LpnDecomposition/Component.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser.LpnDecomposition; import java.util.ArrayList; diff --git a/src/dataModels/lpn/parser/LpnDecomposition/Edge.java b/src/dataModels/lpn/parser/LpnDecomposition/Edge.java index 63e9eae81..f18185821 100644 --- a/src/dataModels/lpn/parser/LpnDecomposition/Edge.java +++ b/src/dataModels/lpn/parser/LpnDecomposition/Edge.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser.LpnDecomposition; diff --git a/src/dataModels/lpn/parser/LpnDecomposition/LpnComponentGraph.java b/src/dataModels/lpn/parser/LpnDecomposition/LpnComponentGraph.java index 343404702..9ed6313e4 100644 --- a/src/dataModels/lpn/parser/LpnDecomposition/LpnComponentGraph.java +++ b/src/dataModels/lpn/parser/LpnDecomposition/LpnComponentGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser.LpnDecomposition; import java.io.BufferedWriter; diff --git a/src/dataModels/lpn/parser/LpnDecomposition/LpnComponentList.java b/src/dataModels/lpn/parser/LpnDecomposition/LpnComponentList.java index 8abe68997..6d5cbbde7 100644 --- a/src/dataModels/lpn/parser/LpnDecomposition/LpnComponentList.java +++ b/src/dataModels/lpn/parser/LpnDecomposition/LpnComponentList.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser.LpnDecomposition; import java.util.ArrayList; diff --git a/src/dataModels/lpn/parser/LpnDecomposition/LpnProcess.java b/src/dataModels/lpn/parser/LpnDecomposition/LpnProcess.java index fe0053d32..a9f59efce 100644 --- a/src/dataModels/lpn/parser/LpnDecomposition/LpnProcess.java +++ b/src/dataModels/lpn/parser/LpnDecomposition/LpnProcess.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser.LpnDecomposition; import java.util.ArrayList; diff --git a/src/dataModels/lpn/parser/LpnDecomposition/Vertex.java b/src/dataModels/lpn/parser/LpnDecomposition/Vertex.java index 3db0c8a07..9eb275127 100644 --- a/src/dataModels/lpn/parser/LpnDecomposition/Vertex.java +++ b/src/dataModels/lpn/parser/LpnDecomposition/Vertex.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser.LpnDecomposition; import java.util.HashMap; diff --git a/src/dataModels/lpn/parser/LpnDecomposition/VertexComparator.java b/src/dataModels/lpn/parser/LpnDecomposition/VertexComparator.java index f6b4e674a..ece9f8f47 100644 --- a/src/dataModels/lpn/parser/LpnDecomposition/VertexComparator.java +++ b/src/dataModels/lpn/parser/LpnDecomposition/VertexComparator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser.LpnDecomposition; import java.util.Comparator; diff --git a/src/dataModels/lpn/parser/ParseException.java b/src/dataModels/lpn/parser/ParseException.java index 513906be7..d3948560e 100644 --- a/src/dataModels/lpn/parser/ParseException.java +++ b/src/dataModels/lpn/parser/ParseException.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* Generated By:JavaCC: Do not edit this line. ParseException.java Version 5.0 */ /* JavaCCOptions:KEEP_LINE_COL=null */ package dataModels.lpn.parser; diff --git a/src/dataModels/lpn/parser/Parser.java b/src/dataModels/lpn/parser/Parser.java index 2c608cf40..d37573b82 100644 --- a/src/dataModels/lpn/parser/Parser.java +++ b/src/dataModels/lpn/parser/Parser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* Generated By:JavaCC: Do not edit this line. Parser.java */ package dataModels.lpn.parser; diff --git a/src/dataModels/lpn/parser/ParserConstants.java b/src/dataModels/lpn/parser/ParserConstants.java index 84f8bf084..d80f90cad 100644 --- a/src/dataModels/lpn/parser/ParserConstants.java +++ b/src/dataModels/lpn/parser/ParserConstants.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* Generated By:JavaCC: Do not edit this line. ParserConstants.java */ package dataModels.lpn.parser; diff --git a/src/dataModels/lpn/parser/ParserTokenManager.java b/src/dataModels/lpn/parser/ParserTokenManager.java index a27d3e2cc..aa74eac3f 100644 --- a/src/dataModels/lpn/parser/ParserTokenManager.java +++ b/src/dataModels/lpn/parser/ParserTokenManager.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* Generated By:JavaCC: Do not edit this line. ParserTokenManager.java */ package dataModels.lpn.parser; diff --git a/src/dataModels/lpn/parser/Place.java b/src/dataModels/lpn/parser/Place.java index 4e9427f36..6d3d4421a 100644 --- a/src/dataModels/lpn/parser/Place.java +++ b/src/dataModels/lpn/parser/Place.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser; import java.util.ArrayList; diff --git a/src/dataModels/lpn/parser/Token.java b/src/dataModels/lpn/parser/Token.java index 559b31e93..b87f8493f 100644 --- a/src/dataModels/lpn/parser/Token.java +++ b/src/dataModels/lpn/parser/Token.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* Generated By:JavaCC: Do not edit this line. Token.java Version 5.0 */ /* JavaCCOptions:TOKEN_EXTENDS=,KEEP_LINE_COL=null,SUPPORT_CLASS_VISIBILITY_PUBLIC=true */ package dataModels.lpn.parser; diff --git a/src/dataModels/lpn/parser/TokenMgrError.java b/src/dataModels/lpn/parser/TokenMgrError.java index 44b6bfe5a..bac951d43 100644 --- a/src/dataModels/lpn/parser/TokenMgrError.java +++ b/src/dataModels/lpn/parser/TokenMgrError.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* Generated By:JavaCC: Do not edit this line. TokenMgrError.java Version 5.0 */ /* JavaCCOptions: */ package dataModels.lpn.parser; diff --git a/src/dataModels/lpn/parser/Transition.java b/src/dataModels/lpn/parser/Transition.java index dd2e3f682..e400dd1db 100644 --- a/src/dataModels/lpn/parser/Transition.java +++ b/src/dataModels/lpn/parser/Transition.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser; import java.util.ArrayList; diff --git a/src/dataModels/lpn/parser/Translator.java b/src/dataModels/lpn/parser/Translator.java index a1fb515f1..f474fc4a1 100644 --- a/src/dataModels/lpn/parser/Translator.java +++ b/src/dataModels/lpn/parser/Translator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser; import java.io.FileNotFoundException; diff --git a/src/dataModels/lpn/parser/Variable.java b/src/dataModels/lpn/parser/Variable.java index a39c3f63a..a3fbf4286 100644 --- a/src/dataModels/lpn/parser/Variable.java +++ b/src/dataModels/lpn/parser/Variable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser; import java.util.ArrayList; diff --git a/src/dataModels/lpn/parser/properties/AbstractionProperty.java b/src/dataModels/lpn/parser/properties/AbstractionProperty.java index b2a27ce6b..b881e5e1a 100644 --- a/src/dataModels/lpn/parser/properties/AbstractionProperty.java +++ b/src/dataModels/lpn/parser/properties/AbstractionProperty.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser.properties; import javax.swing.DefaultListModel; diff --git a/src/dataModels/lpn/parser/properties/BuildProperty.java b/src/dataModels/lpn/parser/properties/BuildProperty.java index 9c5ee4243..045a13463 100644 --- a/src/dataModels/lpn/parser/properties/BuildProperty.java +++ b/src/dataModels/lpn/parser/properties/BuildProperty.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.lpn.parser.properties; import java.awt.List; diff --git a/src/dataModels/lpn/parser/properties/PropertyLexer.java b/src/dataModels/lpn/parser/properties/PropertyLexer.java index dba3486fc..4666f79b9 100644 --- a/src/dataModels/lpn/parser/properties/PropertyLexer.java +++ b/src/dataModels/lpn/parser/properties/PropertyLexer.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ // $ANTLR 3.5 /Users/myers/research/nobackup/workspace/BioSim/gui/src/lpn/parser/properties/Property.g 2016-09-01 11:02:46 package dataModels.lpn.parser.properties; diff --git a/src/dataModels/lpn/parser/properties/PropertyParser.java b/src/dataModels/lpn/parser/properties/PropertyParser.java index 7b6f6d0cb..c4a486112 100644 --- a/src/dataModels/lpn/parser/properties/PropertyParser.java +++ b/src/dataModels/lpn/parser/properties/PropertyParser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ // $ANTLR 3.5 /Users/myers/research/nobackup/workspace/BioSim/gui/src/lpn/parser/properties/Property.g 2016-09-01 11:02:46 package dataModels.lpn.parser.properties; diff --git a/src/dataModels/util/GlobalConstants.java b/src/dataModels/util/GlobalConstants.java index 977e3fae1..dc40e2fdd 100644 --- a/src/dataModels/util/GlobalConstants.java +++ b/src/dataModels/util/GlobalConstants.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util; import java.io.File; diff --git a/src/dataModels/util/Message.java b/src/dataModels/util/Message.java index faee42eb5..278b01b95 100644 --- a/src/dataModels/util/Message.java +++ b/src/dataModels/util/Message.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util; diff --git a/src/dataModels/util/MutableString.java b/src/dataModels/util/MutableString.java index ee857a9fb..4bf3311a1 100644 --- a/src/dataModels/util/MutableString.java +++ b/src/dataModels/util/MutableString.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util; import java.io.Serializable; diff --git a/src/dataModels/util/dataparser/CSVParser.java b/src/dataModels/util/dataparser/CSVParser.java index 7994bfc8a..7fefc4b37 100644 --- a/src/dataModels/util/dataparser/CSVParser.java +++ b/src/dataModels/util/dataparser/CSVParser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util.dataparser; import java.io.*; diff --git a/src/dataModels/util/dataparser/DATParser.java b/src/dataModels/util/dataparser/DATParser.java index 15f076f0f..ec419b25b 100644 --- a/src/dataModels/util/dataparser/DATParser.java +++ b/src/dataModels/util/dataparser/DATParser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util.dataparser; import java.io.*; diff --git a/src/dataModels/util/dataparser/DTSDParser.java b/src/dataModels/util/dataparser/DTSDParser.java index 7b8fbd2b1..758a88a33 100644 --- a/src/dataModels/util/dataparser/DTSDParser.java +++ b/src/dataModels/util/dataparser/DTSDParser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util.dataparser; import java.awt.Point; diff --git a/src/dataModels/util/dataparser/DataParser.java b/src/dataModels/util/dataparser/DataParser.java index ba18a3c7f..9a53909a4 100644 --- a/src/dataModels/util/dataparser/DataParser.java +++ b/src/dataModels/util/dataparser/DataParser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util.dataparser; import java.awt.*; diff --git a/src/dataModels/util/dataparser/TSDParser.java b/src/dataModels/util/dataparser/TSDParser.java index edb100bc0..a1562f72a 100644 --- a/src/dataModels/util/dataparser/TSDParser.java +++ b/src/dataModels/util/dataparser/TSDParser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util.dataparser; import java.io.*; diff --git a/src/dataModels/util/exceptions/BioSimException.java b/src/dataModels/util/exceptions/BioSimException.java index 3b51b59b4..a1ed54ee8 100644 --- a/src/dataModels/util/exceptions/BioSimException.java +++ b/src/dataModels/util/exceptions/BioSimException.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util.exceptions; public class BioSimException extends Exception{ diff --git a/src/dataModels/util/exceptions/SBOLException.java b/src/dataModels/util/exceptions/SBOLException.java index 5268d9630..7ac7c60a0 100644 --- a/src/dataModels/util/exceptions/SBOLException.java +++ b/src/dataModels/util/exceptions/SBOLException.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package dataModels.util.exceptions; public class SBOLException extends BioSimException{ diff --git a/src/frontend/analysis/AnalysisThread.java b/src/frontend/analysis/AnalysisThread.java index 00627b063..e541eed1d 100644 --- a/src/frontend/analysis/AnalysisThread.java +++ b/src/frontend/analysis/AnalysisThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.analysis; public class AnalysisThread extends Thread { diff --git a/src/frontend/analysis/AnalysisView.java b/src/frontend/analysis/AnalysisView.java index dc5f4bc0e..5ebf2f77e 100644 --- a/src/frontend/analysis/AnalysisView.java +++ b/src/frontend/analysis/AnalysisView.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.analysis; import java.awt.AWTError; diff --git a/src/frontend/analysis/ConstraintTermThread.java b/src/frontend/analysis/ConstraintTermThread.java index 11ac7af23..8ae0c1857 100644 --- a/src/frontend/analysis/ConstraintTermThread.java +++ b/src/frontend/analysis/ConstraintTermThread.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.analysis; import java.util.ArrayList; diff --git a/src/frontend/analysis/Nary_Run.java b/src/frontend/analysis/Nary_Run.java index 46bfe1210..448e186cf 100644 --- a/src/frontend/analysis/Nary_Run.java +++ b/src/frontend/analysis/Nary_Run.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.analysis; import java.awt.AWTError; diff --git a/src/frontend/analysis/Run.java b/src/frontend/analysis/Run.java index 3680f981c..364ad84ba 100644 --- a/src/frontend/analysis/Run.java +++ b/src/frontend/analysis/Run.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.analysis; import java.awt.Component; diff --git a/src/frontend/analysis/incrementalsim/EventQueueComparator.java b/src/frontend/analysis/incrementalsim/EventQueueComparator.java index f56f57241..0aed444ff 100644 --- a/src/frontend/analysis/incrementalsim/EventQueueComparator.java +++ b/src/frontend/analysis/incrementalsim/EventQueueComparator.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.analysis.incrementalsim; import java.util.Comparator; diff --git a/src/frontend/analysis/incrementalsim/EventQueueElement.java b/src/frontend/analysis/incrementalsim/EventQueueElement.java index 3868f4451..c47c4a219 100644 --- a/src/frontend/analysis/incrementalsim/EventQueueElement.java +++ b/src/frontend/analysis/incrementalsim/EventQueueElement.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.analysis.incrementalsim; diff --git a/src/frontend/analysis/incrementalsim/GillespieSSAJavaSingleStep.java b/src/frontend/analysis/incrementalsim/GillespieSSAJavaSingleStep.java index 178a7f77b..f0196411a 100644 --- a/src/frontend/analysis/incrementalsim/GillespieSSAJavaSingleStep.java +++ b/src/frontend/analysis/incrementalsim/GillespieSSAJavaSingleStep.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.analysis.incrementalsim; import java.util.ArrayList; diff --git a/src/frontend/analysis/incrementalsim/SimResultsTable.java b/src/frontend/analysis/incrementalsim/SimResultsTable.java index 72888139a..88aa9aefc 100644 --- a/src/frontend/analysis/incrementalsim/SimResultsTable.java +++ b/src/frontend/analysis/incrementalsim/SimResultsTable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.analysis.incrementalsim; import java.awt.Dimension; diff --git a/src/frontend/biomodel/gui/comp/ComponentsPanel.java b/src/frontend/biomodel/gui/comp/ComponentsPanel.java index 3d33e106d..373752ff9 100644 --- a/src/frontend/biomodel/gui/comp/ComponentsPanel.java +++ b/src/frontend/biomodel/gui/comp/ComponentsPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.comp; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/comp/DropComponentPanel.java b/src/frontend/biomodel/gui/comp/DropComponentPanel.java index c9229f74f..438c3a495 100644 --- a/src/frontend/biomodel/gui/comp/DropComponentPanel.java +++ b/src/frontend/biomodel/gui/comp/DropComponentPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.comp; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/comp/Grid.java b/src/frontend/biomodel/gui/comp/Grid.java index 0ca5fdb34..358129cc2 100644 --- a/src/frontend/biomodel/gui/comp/Grid.java +++ b/src/frontend/biomodel/gui/comp/Grid.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.comp; import java.awt.Color; diff --git a/src/frontend/biomodel/gui/comp/GridAction.java b/src/frontend/biomodel/gui/comp/GridAction.java index 0a9fab8ad..3fdbaf568 100644 --- a/src/frontend/biomodel/gui/comp/GridAction.java +++ b/src/frontend/biomodel/gui/comp/GridAction.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.comp; diff --git a/src/frontend/biomodel/gui/comp/GridPanel.java b/src/frontend/biomodel/gui/comp/GridPanel.java index 3e5aa8332..bb2de0db6 100644 --- a/src/frontend/biomodel/gui/comp/GridPanel.java +++ b/src/frontend/biomodel/gui/comp/GridPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.comp; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/fba/FBAObjective.java b/src/frontend/biomodel/gui/fba/FBAObjective.java index 7364730fe..08e6722d4 100644 --- a/src/frontend/biomodel/gui/fba/FBAObjective.java +++ b/src/frontend/biomodel/gui/fba/FBAObjective.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.fba; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/gcm/InfluencePanel.java b/src/frontend/biomodel/gui/gcm/InfluencePanel.java index 4cb32da03..ede1d1cb4 100644 --- a/src/frontend/biomodel/gui/gcm/InfluencePanel.java +++ b/src/frontend/biomodel/gui/gcm/InfluencePanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.gcm; diff --git a/src/frontend/biomodel/gui/gcm/PromoterPanel.java b/src/frontend/biomodel/gui/gcm/PromoterPanel.java index 999a8acc1..0aa2167b6 100644 --- a/src/frontend/biomodel/gui/gcm/PromoterPanel.java +++ b/src/frontend/biomodel/gui/gcm/PromoterPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.gcm; diff --git a/src/frontend/biomodel/gui/movie/MovieAppearance.java b/src/frontend/biomodel/gui/movie/MovieAppearance.java index 694993bfa..64b0b3582 100644 --- a/src/frontend/biomodel/gui/movie/MovieAppearance.java +++ b/src/frontend/biomodel/gui/movie/MovieAppearance.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.movie; import java.awt.Color; diff --git a/src/frontend/biomodel/gui/movie/MovieContainer.java b/src/frontend/biomodel/gui/movie/MovieContainer.java index 5fb77015b..9486439b4 100644 --- a/src/frontend/biomodel/gui/movie/MovieContainer.java +++ b/src/frontend/biomodel/gui/movie/MovieContainer.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.movie; diff --git a/src/frontend/biomodel/gui/movie/MovieScheme.java b/src/frontend/biomodel/gui/movie/MovieScheme.java index c94da90f5..69b801acd 100644 --- a/src/frontend/biomodel/gui/movie/MovieScheme.java +++ b/src/frontend/biomodel/gui/movie/MovieScheme.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.movie; diff --git a/src/frontend/biomodel/gui/movie/SchemeChooserPanel.java b/src/frontend/biomodel/gui/movie/SchemeChooserPanel.java index 4d725c28d..0ad8dede6 100644 --- a/src/frontend/biomodel/gui/movie/SchemeChooserPanel.java +++ b/src/frontend/biomodel/gui/movie/SchemeChooserPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.movie; diff --git a/src/frontend/biomodel/gui/movie/SerializableScheme.java b/src/frontend/biomodel/gui/movie/SerializableScheme.java index 85cfa4904..6df90815f 100644 --- a/src/frontend/biomodel/gui/movie/SerializableScheme.java +++ b/src/frontend/biomodel/gui/movie/SerializableScheme.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.movie; import java.awt.GradientPaint; diff --git a/src/frontend/biomodel/gui/sbmlcore/Compartments.java b/src/frontend/biomodel/gui/sbmlcore/Compartments.java index fd4ecf26f..ce2732466 100644 --- a/src/frontend/biomodel/gui/sbmlcore/Compartments.java +++ b/src/frontend/biomodel/gui/sbmlcore/Compartments.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/Constraints.java b/src/frontend/biomodel/gui/sbmlcore/Constraints.java index c4805c7aa..b902573ff 100644 --- a/src/frontend/biomodel/gui/sbmlcore/Constraints.java +++ b/src/frontend/biomodel/gui/sbmlcore/Constraints.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/ElementsPanel.java b/src/frontend/biomodel/gui/sbmlcore/ElementsPanel.java index d83399e06..91e5f5d25 100644 --- a/src/frontend/biomodel/gui/sbmlcore/ElementsPanel.java +++ b/src/frontend/biomodel/gui/sbmlcore/ElementsPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.FlowLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/Events.java b/src/frontend/biomodel/gui/sbmlcore/Events.java index bc6dca92d..f0f0d3e11 100644 --- a/src/frontend/biomodel/gui/sbmlcore/Events.java +++ b/src/frontend/biomodel/gui/sbmlcore/Events.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/Functions.java b/src/frontend/biomodel/gui/sbmlcore/Functions.java index 767268fdb..bc8180a8f 100644 --- a/src/frontend/biomodel/gui/sbmlcore/Functions.java +++ b/src/frontend/biomodel/gui/sbmlcore/Functions.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/InitialAssignments.java b/src/frontend/biomodel/gui/sbmlcore/InitialAssignments.java index da5177a2d..36eb52d77 100644 --- a/src/frontend/biomodel/gui/sbmlcore/InitialAssignments.java +++ b/src/frontend/biomodel/gui/sbmlcore/InitialAssignments.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/ModelPanel.java b/src/frontend/biomodel/gui/sbmlcore/ModelPanel.java index 241d335ce..bafcbc785 100644 --- a/src/frontend/biomodel/gui/sbmlcore/ModelPanel.java +++ b/src/frontend/biomodel/gui/sbmlcore/ModelPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.GridLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/MySpecies.java b/src/frontend/biomodel/gui/sbmlcore/MySpecies.java index df561a278..7502e7cc8 100644 --- a/src/frontend/biomodel/gui/sbmlcore/MySpecies.java +++ b/src/frontend/biomodel/gui/sbmlcore/MySpecies.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/Parameters.java b/src/frontend/biomodel/gui/sbmlcore/Parameters.java index 224b42ee1..c2d8dbb2b 100644 --- a/src/frontend/biomodel/gui/sbmlcore/Parameters.java +++ b/src/frontend/biomodel/gui/sbmlcore/Parameters.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/Reactions.java b/src/frontend/biomodel/gui/sbmlcore/Reactions.java index 3ba847367..06a1ec669 100644 --- a/src/frontend/biomodel/gui/sbmlcore/Reactions.java +++ b/src/frontend/biomodel/gui/sbmlcore/Reactions.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/Rules.java b/src/frontend/biomodel/gui/sbmlcore/Rules.java index 60f24b496..998b5281d 100644 --- a/src/frontend/biomodel/gui/sbmlcore/Rules.java +++ b/src/frontend/biomodel/gui/sbmlcore/Rules.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbmlcore/SpeciesPanel.java b/src/frontend/biomodel/gui/sbmlcore/SpeciesPanel.java index 20c24fe34..c4e8ae7a1 100644 --- a/src/frontend/biomodel/gui/sbmlcore/SpeciesPanel.java +++ b/src/frontend/biomodel/gui/sbmlcore/SpeciesPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; diff --git a/src/frontend/biomodel/gui/sbmlcore/Units.java b/src/frontend/biomodel/gui/sbmlcore/Units.java index c09dd2085..f00f98049 100644 --- a/src/frontend/biomodel/gui/sbmlcore/Units.java +++ b/src/frontend/biomodel/gui/sbmlcore/Units.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbmlcore; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/sbol/SBOLAssociationPanel2.java b/src/frontend/biomodel/gui/sbol/SBOLAssociationPanel2.java index 94cd1a4b7..2c017ef01 100644 --- a/src/frontend/biomodel/gui/sbol/SBOLAssociationPanel2.java +++ b/src/frontend/biomodel/gui/sbol/SBOLAssociationPanel2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbol; import java.awt.*; diff --git a/src/frontend/biomodel/gui/sbol/SBOLDescriptorPanel2.java b/src/frontend/biomodel/gui/sbol/SBOLDescriptorPanel2.java index 85bb9e383..49f6ea400 100644 --- a/src/frontend/biomodel/gui/sbol/SBOLDescriptorPanel2.java +++ b/src/frontend/biomodel/gui/sbol/SBOLDescriptorPanel2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbol; import java.awt.GridLayout; diff --git a/src/frontend/biomodel/gui/sbol/SBOLField2.java b/src/frontend/biomodel/gui/sbol/SBOLField2.java index 322e665b4..8d48065fd 100644 --- a/src/frontend/biomodel/gui/sbol/SBOLField2.java +++ b/src/frontend/biomodel/gui/sbol/SBOLField2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.sbol; import java.awt.GridLayout; diff --git a/src/frontend/biomodel/gui/schematic/BioGraph.java b/src/frontend/biomodel/gui/schematic/BioGraph.java index 83d09b392..a25bef61c 100644 --- a/src/frontend/biomodel/gui/schematic/BioGraph.java +++ b/src/frontend/biomodel/gui/schematic/BioGraph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /** * */ diff --git a/src/frontend/biomodel/gui/schematic/EditorPopupMenu.java b/src/frontend/biomodel/gui/schematic/EditorPopupMenu.java index 79bf87f11..1ce94283a 100644 --- a/src/frontend/biomodel/gui/schematic/EditorPopupMenu.java +++ b/src/frontend/biomodel/gui/schematic/EditorPopupMenu.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.schematic; diff --git a/src/frontend/biomodel/gui/schematic/Layouting.java b/src/frontend/biomodel/gui/schematic/Layouting.java index af910349f..e497564a2 100644 --- a/src/frontend/biomodel/gui/schematic/Layouting.java +++ b/src/frontend/biomodel/gui/schematic/Layouting.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.schematic; import java.awt.event.ActionListener; diff --git a/src/frontend/biomodel/gui/schematic/ListChooser.java b/src/frontend/biomodel/gui/schematic/ListChooser.java index e3de7a36c..695935a3e 100644 --- a/src/frontend/biomodel/gui/schematic/ListChooser.java +++ b/src/frontend/biomodel/gui/schematic/ListChooser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.schematic; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/schematic/ModelEditor.java b/src/frontend/biomodel/gui/schematic/ModelEditor.java index be4cf08dc..47aabcb02 100644 --- a/src/frontend/biomodel/gui/schematic/ModelEditor.java +++ b/src/frontend/biomodel/gui/schematic/ModelEditor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.schematic; diff --git a/src/frontend/biomodel/gui/schematic/ModelToolBar.java b/src/frontend/biomodel/gui/schematic/ModelToolBar.java index e92144849..128990fb6 100644 --- a/src/frontend/biomodel/gui/schematic/ModelToolBar.java +++ b/src/frontend/biomodel/gui/schematic/ModelToolBar.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.schematic; import javax.swing.JToolBar; diff --git a/src/frontend/biomodel/gui/schematic/Schematic.java b/src/frontend/biomodel/gui/schematic/Schematic.java index 382fdedc6..afba748de 100644 --- a/src/frontend/biomodel/gui/schematic/Schematic.java +++ b/src/frontend/biomodel/gui/schematic/Schematic.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.schematic; diff --git a/src/frontend/biomodel/gui/schematic/TreeChooser.java b/src/frontend/biomodel/gui/schematic/TreeChooser.java index cde631f51..a36ae1fe5 100644 --- a/src/frontend/biomodel/gui/schematic/TreeChooser.java +++ b/src/frontend/biomodel/gui/schematic/TreeChooser.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.schematic; import java.awt.BorderLayout; diff --git a/src/frontend/biomodel/gui/schematic/Utils.java b/src/frontend/biomodel/gui/schematic/Utils.java index d8410cb7f..d08204e31 100644 --- a/src/frontend/biomodel/gui/schematic/Utils.java +++ b/src/frontend/biomodel/gui/schematic/Utils.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.schematic; import java.awt.Dimension; diff --git a/src/frontend/biomodel/gui/util/AbstractRunnableNamedButton.java b/src/frontend/biomodel/gui/util/AbstractRunnableNamedButton.java index 3a15f7d54..844f02680 100644 --- a/src/frontend/biomodel/gui/util/AbstractRunnableNamedButton.java +++ b/src/frontend/biomodel/gui/util/AbstractRunnableNamedButton.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; import javax.swing.JButton; diff --git a/src/frontend/biomodel/gui/util/ComponentAction.java b/src/frontend/biomodel/gui/util/ComponentAction.java index c6f194631..647f643ae 100644 --- a/src/frontend/biomodel/gui/util/ComponentAction.java +++ b/src/frontend/biomodel/gui/util/ComponentAction.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; import java.awt.event.ActionEvent; diff --git a/src/frontend/biomodel/gui/util/EnableElement.java b/src/frontend/biomodel/gui/util/EnableElement.java index 286d99256..16a798d3d 100755 --- a/src/frontend/biomodel/gui/util/EnableElement.java +++ b/src/frontend/biomodel/gui/util/EnableElement.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; diff --git a/src/frontend/biomodel/gui/util/FieldPanel.java b/src/frontend/biomodel/gui/util/FieldPanel.java index 2195f5a26..04b711f3d 100755 --- a/src/frontend/biomodel/gui/util/FieldPanel.java +++ b/src/frontend/biomodel/gui/util/FieldPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; import java.awt.GridLayout; diff --git a/src/frontend/biomodel/gui/util/NamedObject.java b/src/frontend/biomodel/gui/util/NamedObject.java index 1b05aca79..b68f66806 100644 --- a/src/frontend/biomodel/gui/util/NamedObject.java +++ b/src/frontend/biomodel/gui/util/NamedObject.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; public interface NamedObject { diff --git a/src/frontend/biomodel/gui/util/PropertyField.java b/src/frontend/biomodel/gui/util/PropertyField.java index 1b0c533cd..5f871a25c 100644 --- a/src/frontend/biomodel/gui/util/PropertyField.java +++ b/src/frontend/biomodel/gui/util/PropertyField.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; diff --git a/src/frontend/biomodel/gui/util/PropertyList.java b/src/frontend/biomodel/gui/util/PropertyList.java index a7e0a2be8..5884733b3 100755 --- a/src/frontend/biomodel/gui/util/PropertyList.java +++ b/src/frontend/biomodel/gui/util/PropertyList.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; import java.util.Collection; diff --git a/src/frontend/biomodel/gui/util/PropertyProvider.java b/src/frontend/biomodel/gui/util/PropertyProvider.java index 86725f8d6..9acc175ea 100644 --- a/src/frontend/biomodel/gui/util/PropertyProvider.java +++ b/src/frontend/biomodel/gui/util/PropertyProvider.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; /** diff --git a/src/frontend/biomodel/gui/util/Runnable.java b/src/frontend/biomodel/gui/util/Runnable.java index 92d4867d6..c38a89664 100755 --- a/src/frontend/biomodel/gui/util/Runnable.java +++ b/src/frontend/biomodel/gui/util/Runnable.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; public interface Runnable { diff --git a/src/frontend/biomodel/gui/util/StateElement.java b/src/frontend/biomodel/gui/util/StateElement.java index b8b73ec4f..88966cb2b 100755 --- a/src/frontend/biomodel/gui/util/StateElement.java +++ b/src/frontend/biomodel/gui/util/StateElement.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.gui.util; import java.util.ArrayList; diff --git a/src/frontend/biomodel/util/UndoManager.java b/src/frontend/biomodel/util/UndoManager.java index 42e7b2f68..bb48f4508 100644 --- a/src/frontend/biomodel/util/UndoManager.java +++ b/src/frontend/biomodel/util/UndoManager.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.biomodel.util; //import java.util.Deque; diff --git a/src/frontend/graph/Graph.java b/src/frontend/graph/Graph.java index e7536ab3f..cbcb42f18 100644 --- a/src/frontend/graph/Graph.java +++ b/src/frontend/graph/Graph.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.graph; import java.awt.BorderLayout; diff --git a/src/frontend/learn/AMSModel/LearnLPN.java b/src/frontend/learn/AMSModel/LearnLPN.java index b58ff943b..d72ce012b 100644 --- a/src/frontend/learn/AMSModel/LearnLPN.java +++ b/src/frontend/learn/AMSModel/LearnLPN.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.learn.AMSModel; import java.awt.*; diff --git a/src/frontend/learn/GCM/LearnGCM.java b/src/frontend/learn/GCM/LearnGCM.java index 8a4abd6d9..fe5f77434 100644 --- a/src/frontend/learn/GCM/LearnGCM.java +++ b/src/frontend/learn/GCM/LearnGCM.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.learn.GCM; import java.awt.AWTError; diff --git a/src/frontend/learn/datamanager/DataManager.java b/src/frontend/learn/datamanager/DataManager.java index e72079197..1c5fddaac 100644 --- a/src/frontend/learn/datamanager/DataManager.java +++ b/src/frontend/learn/datamanager/DataManager.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.learn.datamanager; import java.awt.*; diff --git a/src/frontend/learn/parameterestimator/ParamEstimatorPanel.java b/src/frontend/learn/parameterestimator/ParamEstimatorPanel.java index 5ff096a51..6fabf887f 100644 --- a/src/frontend/learn/parameterestimator/ParamEstimatorPanel.java +++ b/src/frontend/learn/parameterestimator/ParamEstimatorPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.learn.parameterestimator; import java.awt.BorderLayout; diff --git a/src/frontend/lpn/gui/AssignmentPanel.java b/src/frontend/lpn/gui/AssignmentPanel.java index 9ffc3eecb..9c0c8a844 100644 --- a/src/frontend/lpn/gui/AssignmentPanel.java +++ b/src/frontend/lpn/gui/AssignmentPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.lpn.gui; import java.awt.GridLayout; diff --git a/src/frontend/lpn/gui/ControlFlowPanel.java b/src/frontend/lpn/gui/ControlFlowPanel.java index 30f417b73..acdd6b7e3 100644 --- a/src/frontend/lpn/gui/ControlFlowPanel.java +++ b/src/frontend/lpn/gui/ControlFlowPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.lpn.gui; import java.awt.GridLayout; diff --git a/src/frontend/lpn/gui/LHPNEditor.java b/src/frontend/lpn/gui/LHPNEditor.java index 5814bcb38..4dfd14952 100644 --- a/src/frontend/lpn/gui/LHPNEditor.java +++ b/src/frontend/lpn/gui/LHPNEditor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.lpn.gui; import java.awt.BorderLayout; diff --git a/src/frontend/lpn/gui/PlacePanel.java b/src/frontend/lpn/gui/PlacePanel.java index 63d9b80b1..18091c3b4 100644 --- a/src/frontend/lpn/gui/PlacePanel.java +++ b/src/frontend/lpn/gui/PlacePanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.lpn.gui; import java.awt.GridLayout; diff --git a/src/frontend/lpn/gui/PropertyField.java b/src/frontend/lpn/gui/PropertyField.java index f2bb25dbb..7664bed93 100644 --- a/src/frontend/lpn/gui/PropertyField.java +++ b/src/frontend/lpn/gui/PropertyField.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.lpn.gui; diff --git a/src/frontend/lpn/gui/PropertyPanel.java b/src/frontend/lpn/gui/PropertyPanel.java index 864522184..afd626ee2 100644 --- a/src/frontend/lpn/gui/PropertyPanel.java +++ b/src/frontend/lpn/gui/PropertyPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.lpn.gui; import java.awt.GridLayout; diff --git a/src/frontend/lpn/gui/TransitionsPanel.java b/src/frontend/lpn/gui/TransitionsPanel.java index 5f4815799..835f15bed 100644 --- a/src/frontend/lpn/gui/TransitionsPanel.java +++ b/src/frontend/lpn/gui/TransitionsPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.lpn.gui; import java.awt.GridLayout; diff --git a/src/frontend/lpn/gui/VariablesPanel.java b/src/frontend/lpn/gui/VariablesPanel.java index 430c0022d..6dcddab75 100644 --- a/src/frontend/lpn/gui/VariablesPanel.java +++ b/src/frontend/lpn/gui/VariablesPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.lpn.gui; import java.awt.GridLayout; diff --git a/src/frontend/main/Gui.java b/src/frontend/main/Gui.java index 12c3a7176..f1ebe9ed4 100644 --- a/src/frontend/main/Gui.java +++ b/src/frontend/main/Gui.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.main; import java.awt.AWTError; diff --git a/src/frontend/main/Log.java b/src/frontend/main/Log.java index 48dde6ef2..5641e61a6 100644 --- a/src/frontend/main/Log.java +++ b/src/frontend/main/Log.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.main; import java.awt.*; diff --git a/src/frontend/main/util/EditPreferences.java b/src/frontend/main/util/EditPreferences.java index 74b235f1c..fa242a22c 100644 --- a/src/frontend/main/util/EditPreferences.java +++ b/src/frontend/main/util/EditPreferences.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.main.util; import java.awt.BorderLayout; diff --git a/src/frontend/main/util/ExampleFileFilter.java b/src/frontend/main/util/ExampleFileFilter.java index f1e5710bb..c964ed0dd 100644 --- a/src/frontend/main/util/ExampleFileFilter.java +++ b/src/frontend/main/util/ExampleFileFilter.java @@ -3,7 +3,7 @@ package frontend.main.util; /* * @(#)ExampleFileFilter.java 1.9 99/04/23 * - * Copyright (c) 1998, 1999 by Sun Microsystems, Inc. All Rights Reserved. + * Copyright (c) 1998, 2017 by Sun Microsystems, Inc. All Rights Reserved. * * Sun grants you ("Licensee") a non-exclusive, royalty free, license to use, * modify and redistribute this software in source and binary code form, diff --git a/src/frontend/main/util/FileTree.java b/src/frontend/main/util/FileTree.java index 276302783..4c761a2b2 100644 --- a/src/frontend/main/util/FileTree.java +++ b/src/frontend/main/util/FileTree.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.main.util; diff --git a/src/frontend/main/util/SpringUtilities.java b/src/frontend/main/util/SpringUtilities.java index 351121b9c..05ff91b41 100644 --- a/src/frontend/main/util/SpringUtilities.java +++ b/src/frontend/main/util/SpringUtilities.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 1995, 2008, Oracle and/or its affiliates. All rights reserved. + * Copyright (c) 1995, 2017, Oracle and/or its affiliates. All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions diff --git a/src/frontend/main/util/Utility.java b/src/frontend/main/util/Utility.java index 6ad41d138..ade766503 100644 --- a/src/frontend/main/util/Utility.java +++ b/src/frontend/main/util/Utility.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.main.util; import java.awt.AWTError; diff --git a/src/frontend/main/util/tabs/CloseAndMaxTabbedPane.java b/src/frontend/main/util/tabs/CloseAndMaxTabbedPane.java index e8a4b45f3..5d445dc9d 100644 --- a/src/frontend/main/util/tabs/CloseAndMaxTabbedPane.java +++ b/src/frontend/main/util/tabs/CloseAndMaxTabbedPane.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * David Bismut, davidou@mageos.com * Intern, SETLabs, Infosys Technologies Ltd. May 2004 - Jul 2004 diff --git a/src/frontend/main/util/tabs/CloseListener.java b/src/frontend/main/util/tabs/CloseListener.java index f55640696..d8c80d87c 100644 --- a/src/frontend/main/util/tabs/CloseListener.java +++ b/src/frontend/main/util/tabs/CloseListener.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * David Bismut, davidou@mageos.com * Intern, SETLabs, Infosys Technologies Ltd. May 2004 - Jul 2004 diff --git a/src/frontend/main/util/tabs/CloseTabPaneEnhancedUI.java b/src/frontend/main/util/tabs/CloseTabPaneEnhancedUI.java index adcd6f0cb..fbd78ade7 100644 --- a/src/frontend/main/util/tabs/CloseTabPaneEnhancedUI.java +++ b/src/frontend/main/util/tabs/CloseTabPaneEnhancedUI.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * David Bismut, davidou@mageos.com * Intern, SETLabs, Infosys Technologies Ltd. May 2004 - Jul 2004 diff --git a/src/frontend/main/util/tabs/CloseTabPaneUI.java b/src/frontend/main/util/tabs/CloseTabPaneUI.java index 10321ed84..6dff761f3 100644 --- a/src/frontend/main/util/tabs/CloseTabPaneUI.java +++ b/src/frontend/main/util/tabs/CloseTabPaneUI.java @@ -9,7 +9,7 @@ * Extended from * @(#)BasicTabbedPaneUI.java 1.126 03/01/23 * - * Copyright 2003 Sun Microsystems, Inc. All rights reserved. + * Copyright 2003, 2017 Sun Microsystems, Inc. All rights reserved. * SUN PROPRIETARY/CONFIDENTIAL. Use is subject to license terms. */ diff --git a/src/frontend/main/util/tabs/DoubleClickListener.java b/src/frontend/main/util/tabs/DoubleClickListener.java index e473dcaaa..b26862fdc 100644 --- a/src/frontend/main/util/tabs/DoubleClickListener.java +++ b/src/frontend/main/util/tabs/DoubleClickListener.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * David Bismut, davidou@mageos.com * Intern, SETLabs, Infosys Technologies Ltd. May 2004 - Jul 2004 diff --git a/src/frontend/main/util/tabs/MaxListener.java b/src/frontend/main/util/tabs/MaxListener.java index 47fa61115..357c7234c 100644 --- a/src/frontend/main/util/tabs/MaxListener.java +++ b/src/frontend/main/util/tabs/MaxListener.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * David Bismut, davidou@mageos.com * Intern, SETLabs, Infosys Technologies Ltd. May 2004 - Jul 2004 diff --git a/src/frontend/main/util/tabs/PopupOutsideListener.java b/src/frontend/main/util/tabs/PopupOutsideListener.java index a29f5c5c8..24e9be49c 100644 --- a/src/frontend/main/util/tabs/PopupOutsideListener.java +++ b/src/frontend/main/util/tabs/PopupOutsideListener.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /* * David Bismut, davidou@mageos.com * Intern, SETLabs, Infosys Technologies Ltd. May 2004 - Jul 2004 diff --git a/src/frontend/sbol/browser/CollectionBrowserPanel2.java b/src/frontend/sbol/browser/CollectionBrowserPanel2.java index 705cf2988..d26d9f610 100644 --- a/src/frontend/sbol/browser/CollectionBrowserPanel2.java +++ b/src/frontend/sbol/browser/CollectionBrowserPanel2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.sbol.browser; import java.awt.*; diff --git a/src/frontend/sbol/browser/ComponentDefinitionBrowserPanel.java b/src/frontend/sbol/browser/ComponentDefinitionBrowserPanel.java index c50c6541d..b3c1fd276 100644 --- a/src/frontend/sbol/browser/ComponentDefinitionBrowserPanel.java +++ b/src/frontend/sbol/browser/ComponentDefinitionBrowserPanel.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.sbol.browser; import java.awt.*; diff --git a/src/frontend/sbol/browser/SBOLBrowser2.java b/src/frontend/sbol/browser/SBOLBrowser2.java index 11f695663..60ddbc42b 100644 --- a/src/frontend/sbol/browser/SBOLBrowser2.java +++ b/src/frontend/sbol/browser/SBOLBrowser2.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.sbol.browser; diff --git a/src/frontend/synthesis/async/Synthesis.java b/src/frontend/synthesis/async/Synthesis.java index c67b729c6..2eaff1ddc 100644 --- a/src/frontend/synthesis/async/Synthesis.java +++ b/src/frontend/synthesis/async/Synthesis.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.synthesis.async; diff --git a/src/frontend/synthesis/genetic/SynthesisView.java b/src/frontend/synthesis/genetic/SynthesisView.java index 607ae81a9..4a60912a0 100644 --- a/src/frontend/synthesis/genetic/SynthesisView.java +++ b/src/frontend/synthesis/genetic/SynthesisView.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.synthesis.genetic; import java.awt.BorderLayout; diff --git a/src/frontend/verification/AbstPane.java b/src/frontend/verification/AbstPane.java index e40f7848c..3434207df 100644 --- a/src/frontend/verification/AbstPane.java +++ b/src/frontend/verification/AbstPane.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.verification; import javax.swing.*; diff --git a/src/frontend/verification/ParamEditor.java b/src/frontend/verification/ParamEditor.java index b158fb0d4..b96e34cf0 100644 --- a/src/frontend/verification/ParamEditor.java +++ b/src/frontend/verification/ParamEditor.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.verification; import javax.swing.*; diff --git a/src/frontend/verification/Verification.java b/src/frontend/verification/Verification.java index 27e613a82..7b66317c3 100644 --- a/src/frontend/verification/Verification.java +++ b/src/frontend/verification/Verification.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package frontend.verification; import java.awt.AWTError; diff --git a/src/test/conversion/ConversionAbstractTests.java b/src/test/conversion/ConversionAbstractTests.java index b98de0c8a..a64b30733 100644 --- a/src/test/conversion/ConversionAbstractTests.java +++ b/src/test/conversion/ConversionAbstractTests.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.conversion; import org.junit.Test; diff --git a/src/test/conversion/RoundtripTest.java b/src/test/conversion/RoundtripTest.java index f791fa57d..0cbe38f21 100644 --- a/src/test/conversion/RoundtripTest.java +++ b/src/test/conversion/RoundtripTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.conversion; import java.io.File; diff --git a/src/test/gcm2sbml/FieldPanelTest.java b/src/test/gcm2sbml/FieldPanelTest.java index e333345a2..0b7ad5ace 100755 --- a/src/test/gcm2sbml/FieldPanelTest.java +++ b/src/test/gcm2sbml/FieldPanelTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.gcm2sbml; import gcm2sbml.gui.FieldPanel; diff --git a/src/test/gcm2sbml/GCM2SBMLEditorTest.java b/src/test/gcm2sbml/GCM2SBMLEditorTest.java index 0c4c70e62..416eea131 100644 --- a/src/test/gcm2sbml/GCM2SBMLEditorTest.java +++ b/src/test/gcm2sbml/GCM2SBMLEditorTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.gcm2sbml; diff --git a/src/test/gcm2sbml/GCMFileTest.java b/src/test/gcm2sbml/GCMFileTest.java index f8ea43821..d0c269cd4 100644 --- a/src/test/gcm2sbml/GCMFileTest.java +++ b/src/test/gcm2sbml/GCMFileTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.gcm2sbml; diff --git a/src/test/gcm2sbml/GCMParserTest.java b/src/test/gcm2sbml/GCMParserTest.java index 2ee761ee9..1dfa9def0 100644 --- a/src/test/gcm2sbml/GCMParserTest.java +++ b/src/test/gcm2sbml/GCMParserTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.gcm2sbml; diff --git a/src/test/gcm2sbml/GCMScriptTest.java b/src/test/gcm2sbml/GCMScriptTest.java index 849e98f53..0554e4eae 100644 --- a/src/test/gcm2sbml/GCMScriptTest.java +++ b/src/test/gcm2sbml/GCMScriptTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ /** * */ diff --git a/src/test/gcm2sbml/SBMLTest.java b/src/test/gcm2sbml/SBMLTest.java index 9159aeecc..f7141375f 100644 --- a/src/test/gcm2sbml/SBMLTest.java +++ b/src/test/gcm2sbml/SBMLTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.gcm2sbml; diff --git a/src/test/gcm2sbml/ScriptTest.java b/src/test/gcm2sbml/ScriptTest.java index 404586cf0..ec2ca3a05 100644 --- a/src/test/gcm2sbml/ScriptTest.java +++ b/src/test/gcm2sbml/ScriptTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.gcm2sbml; import gcm2sbml.scripts.GCMScript; diff --git a/src/test/gcm2sbml/SpeciesThresholdTesterTest.java b/src/test/gcm2sbml/SpeciesThresholdTesterTest.java index 7074c5ff9..4de73d16f 100644 --- a/src/test/gcm2sbml/SpeciesThresholdTesterTest.java +++ b/src/test/gcm2sbml/SpeciesThresholdTesterTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.gcm2sbml; import gcm2sbml.scripts.GCMScript; diff --git a/src/test/gcm2sbml/UtilityTest.java b/src/test/gcm2sbml/UtilityTest.java index 3ae869a23..87850a9dd 100644 --- a/src/test/gcm2sbml/UtilityTest.java +++ b/src/test/gcm2sbml/UtilityTest.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.gcm2sbml; diff --git a/src/test/scripts/AbstractTester.java b/src/test/scripts/AbstractTester.java index 270850911..4229dc86d 100644 --- a/src/test/scripts/AbstractTester.java +++ b/src/test/scripts/AbstractTester.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.scripts; diff --git a/src/test/scripts/GCMScript.java b/src/test/scripts/GCMScript.java index a9a3212f1..b6eb35da6 100644 --- a/src/test/scripts/GCMScript.java +++ b/src/test/scripts/GCMScript.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.scripts; import java.util.ArrayList; diff --git a/src/test/scripts/ProbabilityScript.java b/src/test/scripts/ProbabilityScript.java index 27e270126..1d46fb85e 100644 --- a/src/test/scripts/ProbabilityScript.java +++ b/src/test/scripts/ProbabilityScript.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.scripts; import java.io.BufferedWriter; diff --git a/src/test/scripts/SpeciesThresholdTester.java b/src/test/scripts/SpeciesThresholdTester.java index 49c0a6356..87a0cf48b 100644 --- a/src/test/scripts/SpeciesThresholdTester.java +++ b/src/test/scripts/SpeciesThresholdTester.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.scripts; import java.util.ArrayList; diff --git a/src/test/scripts/TesterInterface.java b/src/test/scripts/TesterInterface.java index c7a773383..13f299a51 100644 --- a/src/test/scripts/TesterInterface.java +++ b/src/test/scripts/TesterInterface.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.scripts; import dataModels.biomodel.util.ExperimentResult; diff --git a/src/test/scripts/TimingScript.java b/src/test/scripts/TimingScript.java index 7b5f2ec6d..1d846ca52 100644 --- a/src/test/scripts/TimingScript.java +++ b/src/test/scripts/TimingScript.java @@ -1,3 +1,16 @@ +/******************************************************************************* + * + * This file is part of iBioSim. Please visit + * for the latest version of iBioSim. + * + * Copyright (C) 2017 University of Utah + * + * This library is free software; you can redistribute it and/or modify it + * under the terms of the Apache License. A copy of the license agreement is provided + * in the file named "LICENSE.txt" included with this software distribution + * and also available online at . + * + *******************************************************************************/ package test.scripts; import java.io.BufferedWriter;