Began mavenization. Removed libSBOlj, batk-*, and antlr libraries.
This commit is contained in:
Zach Zundel
parent
21158b8c9c
commit
bfd58a1ca4
28 changed files with 252 additions and 86 deletions
169
.classpath
169
.classpath
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@ -1,86 +1,83 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry excluding="biomodel/gui/sbol/SBOLField.java|biomodel/gui/sbol/SBOLDescriptorPanel.java|biomodel/gui/sbol/SBOLAssociationPanel.java|backend/biomodel/gui/sbol/SBOLAssociationPanel.java|backend/biomodel/gui/sbol/SBOLDescriptorPanel.java|backend/biomodel/gui/sbol/SBOLField.java|backend/biomodel/scripts/|frontend/biomodel/gui/sbol/SBOLAssociationPanel.java|frontend/biomodel/gui/sbol/SBOLDescriptorPanel.java|frontend/biomodel/gui/sbol/SBOLField.java|backend/biomodel/util/Validation.java|backend/sbol/util/SBOLFileManager.java|backend/sbol/util/SBOLIdentityManager.java|backend/sbol/util/SBOLUtility.java|backend/sbol/assembly/Assembler.java|backend/sbol/assembly/AssemblyGraph.java|backend/sbol/assembly/AssemblyNode.java|frontend/sbol/browser/CollectionBrowserPanel.java|frontend/sbol/browser/DNAComponentBrowserPanel.java|frontend/sbol/browser/SBOLBrowser.java" kind="src" path="src"/>
|
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<classpathentry kind="lib" path="lib/epsgraphics.jar"/>
|
||||
<classpathentry kind="lib" path="lib/js.jar"/>
|
||||
<classpathentry kind="lib" path="lib/junit.jar"/>
|
||||
<classpathentry kind="lib" path="lib/org-jdesktop-layout.jar"/>
|
||||
<classpathentry kind="lib" path="lib/pdf-transcoder.jar"/>
|
||||
<classpathentry kind="lib" path="lib/xalan-2.6.0.jar"/>
|
||||
<classpathentry kind="lib" path="lib/xml-apis-ext.jar"/>
|
||||
<classpathentry kind="lib" path="lib/xml-apis.jar"/>
|
||||
<classpathentry kind="lib" path="lib/swing-layout-1.0.3.jar"/>
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||||
<classpathentry kind="lib" path="lib/activation.jar"/>
|
||||
<classpathentry kind="lib" path="lib/mail.jar"/>
|
||||
<classpathentry kind="lib" path="lib/iText-2.1.5.jar"/>
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||||
<classpathentry kind="lib" path="lib/jgraphx.jar"/>
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<classpathentry kind="lib" path="lib/commons-primitives-20070823.jar"/>
|
||||
<classpathentry kind="lib" path="lib/hppc-0.3.1.jar"/>
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||||
<classpathentry kind="lib" path="lib/SourceLibrary.jar"/>
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||||
<classpathentry kind="lib" path="lib/trove-3.0.0.jar"/>
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<classpathentry kind="lib" path="lib/openmali.jar"/>
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<classpathentry kind="lib" path="lib/jafama.jar"/>
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<classpathentry kind="lib" path="lib/flanagan.jar"/>
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<classpathentry kind="lib" path="lib/jcommon-1.0.17.jar"/>
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<classpathentry kind="lib" path="lib/jfreechart-1.0.14.jar"/>
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<classpathentry kind="lib" path="lib/antlr-3.4-complete.jar"/>
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<classpathentry kind="lib" path="lib/biomodels-wslib-1.21.jar"/>
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<classpathentry kind="lib" path="lib/axis.jar"/>
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<classpathentry kind="lib" path="lib/commons-discovery-0.5.jar"/>
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<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
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<classpathentry kind="lib" path="lib/wsdl4j.jar"/>
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<classpathentry kind="lib" path="lib/saaj.jar"/>
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<classpathentry kind="lib" path="lib/w3c-dom.jar"/>
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<classpathentry kind="lib" path="lib/batik-awt-util.jar"/>
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<classpathentry kind="lib" path="lib/batik-ext.jar"/>
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<classpathentry kind="lib" path="lib/batik-svggen.jar"/>
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<classpathentry kind="lib" path="lib/batik-util.jar"/>
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<classpathentry kind="lib" path="lib/batik-xml.jar"/>
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<classpathentry kind="lib" path="lib/javax.servlet-api-3.0.1.jar"/>
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<classpathentry kind="lib" path="lib/jdom-contrib.jar"/>
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<classpathentry kind="lib" path="lib/batik-dom.jar"/>
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<classpathentry kind="lib" path="lib/batik-css.jar"/>
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<classpathentry kind="lib" path="lib/batik-gui-util.jar"/>
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<classpathentry kind="lib" path="lib/batik-bridge.jar"/>
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<classpathentry kind="lib" path="lib/batik-transcoder.jar"/>
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<classpathentry kind="lib" path="lib/batik-svg-dom.jar"/>
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<classpathentry kind="lib" path="lib/batik-anim.jar"/>
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<classpathentry kind="lib" path="lib/batik-parser.jar"/>
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<classpathentry kind="lib" path="lib/batik-gvt.jar"/>
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<classpathentry kind="lib" path="lib/batik-script.jar"/>
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<classpathentry kind="lib" path="lib/SBOLDesigner.jar"/>
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<classpathentry kind="lib" path="lib/simpleeventbus-1.2.jar"/>
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<classpathentry kind="lib" path="lib/guava-18.0.jar"/>
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<classpathentry kind="lib" path="lib/openrdf-sesame-2.6.9-onejar.jar"/>
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<classpathentry kind="lib" path="lib/AppleJavaExtensions.jar"/>
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<classpathentry kind="lib" path="lib/commons-httpclient-3.1.jar"/>
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<classpathentry kind="lib" path="lib/commons-codec-1.4.jar"/>
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<classpathentry kind="lib" path="lib/httpclient-4.5.2.jar"/>
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<classpathentry kind="lib" path="lib/httpclient-cache-4.5.2.jar"/>
|
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<classpathentry kind="lib" path="lib/httpcore-4.4.4.jar"/>
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<classpathentry kind="lib" path="lib/httpmime-4.5.2.jar"/>
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<classpathentry kind="lib" path="lib/gson-2.3.1.jar"/>
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<classpathentry kind="lib" path="lib/sbolstack-frontend-1.0-SNAPSHOT.jar"/>
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<classpathentry kind="lib" path="lib/CombineArchive-1.1.1-jar-with-dependencies.jar"/>
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||||
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
|
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<classpathentry kind="lib" path="lib/jaxen-1.1.1.jar"/>
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<classpathentry kind="lib" path="lib/jlibsedml.jar"/>
|
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<classpathentry kind="lib" path="lib/xom-1.2.1.jar"/>
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<classpathentry kind="lib" path="lib/jmathml.jar"/>
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<classpathentry kind="lib" path="lib/architecture-rules-3.0.0-M1.jar"/>
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<classpathentry kind="lib" path="lib/colt-1.2.0.jar"/>
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<classpathentry kind="lib" path="lib/commons-beanutils-1.6.jar"/>
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<classpathentry kind="lib" path="lib/commons-collections-2.1.jar"/>
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<classpathentry kind="lib" path="lib/commons-digester-1.6.jar"/>
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<classpathentry kind="lib" path="lib/commons-io-1.4.jar"/>
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<classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
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<classpathentry kind="lib" path="lib/jdepend-2.9.1.jar"/>
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<classpathentry kind="lib" path="lib/joptimizer-3.3.0.jar"/>
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<classpathentry kind="lib" path="lib/commons-lang3-3.3.2.jar"/>
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<classpathentry kind="lib" path="lib/csparsej-1.1.1.jar"/>
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<classpathentry kind="lib" path="lib/libsbmlj.jar"/>
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<classpathentry kind="lib" path="lib/commons-math3-3.6.1.jar" sourcepath="lib/commons-math3-3.6.1-sources.jar"/>
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<classpathentry kind="lib" path="lib/libSBOLj-2.1.1-SNAPSHOT-withDependencies.jar"/>
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<classpathentry kind="lib" path="lib/jsbml-1.2-with-dependencies.jar"/>
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<classpathentry kind="output" path="dist/classes"/>
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</classpath>
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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry including="**/*.java" kind="src" output="target/classes" path="src">
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<attributes>
|
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="lib" path="lib/epsgraphics.jar"/>
|
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<classpathentry kind="lib" path="lib/js.jar"/>
|
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<classpathentry kind="lib" path="lib/junit.jar"/>
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<classpathentry kind="lib" path="lib/org-jdesktop-layout.jar"/>
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<classpathentry kind="lib" path="lib/pdf-transcoder.jar"/>
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<classpathentry kind="lib" path="lib/xalan-2.6.0.jar"/>
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<classpathentry kind="lib" path="lib/xml-apis-ext.jar"/>
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<classpathentry kind="lib" path="lib/xml-apis.jar"/>
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<classpathentry kind="lib" path="lib/swing-layout-1.0.3.jar"/>
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<classpathentry kind="lib" path="lib/activation.jar"/>
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<classpathentry kind="lib" path="lib/mail.jar"/>
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<classpathentry kind="lib" path="lib/iText-2.1.5.jar"/>
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<classpathentry kind="lib" path="lib/jgraphx.jar"/>
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<classpathentry kind="lib" path="lib/commons-primitives-20070823.jar"/>
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<classpathentry kind="lib" path="lib/hppc-0.3.1.jar"/>
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<classpathentry kind="lib" path="lib/SourceLibrary.jar"/>
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<classpathentry kind="lib" path="lib/trove-3.0.0.jar"/>
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<classpathentry kind="lib" path="lib/openmali.jar"/>
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<classpathentry kind="lib" path="lib/jafama.jar"/>
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<classpathentry kind="lib" path="lib/flanagan.jar"/>
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<classpathentry kind="lib" path="lib/jcommon-1.0.17.jar"/>
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||||
<classpathentry kind="lib" path="lib/jfreechart-1.0.14.jar"/>
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<classpathentry kind="lib" path="lib/biomodels-wslib-1.21.jar"/>
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<classpathentry kind="lib" path="lib/axis.jar"/>
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<classpathentry kind="lib" path="lib/commons-discovery-0.5.jar"/>
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<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
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<classpathentry kind="lib" path="lib/wsdl4j.jar"/>
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<classpathentry kind="lib" path="lib/saaj.jar"/>
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<classpathentry kind="lib" path="lib/w3c-dom.jar"/>
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<classpathentry kind="lib" path="lib/javax.servlet-api-3.0.1.jar"/>
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<classpathentry kind="lib" path="lib/jdom-contrib.jar"/>
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<classpathentry kind="lib" path="lib/SBOLDesigner.jar"/>
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<classpathentry kind="lib" path="lib/simpleeventbus-1.2.jar"/>
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<classpathentry kind="lib" path="lib/guava-18.0.jar"/>
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<classpathentry kind="lib" path="lib/openrdf-sesame-2.6.9-onejar.jar"/>
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<classpathentry kind="lib" path="lib/AppleJavaExtensions.jar"/>
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<classpathentry kind="lib" path="lib/commons-httpclient-3.1.jar"/>
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<classpathentry kind="lib" path="lib/commons-codec-1.4.jar"/>
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<classpathentry kind="lib" path="lib/httpclient-4.5.2.jar"/>
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<classpathentry kind="lib" path="lib/httpclient-cache-4.5.2.jar"/>
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<classpathentry kind="lib" path="lib/httpcore-4.4.4.jar"/>
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<classpathentry kind="lib" path="lib/httpmime-4.5.2.jar"/>
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<classpathentry kind="lib" path="lib/gson-2.3.1.jar"/>
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<classpathentry kind="lib" path="lib/sbolstack-frontend-1.0-SNAPSHOT.jar"/>
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<classpathentry kind="lib" path="lib/CombineArchive-1.1.1-jar-with-dependencies.jar"/>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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||||
</classpathentry>
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<classpathentry kind="lib" path="lib/jaxen-1.1.1.jar"/>
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<classpathentry kind="lib" path="lib/jlibsedml.jar"/>
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<classpathentry kind="lib" path="lib/xom-1.2.1.jar"/>
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<classpathentry kind="lib" path="lib/jmathml.jar"/>
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<classpathentry kind="lib" path="lib/architecture-rules-3.0.0-M1.jar"/>
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<classpathentry kind="lib" path="lib/colt-1.2.0.jar"/>
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<classpathentry kind="lib" path="lib/commons-beanutils-1.6.jar"/>
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<classpathentry kind="lib" path="lib/commons-collections-2.1.jar"/>
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<classpathentry kind="lib" path="lib/commons-digester-1.6.jar"/>
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<classpathentry kind="lib" path="lib/commons-io-1.4.jar"/>
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||||
<classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
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||||
<classpathentry kind="lib" path="lib/jdepend-2.9.1.jar"/>
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<classpathentry kind="lib" path="lib/joptimizer-3.3.0.jar"/>
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<classpathentry kind="lib" path="lib/commons-lang3-3.3.2.jar"/>
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<classpathentry kind="lib" path="lib/csparsej-1.1.1.jar"/>
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<classpathentry kind="lib" path="lib/libsbmlj.jar"/>
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<classpathentry kind="lib" path="lib/commons-math3-3.6.1.jar" sourcepath="lib/commons-math3-3.6.1-sources.jar"/>
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||||
<classpathentry kind="lib" path="lib/jsbml-1.2-with-dependencies.jar"/>
|
||||
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
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||||
<attributes>
|
||||
<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="output" path="target/classes"/>
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</classpath>
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1
.gitignore
vendored
1
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vendored
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/dist/
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/target/
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6
.project
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.project
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@ -20,8 +20,14 @@
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<arguments>
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</arguments>
|
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</buildCommand>
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<buildCommand>
|
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<name>org.eclipse.m2e.core.maven2Builder</name>
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<arguments>
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</arguments>
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</buildCommand>
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</buildSpec>
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<natures>
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<nature>org.eclipse.m2e.core.maven2Nature</nature>
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<nature>org.eclipse.jdt.core.javanature</nature>
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<nature>org.deved.antlride.core.nature</nature>
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<nature>org.eclipse.wst.jsdt.core.jsNature</nature>
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@ -8,4 +8,5 @@ org.eclipse.jdt.core.compiler.debug.localVariable=generate
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org.eclipse.jdt.core.compiler.debug.sourceFile=generate
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org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
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org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
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org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
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org.eclipse.jdt.core.compiler.source=1.6
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.settings/org.eclipse.m2e.core.prefs
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4
.settings/org.eclipse.m2e.core.prefs
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activeProfiles=
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eclipse.preferences.version=1
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resolveWorkspaceProjects=true
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version=1
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157
pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<groupId>MyersResearchGroup</groupId>
|
||||
<artifactId>iBioSim</artifactId>
|
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<version>0.0.1-SNAPSHOT</version>
|
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<name>iBioSim</name>
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<build>
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||||
<sourceDirectory>src</sourceDirectory>
|
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<resources>
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<resource>
|
||||
<directory>src</directory>
|
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<excludes>
|
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<exclude>**/*.java</exclude>
|
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</excludes>
|
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</resource>
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</resources>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<artifactId>maven-compiler-plugin</artifactId>
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<version>3.5.1</version>
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||||
<configuration>
|
||||
<source>1.6</source>
|
||||
<target>1.6</target>
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</configuration>
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</plugin>
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</plugins>
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</build>
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<dependencies>
|
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<dependency>
|
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<groupId>org.sbolstandard</groupId>
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||||
<artifactId>libSBOLj</artifactId>
|
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</dependency>
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<dependency>
|
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<groupId>org.sbolstandard</groupId>
|
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<artifactId>libSBOLj</artifactId>
|
||||
<version>2.1.1</version>
|
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</dependency>
|
||||
<dependency>
|
||||
<groupId>org.antlr</groupId>
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<artifactId>antlr</artifactId>
|
||||
<version>3.4</version>
|
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</dependency>
|
||||
<dependency>
|
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<groupId>org.antlr</groupId>
|
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<artifactId>antlr-runtime</artifactId>
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||||
<version>3.4</version>
|
||||
</dependency>
|
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<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
|
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<artifactId>batik-awt-util</artifactId>
|
||||
<version>1.8</version>
|
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</dependency>
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<dependency>
|
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<groupId>org.apache.xmlgraphics</groupId>
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||||
<artifactId>batik-anim</artifactId>
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||||
<version>1.8</version>
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</dependency>
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<dependency>
|
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<groupId>org.apache.xmlgraphics</groupId>
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||||
<artifactId>batik-bridge</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-codec</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-css</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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||||
<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-dom</artifactId>
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||||
<version>1.8</version>
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</dependency>
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<dependency>
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||||
<groupId>org.apache.xmlgraphics</groupId>
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||||
<artifactId>batik-ext</artifactId>
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||||
<version>1.8</version>
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||||
</dependency>
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<dependency>
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||||
<groupId>org.apache.xmlgraphics</groupId>
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||||
<artifactId>batik-extension</artifactId>
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||||
<version>1.8</version>
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</dependency>
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<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
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||||
<artifactId>batik-gui-util</artifactId>
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||||
<version>1.8</version>
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</dependency>
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<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
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||||
<artifactId>batik-gvt</artifactId>
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||||
<version>1.8</version>
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</dependency>
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<dependency>
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||||
<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-parser</artifactId>
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<version>1.8</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
|
||||
<artifactId>batik-script</artifactId>
|
||||
<version>1.8</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
|
||||
<artifactId>batik-svg-dom</artifactId>
|
||||
<version>1.8</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
|
||||
<artifactId>batik-svggen</artifactId>
|
||||
<version>1.8</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
|
||||
<artifactId>batik-swing</artifactId>
|
||||
<version>1.8</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
|
||||
<artifactId>batik-transcoder</artifactId>
|
||||
<version>1.8</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
|
||||
<artifactId>batik-util</artifactId>
|
||||
<version>1.8</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.xmlgraphics</groupId>
|
||||
<artifactId>batik-xml</artifactId>
|
||||
<version>1.8</version>
|
||||
</dependency>
|
||||
|
||||
|
||||
</dependencies>
|
||||
<dependencyManagement>
|
||||
<dependencies>
|
||||
|
||||
</dependencies>
|
||||
</dependencyManagement>
|
||||
</project>
|
||||
Loading…
Add table
Add a link
Reference in a new issue