Added license header to source code files

.gitignore

@@ -1,3 +1,4 @@
 /dist/
 /target/
 jsbml.log
+/bin/

bin/ATACSGUI.bat

@@ -1,3 +1,16 @@
+@rem ***************************************************************************
+@rem  
+@rem This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+@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 <http://www.async.ece.utah.edu/ibiosim/License>.
+@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"

bin/LEMA.bat

@@ -1,3 +1,16 @@
+@rem ***************************************************************************
+@rem  
+@rem This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+@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 <http://www.async.ece.utah.edu/ibiosim/License>.
+@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"

bin/apply_post_filter.pl

@@ -1,4 +1,17 @@
 #!/usr/bin/perl
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 
 if ($#ARGV != 3){
     print "Usage: ./recheck_results.pl cutoff file_method_dot file_correct.dot file_output\n";

bin/checkHpn.pl

@@ -1,4 +1,17 @@
 #!/usr/bin/perl
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 
 ###############################################################################
 ##

bin/check_dot.pl

@@ -1,4 +1,17 @@
 #!/usr/bin/perl
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 
 #This file writes the checked dot file.
 

bin/detect-java.sh

@@ -1,4 +1,17 @@
 #!/bin/bash
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 # 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.

bin/gcm2sbml.pl

@@ -1,4 +1,17 @@
 #!/usr/bin/perl -w
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 
 use Getopt::Std;
 

bin/genBackgroundGCM.pl

@@ -1,4 +1,17 @@
 #!/usr/bin/perl
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 
 open (IN, "run-1.tsd");
 @in = <IN>;

bin/gen_GeneNet_report.pl

@@ -1,4 +1,17 @@
 #!/usr/bin/perl
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 
 
 $genenet_dir = $ARGV[0];

bin/iBioSim.bat

@@ -1,3 +1,16 @@
+@rem ***************************************************************************
+@rem  
+@rem This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+@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 <http://www.async.ece.utah.edu/ibiosim/License>.
+@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"

bin/remote.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 scp $2.xml $1:/tmp/.
 scp $2.properties $1:/tmp/.
 ssh $1 "reb2sac --target.encoding=$3 /tmp/$2.xml"

bin/remoteATACS.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 scp $3.lpn $1:/tmp/.
 ssh $1 "atacs $2 /tmp/$3.lpn"
 scp $1:"atacs.log" .

bin/remoteTangATACS.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 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" .

bin/remoteTangSim.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 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"

makeATACS.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 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/.

makeATACS64.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 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/.

makeLEMA.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 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/.

makeLEMA64.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 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

makedmg.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 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/.

makedmg64.sh

@@ -1,4 +1,17 @@
 #!/bin/sh
+#*******************************************************************************
+#  
+# This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+# for the latest version of iBioSim.
+#
+# Copyright (C) 2017 University of Utah
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the Apache License. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+#  
+#*******************************************************************************
 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

src/backend/analysis/dynamicsim/DynamicSimulation.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim;
 
 import java.awt.Dimension;

src/backend/analysis/dynamicsim/ParentSimulator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim;
 
 import java.io.IOException;

src/backend/analysis/dynamicsim/flattened/DynSim.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.flattened;
 
 import java.io.File;

src/backend/analysis/dynamicsim/flattened/Simulator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.flattened;
 
 import flanagan.math.Fmath;

src/backend/analysis/dynamicsim/flattened/SimulatorODERK.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.flattened;
 
 import java.io.IOException;

src/backend/analysis/dynamicsim/flattened/SimulatorSSACR.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.flattened;
 
 import gnu.trove.map.hash.TIntDoubleHashMap;

src/backend/analysis/dynamicsim/flattened/SimulatorSSADirect.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.flattened;
 
 import java.io.IOException;

src/backend/analysis/dynamicsim/flattened/SpeciesDimensions.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.flattened;
 
 public class SpeciesDimensions {

src/backend/analysis/dynamicsim/flattened/XORShiftRandom.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.flattened;
 
 /*

src/backend/analysis/dynamicsim/hierarchical/HierarchicalSimulation.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical;
 
 import java.io.BufferedWriter;

src/backend/analysis/dynamicsim/hierarchical/io/HierarchicalWriter.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.io;
 
 import java.io.BufferedWriter;

src/backend/analysis/dynamicsim/hierarchical/math/AbstractHierarchicalNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 public abstract class AbstractHierarchicalNode

src/backend/analysis/dynamicsim/hierarchical/math/ArrayDimensionNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 public class ArrayDimensionNode extends VariableNode

src/backend/analysis/dynamicsim/hierarchical/math/ArrayNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 import java.util.ArrayList;

src/backend/analysis/dynamicsim/hierarchical/math/ConstraintNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 public class ConstraintNode extends HierarchicalNode

src/backend/analysis/dynamicsim/hierarchical/math/Evaluator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 import odk.lang.FastMath;

src/backend/analysis/dynamicsim/hierarchical/math/EventNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 import java.util.ArrayList;

src/backend/analysis/dynamicsim/hierarchical/math/FunctionNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 import java.util.ArrayList;

src/backend/analysis/dynamicsim/hierarchical/math/HierarchicalNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 import java.util.ArrayList;

src/backend/analysis/dynamicsim/hierarchical/math/ReactionNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 import java.util.ArrayList;

src/backend/analysis/dynamicsim/hierarchical/math/SpeciesNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 import java.util.ArrayList;

src/backend/analysis/dynamicsim/hierarchical/math/SpeciesReferenceNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 public class SpeciesReferenceNode extends VariableNode

src/backend/analysis/dynamicsim/hierarchical/math/VariableNode.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.math;
 
 import java.util.ArrayList;

src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalFBASimulator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.methods;
 
 import java.io.IOException;

src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalHybridSimulator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.methods;
 
 

src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalMixedSimulator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.methods;
 
 import java.io.IOException;

src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalODERKSimulator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.methods;
 
 import java.io.IOException;

src/backend/analysis/dynamicsim/hierarchical/methods/HierarchicalSSADirectSimulator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.methods;
 
 import java.io.IOException;

src/backend/analysis/dynamicsim/hierarchical/model/HierarchicalModel.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.model;
 
 import java.util.ArrayList;

src/backend/analysis/dynamicsim/hierarchical/states/DenseState.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 
 package backend.analysis.dynamicsim.hierarchical.states;
 

src/backend/analysis/dynamicsim/hierarchical/states/HierarchicalState.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 
 package backend.analysis.dynamicsim.hierarchical.states;
 

src/backend/analysis/dynamicsim/hierarchical/states/SparseState.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 
 package backend.analysis.dynamicsim.hierarchical.states;
 

src/backend/analysis/dynamicsim/hierarchical/states/TreeState.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 
 package backend.analysis.dynamicsim.hierarchical.states;
 

src/backend/analysis/dynamicsim/hierarchical/states/ValueState.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 
 package backend.analysis.dynamicsim.hierarchical.states;
 

src/backend/analysis/dynamicsim/hierarchical/states/VectorState.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.states;
 
 public class VectorState extends HierarchicalState{

src/backend/analysis/dynamicsim/hierarchical/states/VectorWrapper.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 
 package backend.analysis.dynamicsim.hierarchical.states;
 

src/backend/analysis/dynamicsim/hierarchical/util/HierarchicalUtilities.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util;
 
 import java.io.File;

src/backend/analysis/dynamicsim/hierarchical/util/comp/HierarchicalEventComparator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.comp;
 
 import java.util.Comparator;

src/backend/analysis/dynamicsim/hierarchical/util/comp/ReplacementHandler.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.comp;
 
 import backend.analysis.dynamicsim.hierarchical.model.HierarchicalModel;

src/backend/analysis/dynamicsim/hierarchical/util/interpreter/MathInterpreter.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.interpreter;
 
 import java.util.Map;

src/backend/analysis/dynamicsim/hierarchical/util/interpreter/RateSplitterInterpreter.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.interpreter;
 
 import java.util.ArrayList;

src/backend/analysis/dynamicsim/hierarchical/util/scripts/HierarchicalSimulatorRunner.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.scripts;
 
 import java.io.File;

src/backend/analysis/dynamicsim/hierarchical/util/setup/ArraysSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import org.sbml.jsbml.ASTNode;

src/backend/analysis/dynamicsim/hierarchical/util/setup/CompartmentSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 

src/backend/analysis/dynamicsim/hierarchical/util/setup/ConstraintSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import org.sbml.jsbml.ASTNode;

src/backend/analysis/dynamicsim/hierarchical/util/setup/CoreSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import java.io.IOException;

src/backend/analysis/dynamicsim/hierarchical/util/setup/EventSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import java.util.Map;

src/backend/analysis/dynamicsim/hierarchical/util/setup/InitAssignmentSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import org.sbml.jsbml.ASTNode;

src/backend/analysis/dynamicsim/hierarchical/util/setup/ModelSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 

src/backend/analysis/dynamicsim/hierarchical/util/setup/ParameterSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import org.sbml.jsbml.KineticLaw;

src/backend/analysis/dynamicsim/hierarchical/util/setup/ReactionSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import org.sbml.jsbml.ASTNode;

src/backend/analysis/dynamicsim/hierarchical/util/setup/ReplacementSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import java.util.List;

src/backend/analysis/dynamicsim/hierarchical/util/setup/RuleSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import java.util.Map;

src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesReferenceSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import org.sbml.jsbml.SpeciesReference;

src/backend/analysis/dynamicsim/hierarchical/util/setup/SpeciesSetup.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.dynamicsim.hierarchical.util.setup;
 
 import java.io.IOException;

src/backend/analysis/fba/FluxBalanceAnalysis.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.fba;
 
 import java.io.BufferedWriter;

src/backend/analysis/markov/BuildStateGraphThread.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.markov;
 
 import javax.swing.JProgressBar;

src/backend/analysis/markov/PerfromSteadyStateMarkovAnalysisThread.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.markov;
 
 import java.util.ArrayList;

src/backend/analysis/markov/PerfromTransientMarkovAnalysisThread.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.markov;
 
 import javax.swing.JProgressBar;

src/backend/analysis/markov/StateGraph.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.markov;
 
 import java.io.BufferedWriter;

src/backend/analysis/markov/TransientMarkovMatrixMultiplyThread.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.markov;
 
 public class TransientMarkovMatrixMultiplyThread extends Thread {

src/backend/analysis/util/SEDMLutilities.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.analysis.util;
 
 import java.util.ArrayList;

src/backend/learn/AMSModel/DMVCrun.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.AMSModel;
 
 import java.util.*;

src/backend/learn/AMSModel/LearnModel.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.AMSModel;
 
 import java.io.*;

src/backend/learn/AMSModel/Variable.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.AMSModel;
 
 

src/backend/learn/genenet/Connection.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.genenet;
 
 import java.util.ArrayList;

src/backend/learn/genenet/Encodings.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.genenet;
 
 import java.util.ArrayList;

src/backend/learn/genenet/Experiments.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.genenet;
 
 import java.util.ArrayList;

src/backend/learn/genenet/Learn.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.genenet;
 
 import java.io.File;

src/backend/learn/genenet/NetCon.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.genenet;
 
 import java.util.ArrayList;

src/backend/learn/genenet/Run.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.genenet;
 
 import java.io.File;

src/backend/learn/genenet/SpeciesCollection.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.genenet;
 
 import java.util.ArrayList;

src/backend/learn/genenet/Thresholds.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.genenet;
 
 public class Thresholds

src/backend/learn/parameterestimator/ParameterEstimator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.parameterestimator;
 
 import java.io.IOException;

src/backend/learn/parameterestimator/methods/AbstractEstimator.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.parameterestimator.methods;
 
 public interface AbstractEstimator

src/backend/learn/parameterestimator/methods/pedi/GeneProduct.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.parameterestimator.methods.pedi;
 
 public class GeneProduct

src/backend/learn/parameterestimator/methods/pedi/PEDIBridge.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.parameterestimator.methods.pedi;
 
 public interface PEDIBridge

src/backend/learn/parameterestimator/methods/sres/EvolutionMethodSetting.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.parameterestimator.methods.sres;
 
 public class EvolutionMethodSetting

src/backend/learn/parameterestimator/methods/sres/Modelsettings.java

@@ -1,3 +1,16 @@
+/*******************************************************************************
+ *  
+ * This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
+ * for the latest version of iBioSim.
+ *
+ * Copyright (C) 2017 University of Utah
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the Apache License. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
+ *  
+ *******************************************************************************/
 package backend.learn.parameterestimator.methods.sres;
 
 import java.io.BufferedReader;