├── .gitattributes ├── .github └── workflows │ └── ant.yml ├── .gitignore ├── .idea ├── .name ├── PathVisio.iml ├── codeStyleSettings.xml ├── compiler.xml ├── copyright │ └── profiles_settings.xml ├── encodings.xml ├── inspectionProfiles │ ├── Project_Default.xml │ └── profiles_settings.xml ├── jsLibraryMappings.xml ├── libraries │ ├── lib.xml │ └── lib_build.xml ├── misc.xml ├── modules.xml ├── org.pathvisio.core.iml ├── org.pathvisio.data.iml ├── org.pathvisio.desktop.iml ├── org.pathvisio.gex.iml ├── org.pathvisio.gui.iml ├── org.pathvisio.launcher.iml ├── org.pathvisio.pluginmanager.iml ├── org.pathvisio.statistics.iml ├── org.pathvisio.visualization.iml └── vcs.xml ├── CHANGELOG.txt ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTORS.txt ├── Info.plist ├── JNLP-INF └── APPLICATION_TEMPLATE.JNLP ├── JavaApplicationStub ├── LICENSE ├── NOTICE.txt ├── example-data ├── Hs_Apoptosis.gpml ├── Hs_Apoptosis.mapp ├── Hs_Cell_cycle_KEGG.gpml ├── Hs_Cell_cycle_KEGG.mapp ├── Hs_DNA_replication_Reactome.gpml ├── Hs_DNA_replication_Reactome.mapp ├── Hs_G13_Signaling_Pathway.gpml ├── Hs_G13_Signaling_Pathway.mapp ├── Label_test.gpml ├── Label_test.mapp ├── Shape_test.gpml ├── Shape_test.mapp ├── fillcolor_test.gpml ├── fillcolor_test.mapp ├── mim-test.gpml ├── position_test.gpml ├── position_test.mapp ├── sample_affymetrix.txt ├── sample_data_1.csv ├── sample_data_1.txt ├── sample_data_1_negatief.txt ├── sample_data_european.csv ├── sample_data_european.txt ├── sample_data_indescriptive_headers.txt ├── sample_data_long_headers.txt ├── sample_data_many_columns.txt ├── sample_data_no_header.txt ├── sample_data_no_syscode.txt ├── sample_data_two_row_header.txt ├── sample_data_with_text.txt └── sample_sgd.txt ├── lib-build ├── bigcateye.icns ├── biz.aQute.bnd.jar ├── checkstyle-all-5.0.jar ├── junit-4.12.jar └── measure.jar ├── lib ├── bindex.jar ├── com.springsource.org.apache.commons.logging-1.1.1.jar ├── com.springsource.org.jdom-2.0.1.jar ├── commons-codec-1.6.jar ├── commons-math-2.0.jar ├── derby.jar ├── derbyclient.jar ├── felix.jar ├── h2.jar ├── hsqldb.jar ├── javax.activation_1.1.0.v201105071233.jar ├── javax.servlet_3.0.0.v201103241727.jar ├── javax.wsdl_1.5.1.v201012040544.jar ├── javax.xml.rpc_1.1.0.v201005080400.jar ├── javax.xml.soap_1.3.0.v201105210645.jar ├── javax.xml_1.3.4.v201005080400.jar ├── jnlp.jar ├── junit.jar ├── licenses │ ├── JGOODIES-BSD-LICENSE.txt │ ├── LGPL.txt │ ├── epl-v10.html │ ├── hypersonic_lic.txt │ ├── jdom │ │ └── LICENSE.txt │ └── wizard.jar.license.html ├── org.apache.axis_1.4.0.v201005080400.jar ├── org.apache.batik.bridge_1.7.0.v201011041433.jar ├── org.apache.batik.css_1.7.0.v201011041433.jar ├── org.apache.batik.dom.svg_1.7.0.v201011041433.jar ├── org.apache.batik.dom_1.7.0.v201011041433.jar ├── org.apache.batik.ext.awt_1.7.0.v201011041433.jar ├── org.apache.batik.extension_1.7.0.v201011041433.jar ├── org.apache.batik.parser_1.7.0.v201011041433.jar ├── org.apache.batik.svggen_1.7.0.v201011041433.jar ├── org.apache.batik.transcoder_1.7.0.v201011041433.jar ├── org.apache.batik.util.gui_1.7.0.v200903091627.jar ├── org.apache.batik.util_1.7.0.v201011041433.jar ├── org.apache.batik.xml_1.7.0.v201011041433.jar ├── org.apache.commons.discovery_0.2.0.v201004190315.jar ├── org.apache.felix.bundlerepository-1.6.6.jar ├── org.apache.xalan_2.7.1.v201005080400.jar ├── org.apache.xerces_2.9.0.v201101211617.jar ├── org.apache.xml.resolver_1.2.0.v201005080400.jar ├── org.apache.xml.serializer_2.7.1.v201005080400.jar ├── org.bridgedb.bio.jar ├── org.bridgedb.gui.jar ├── org.bridgedb.jar ├── org.bridgedb.rdb.construct.jar ├── org.bridgedb.rdb.jar ├── org.bridgedb.webservice.bridgerest.jar ├── org.eclipse.osgi.jar ├── org.hamcrest.core_1.1.0.v20090501071000.jar ├── org.pathvisio.jgoodies.forms.jar ├── org.pathvisio.pdftranscoder.jar ├── org.pathvisio.ws.commons.util.jar ├── org.pathvisio.xerces.jar ├── org.pathvisio.xmlrpc.client.jar ├── org.pathvisio.xmlrpc.common.jar ├── org.w3c.css.sac_1.3.1.v200903091627.jar ├── org.w3c.dom.events_3.0.0.draft20060413_v201105210656.jar ├── org.w3c.dom.smil_1.0.1.v200903091627.jar └── org.w3c.dom.svg_1.1.0.v201011041433.jar ├── modules ├── README.txt ├── org.pathvisio.core │ ├── .classpath │ ├── .gitignore │ ├── .project │ ├── META-INF │ │ └── MANIFEST.MF │ ├── build.properties │ ├── build.xml │ ├── resources │ │ ├── GPML2007.xsd │ │ ├── GPML2008a.xsd │ │ ├── GPML2010a.xsd │ │ ├── GPML2013a.xsd │ │ ├── alignbottom.gif │ │ ├── aligncenterx.gif │ │ ├── aligncentery.gif │ │ ├── alignleft.gif │ │ ├── alignright.gif │ │ ├── aligntop.gif │ │ ├── apply.gif │ │ ├── bigcateye.gif │ │ ├── bigcateye.svg │ │ ├── botresult.css │ │ ├── bottom.gif │ │ ├── cancel.gif │ │ ├── checked.gif │ │ ├── close.gif │ │ ├── colorpicker.gif │ │ ├── colorset.gif │ │ ├── copy.gif │ │ ├── data_icons.ai │ │ ├── down.gif │ │ ├── edit.gif │ │ ├── export.gif │ │ ├── fullscreen.gif │ │ ├── header.html │ │ ├── import.gif │ │ ├── legend.gif │ │ ├── logo-fullsize.png │ │ ├── logo-tiny.jpg │ │ ├── logo.jpg │ │ ├── mRNA.bmp │ │ ├── mRNA_hi.bmp │ │ ├── minimize.gif │ │ ├── new-logo-small.png │ │ ├── new.gif │ │ ├── newarc.gif │ │ ├── newarrow.gif │ │ ├── newbinding.gif │ │ ├── newbrace.gif │ │ ├── newbranching left.gif │ │ ├── newbranching right.gif │ │ ├── newcatalysis.gif │ │ ├── newcell.gif │ │ ├── newcella.gif │ │ ├── newcleavage.gif │ │ ├── newcomplex-brown.gif │ │ ├── newcomplex.gif │ │ ├── newconversion.gif │ │ ├── newcovalent bond.gif │ │ ├── newcurve.gif │ │ ├── newcytosol region.gif │ │ ├── newdashedarrow.gif │ │ ├── newdashedline.gif │ │ ├── newdatanodemenu.gif │ │ ├── newelbow.gif │ │ ├── newendoplasmic reticulum.gif │ │ ├── newextracellular region.gif │ │ ├── newgap.gif │ │ ├── newgeneproduct.gif │ │ ├── newgolgi apparatus.gif │ │ ├── newhexagon.gif │ │ ├── newinhibition interaction.gif │ │ ├── newinhibition.gif │ │ ├── newinteraction.gif │ │ ├── newinteractionmenu.gif │ │ ├── newitemmenu.gif │ │ ├── newlabel.gif │ │ ├── newligandround.gif │ │ ├── newligandsquare.gif │ │ ├── newline.gif │ │ ├── newlinemenu.gif │ │ ├── newlineshapemenu.gif │ │ ├── newlysosome.gif │ │ ├── newmembrane region.gif │ │ ├── newmetabolite.gif │ │ ├── newmim-degradation.gif │ │ ├── newmim-interaction.gif │ │ ├── newmim-phosphorylated.gif │ │ ├── newmitochondria.gif │ │ ├── newmodification.gif │ │ ├── newmy line.gif │ │ ├── newmy-shape.gif │ │ ├── newnecessary stimulation.gif │ │ ├── newnucleolus.gif │ │ ├── newnucleus.gif │ │ ├── neworgana.gif │ │ ├── neworganb.gif │ │ ├── neworganc.gif │ │ ├── neworganelle.gif │ │ ├── newoval.gif │ │ ├── newpathway.gif │ │ ├── newpentagon.gif │ │ ├── newphosphorylation.gif │ │ ├── newprotein.gif │ │ ├── newproteincomplex.gif │ │ ├── newreaction.gif │ │ ├── newreceptorround.gif │ │ ├── newreceptorsquare.gif │ │ ├── newrectangle.gif │ │ ├── newreversiblereaction.gif │ │ ├── newribosome.gif │ │ ├── newrna-purple.gif │ │ ├── newrna.gif │ │ ├── newroundedrectangle.gif │ │ ├── newsarcoplasmic reticulum.gif │ │ ├── newstimulation interaction.gif │ │ ├── newstimulation.gif │ │ ├── newtbar.gif │ │ ├── newtemplatemenu.gif │ │ ├── newtranscription-translation.gif │ │ ├── newtranslocation.gif │ │ ├── newtriangle.gif │ │ ├── newunknown.gif │ │ ├── newvacuole.gif │ │ ├── newvesicle.gif │ │ ├── open.gif │ │ ├── paste.gif │ │ ├── plugin.png │ │ ├── protein.bmp │ │ ├── protein_hi.bmp │ │ ├── redo.gif │ │ ├── restorescreen.gif │ │ ├── save.gif │ │ ├── saveas.gif │ │ ├── savetoweb.gif │ │ ├── select.gif │ │ ├── sizeheight.gif │ │ ├── sizewidth.gif │ │ ├── sorttable.js │ │ ├── stackhorizontalbottom.gif │ │ ├── stackhorizontalcenter.gif │ │ ├── stackhorizontaltop.gif │ │ ├── stackverticalcenter.gif │ │ ├── stackverticalleft.gif │ │ ├── stackverticalright.gif │ │ ├── top.gif │ │ ├── tree_collapsed.gif │ │ ├── tree_expanded.gif │ │ ├── unchecked.gif │ │ ├── unchecked_unavailable.gif │ │ ├── undo.gif │ │ ├── up.gif │ │ └── visualizations.gif │ ├── src │ │ └── org │ │ │ └── pathvisio │ │ │ └── core │ │ │ ├── ApplicationEvent.java │ │ │ ├── Engine.java │ │ │ ├── Globals.java │ │ │ ├── biopax │ │ │ ├── BiopaxElement.java │ │ │ ├── BiopaxNode.java │ │ │ ├── BiopaxProperty.java │ │ │ ├── BiopaxReferenceManager.java │ │ │ ├── Namespaces.java │ │ │ ├── PropertyType.java │ │ │ ├── PublicationXref.java │ │ │ └── package.html │ │ │ ├── data │ │ │ ├── GdbEvent.java │ │ │ ├── GdbManager.java │ │ │ ├── PubMedQuery.java │ │ │ ├── PubMedResult.java │ │ │ ├── XrefWithSymbol.java │ │ │ └── package.html │ │ │ ├── debug │ │ │ ├── DebugList.java │ │ │ ├── EventDispatchThreadOnly.java │ │ │ ├── Logger.java │ │ │ ├── StopWatch.java │ │ │ ├── ThreadSafe.java │ │ │ ├── WorkerThreadOnly.java │ │ │ └── package.html │ │ │ ├── gpmldiff │ │ │ ├── BasicCost.java │ │ │ ├── BasicOutputter.java │ │ │ ├── BasicSim.java │ │ │ ├── BetterSim.java │ │ │ ├── CostFunction.java │ │ │ ├── DgpmlOutputter.java │ │ │ ├── DiffOutputter.java │ │ │ ├── GlassPane.java │ │ │ ├── GpmlDiff.java │ │ │ ├── Map2D.java │ │ │ ├── PanelOutputter.java │ │ │ ├── Patch.java │ │ │ ├── PatchMain.java │ │ │ ├── PwyDoc.java │ │ │ ├── PwyElt.java │ │ │ ├── SearchNode.java │ │ │ ├── SimilarityFunction.java │ │ │ └── package.html │ │ │ ├── gui │ │ │ ├── PathwayTransferable.java │ │ │ ├── SwingKeyEvent.java │ │ │ ├── SwingMouseEvent.java │ │ │ └── ToolTipProvider.java │ │ │ ├── model │ │ │ ├── AStar.java │ │ │ ├── AbstractConnector.java │ │ │ ├── AbstractPathwayFormat.java │ │ │ ├── AbstractShape.java │ │ │ ├── AlignType.java │ │ │ ├── AnchorType.java │ │ │ ├── BatikImageExporter.java │ │ │ ├── CellularComponentType.java │ │ │ ├── ConnectorRestrictions.java │ │ │ ├── ConnectorShape.java │ │ │ ├── ConnectorShapeFactory.java │ │ │ ├── ConnectorType.java │ │ │ ├── ConverterException.java │ │ │ ├── CurvedConnectorShape.java │ │ │ ├── DataNodeListExporter.java │ │ │ ├── DataNodeType.java │ │ │ ├── EUGeneExporter.java │ │ │ ├── ElbowConnectorShape.java │ │ │ ├── FreeConnectorShape.java │ │ │ ├── GpmlFormat.java │ │ │ ├── GpmlFormat200X.java │ │ │ ├── GpmlFormat2010a.java │ │ │ ├── GpmlFormat2013a.java │ │ │ ├── GpmlFormatAbstract.java │ │ │ ├── GpmlFormatReader.java │ │ │ ├── GpmlFormatVersion.java │ │ │ ├── GpmlFormatWriter.java │ │ │ ├── GraphLink.java │ │ │ ├── GroupStyle.java │ │ │ ├── IShape.java │ │ │ ├── ImageExporter.java │ │ │ ├── LineStyle.java │ │ │ ├── LineType.java │ │ │ ├── MGroup.java │ │ │ ├── MLine.java │ │ │ ├── MState.java │ │ │ ├── MappFormat.java │ │ │ ├── ObjectType.java │ │ │ ├── OntologyTag.java │ │ │ ├── OrientationType.java │ │ │ ├── Pathway.java │ │ │ ├── PathwayElement.java │ │ │ ├── PathwayElementEvent.java │ │ │ ├── PathwayElementListener.java │ │ │ ├── PathwayEvent.java │ │ │ ├── PathwayExporter.java │ │ │ ├── PathwayIO.java │ │ │ ├── PathwayImporter.java │ │ │ ├── PathwayListener.java │ │ │ ├── Property.java │ │ │ ├── PropertyManager.java │ │ │ ├── PropertyType.java │ │ │ ├── RasterImageExporter.java │ │ │ ├── SegmentedConnector.java │ │ │ ├── ShapeType.java │ │ │ ├── StaticProperty.java │ │ │ ├── StaticPropertyType.java │ │ │ ├── StraightConnectorShape.java │ │ │ ├── ValignType.java │ │ │ └── package.html │ │ │ ├── package.html │ │ │ ├── preferences │ │ │ ├── GlobalPreference.java │ │ │ ├── Preference.java │ │ │ ├── PreferenceEvent.java │ │ │ ├── PreferenceListener.java │ │ │ └── PreferenceManager.java │ │ │ ├── util │ │ │ ├── ColorConverter.java │ │ │ ├── ColorExporter.java │ │ │ ├── CommonsFileUtils.java │ │ │ ├── Converter.java │ │ │ ├── FileUtils.java │ │ │ ├── JarUtils.java │ │ │ ├── PathwayParser.java │ │ │ ├── ProgressKeeper.java │ │ │ ├── Relation.java │ │ │ ├── Resources.java │ │ │ ├── RootElementFinder.java │ │ │ ├── Stats.java │ │ │ ├── Utils.java │ │ │ └── package.html │ │ │ └── view │ │ │ ├── AbstractLinkAnchorDelegate.java │ │ │ ├── Adjustable.java │ │ │ ├── AnchorShape.java │ │ │ ├── ArrowShape.java │ │ │ ├── BasicShapes.java │ │ │ ├── Citation.java │ │ │ ├── DefaultLinkAnchorDelegate.java │ │ │ ├── DefaultTemplates.java │ │ │ ├── GenMAPPShapes.java │ │ │ ├── GeneProduct.java │ │ │ ├── Graphics.java │ │ │ ├── GraphicsShape.java │ │ │ ├── Group.java │ │ │ ├── GroupPainter.java │ │ │ ├── GroupPainterRegistry.java │ │ │ ├── Handle.java │ │ │ ├── InfoBox.java │ │ │ ├── InputEvent.java │ │ │ ├── KeyEvent.java │ │ │ ├── Label.java │ │ │ ├── LayoutType.java │ │ │ ├── Legend.java │ │ │ ├── LinAlg.java │ │ │ ├── Line.java │ │ │ ├── LinkAnchor.java │ │ │ ├── LinkProvider.java │ │ │ ├── MIMShapes.java │ │ │ ├── MouseEvent.java │ │ │ ├── SelectionBox.java │ │ │ ├── Shape.java │ │ │ ├── ShapeRegistry.java │ │ │ ├── State.java │ │ │ ├── Template.java │ │ │ ├── UndoAction.java │ │ │ ├── UndoManager.java │ │ │ ├── UndoManagerEvent.java │ │ │ ├── UndoManagerListener.java │ │ │ ├── VAnchor.java │ │ │ ├── VElementMouseEvent.java │ │ │ ├── VElementMouseListener.java │ │ │ ├── VPathway.java │ │ │ ├── VPathwayElement.java │ │ │ ├── VPathwayEvent.java │ │ │ ├── VPathwayListener.java │ │ │ ├── VPathwayWrapper.java │ │ │ ├── VPoint.java │ │ │ ├── ViewActions.java │ │ │ └── package.html │ └── test │ │ └── org │ │ └── pathvisio │ │ └── core │ │ ├── biopax │ │ └── Test.java │ │ ├── data │ │ ├── Test.java │ │ └── TestOnline.java │ │ ├── debug │ │ └── TestDebug.java │ │ ├── gpmldiff │ │ └── Test.java │ │ ├── model │ │ ├── Test.java │ │ ├── TestGpml.java │ │ ├── TestGraph.java │ │ ├── TestMGroup.java │ │ ├── TestParser.java │ │ └── TestSegmentedConnector.java │ │ ├── preferences │ │ └── Test.java │ │ ├── util │ │ └── Test.java │ │ └── view │ │ ├── Test.java │ │ └── TestGroups.java ├── org.pathvisio.data │ ├── .classpath │ ├── .project │ ├── META-INF │ │ └── MANIFEST.MF │ ├── build.properties │ ├── build.xml │ └── src │ │ └── org │ │ └── pathvisio │ │ └── data │ │ ├── Criterion.java │ │ ├── DataException.java │ │ ├── DataInterface.java │ │ ├── Functions.java │ │ ├── IRow.java │ │ └── ISample.java ├── org.pathvisio.desktop │ ├── .classpath │ ├── .project │ ├── META-INF │ │ └── MANIFEST.MF │ ├── build.properties │ ├── build.xml │ ├── resources │ │ └── com │ │ │ └── nexes │ │ │ └── wizard │ │ │ ├── backIcon.gif │ │ │ ├── cancelIcon.gif │ │ │ ├── finishIcon.gif │ │ │ ├── nextIcon.gif │ │ │ └── wizard.properties │ ├── src │ │ ├── com │ │ │ └── nexes │ │ │ │ ├── test │ │ │ │ ├── Main.java │ │ │ │ ├── TestPanel1.java │ │ │ │ ├── TestPanel1Descriptor.java │ │ │ │ ├── TestPanel2.java │ │ │ │ ├── TestPanel2Descriptor.java │ │ │ │ ├── TestPanel3.java │ │ │ │ ├── TestPanel3Descriptor.java │ │ │ │ └── clouds.jpg │ │ │ │ └── wizard │ │ │ │ ├── Wizard.java │ │ │ │ ├── WizardController.java │ │ │ │ ├── WizardModel.java │ │ │ │ ├── WizardPanelDescriptor.java │ │ │ │ └── WizardPanelNotFoundException.java │ │ └── org │ │ │ └── pathvisio │ │ │ └── desktop │ │ │ ├── Activator.java │ │ │ ├── AutoSave.java │ │ │ ├── DataPane.java │ │ │ ├── GuiMain.java │ │ │ ├── MainPanelStandalone.java │ │ │ ├── PreferencePanel.java │ │ │ ├── PreferencesDlg.java │ │ │ ├── PvDesktop.java │ │ │ ├── SearchPane.java │ │ │ ├── StandaloneActions.java │ │ │ ├── data │ │ │ ├── DBConnDerby.java │ │ │ └── DBConnectorSwing.java │ │ │ ├── dialog │ │ │ └── RunLocalPluginDialog.java │ │ │ ├── gex │ │ │ ├── BackpageExpression.java │ │ │ ├── CachedData.java │ │ │ ├── GexManager.java │ │ │ ├── ReporterData.java │ │ │ ├── Sample.java │ │ │ └── SimpleGex.java │ │ │ ├── model │ │ │ ├── BatikImageWithDataExporter.java │ │ │ └── RasterImageWithDataExporter.java │ │ │ ├── parameter │ │ │ └── SimpleDialogBuilder.java │ │ │ ├── plugin │ │ │ ├── IPVBundle.java │ │ │ ├── IPluginManager.java │ │ │ ├── Plugin.java │ │ │ └── PluginRepoPreference.java │ │ │ ├── util │ │ │ ├── BrowseButtonActionListener.java │ │ │ ├── JScrollPaneAdjuster.java │ │ │ ├── JTableRowHeaderResizer.java │ │ │ ├── ListWithPropertiesTableModel.java │ │ │ ├── MatchResult.java │ │ │ ├── PropertyColumn.java │ │ │ ├── RowHeaderRenderer.java │ │ │ ├── RowHeaderResizer.java │ │ │ ├── RowNumberHeader.java │ │ │ ├── RowWithProperties.java │ │ │ ├── SearchMethods.java │ │ │ ├── SearchTableModel.java │ │ │ ├── StandaloneCompat.java │ │ │ └── TextFieldUtils.java │ │ │ └── visualization │ │ │ ├── AbstractVisualizationMethod.java │ │ │ ├── ColorGradient.java │ │ │ ├── ColorRule.java │ │ │ ├── ColorSet.java │ │ │ ├── ColorSetEvent.java │ │ │ ├── ColorSetManager.java │ │ │ ├── ColorSetObject.java │ │ │ ├── Criterion.java │ │ │ ├── Functions.java │ │ │ ├── Visualization.java │ │ │ ├── VisualizationEvent.java │ │ │ ├── VisualizationManager.java │ │ │ ├── VisualizationMethod.java │ │ │ ├── VisualizationMethodProvider.java │ │ │ └── VisualizationMethodRegistry.java │ └── test │ │ └── org │ │ └── pathvisio │ │ └── desktop │ │ ├── debug │ │ └── TestAndMeasure.java │ │ └── visualization │ │ ├── Test.java │ │ └── TestColorset.java ├── org.pathvisio.gex │ ├── .classpath │ ├── .project │ ├── META-INF │ │ └── MANIFEST.MF │ ├── build.properties │ ├── build.xml │ ├── src │ │ └── org │ │ │ └── pathvisio │ │ │ └── gexplugin │ │ │ ├── Activator.java │ │ │ ├── ColumnTableModel.java │ │ │ ├── GexImportWizard.java │ │ │ ├── GexPlugin.java │ │ │ ├── GexTxtImporter.java │ │ │ ├── ImportInformation.java │ │ │ └── PreviewTableModel.java │ └── test │ │ └── org │ │ └── pathvisio │ │ └── gexplugin │ │ └── Test.java ├── org.pathvisio.gui │ ├── .classpath │ ├── .project │ ├── META-INF │ │ └── MANIFEST.MF │ ├── build.properties │ ├── build.xml │ └── src │ │ ├── com │ │ ├── jroller │ │ │ └── completer │ │ │ │ ├── AbstractCompleterFilter.java │ │ │ │ ├── CompleterFilter.java │ │ │ │ ├── CompleterFilterWithWindow.java │ │ │ │ ├── CompleterTextField.java │ │ │ │ └── FilterListModel.java │ │ └── mammothsoftware │ │ │ └── frwk │ │ │ └── ddb │ │ │ ├── DropDownButton.java │ │ │ └── RolloverButton.java │ │ └── org │ │ └── pathvisio │ │ └── gui │ │ ├── BackpagePane.java │ │ ├── BackpageTextProvider.java │ │ ├── CommonActions.java │ │ ├── DataPaneTextProvider.java │ │ ├── DataSourceModel.java │ │ ├── GraphicsChoiceButton.java │ │ ├── ImageButton.java │ │ ├── MainPanel.java │ │ ├── ObjectsPane.java │ │ ├── PathwayElementMenuListener.java │ │ ├── PathwayFileFilter.java │ │ ├── ProgressDialog.java │ │ ├── SwingEngine.java │ │ ├── WrapLayout.java │ │ ├── completer │ │ ├── CompleterQueryFilter.java │ │ ├── CompleterQueryTextArea.java │ │ ├── CompleterQueryTextField.java │ │ ├── CompleterTextArea.java │ │ └── OptionProvider.java │ │ ├── dialogs │ │ ├── AboutDlg.java │ │ ├── DataNodeDialog.java │ │ ├── DatabaseSearchDialog.java │ │ ├── LabelDialog.java │ │ ├── LineDialog.java │ │ ├── NewPathwayDialog.java │ │ ├── OkCancelDialog.java │ │ ├── PathwayElementDialog.java │ │ ├── PathwayPropertiesDialog.java │ │ ├── PopupDialogHandler.java │ │ └── PublicationXRefDialog.java │ │ ├── dnd │ │ └── PathwayImportHandler.java │ │ ├── handler │ │ ├── AngleHandler.java │ │ ├── BooleanHandler.java │ │ ├── ColorHandler.java │ │ ├── ComboHandler.java │ │ ├── CommentsHandler.java │ │ ├── ContextSensitiveEditor.java │ │ ├── DataSourceHandler.java │ │ ├── FontHandler.java │ │ ├── NumberHandler.java │ │ ├── PathwayTableModel.java │ │ ├── PropertyDisplayManager.java │ │ ├── PropertyLabelRenderer.java │ │ ├── PropertyView.java │ │ └── TypeHandler.java │ │ ├── panels │ │ ├── CommentPanel.java │ │ ├── LitReferencePanel.java │ │ └── PathwayElementPanel.java │ │ ├── util │ │ ├── Compat.java │ │ ├── FontChooser.java │ │ ├── FontNameRenderer.java │ │ └── PermissiveComboBox.java │ │ └── view │ │ └── VPathwaySwing.java ├── org.pathvisio.launcher │ ├── .classpath │ ├── .project │ ├── META-INF │ │ └── MANIFEST.MF │ ├── build.properties │ ├── build.xml │ ├── resources │ │ └── version.props │ └── src │ │ └── org │ │ └── pathvisio │ │ └── launcher │ │ ├── BundleLoader.java │ │ ├── PathVisioMain.java │ │ └── SplashFrame.java ├── org.pathvisio.pluginmanager │ ├── .classpath │ ├── .project │ ├── META-INF │ │ └── MANIFEST.MF │ ├── build.properties │ ├── build.xml │ └── src │ │ └── org │ │ └── pathvisio │ │ └── pluginmanager │ │ ├── Activator.java │ │ └── impl │ │ ├── LocalRepositoryHandler.java │ │ ├── PluginManager.java │ │ ├── StatusMessage.java │ │ ├── Utils.java │ │ ├── data │ │ ├── Affiliation.java │ │ ├── BundleAuthor.java │ │ ├── BundleVersion.java │ │ ├── Category.java │ │ ├── Developer.java │ │ ├── PVBundle.java │ │ ├── PVRepository.java │ │ └── Profile.java │ │ ├── dialogs │ │ ├── AvailablePluginsPanel.java │ │ ├── InstalledPluginsPanel.java │ │ ├── PluginCell.java │ │ ├── PluginManagerDialog.java │ │ ├── PluginTableModel.java │ │ └── StatusPanel.java │ │ └── io │ │ ├── RepoXmlFactory.java │ │ └── RepoXmlReader.java ├── org.pathvisio.statistics │ ├── .classpath │ ├── .project │ ├── META-INF │ │ └── MANIFEST.MF │ ├── build.properties │ ├── build.xml │ ├── src │ │ └── org │ │ │ └── pathvisio │ │ │ └── statistics │ │ │ ├── Activator.java │ │ │ ├── Column.java │ │ │ ├── IsDataInPathways.java │ │ │ ├── PathwayMap.java │ │ │ ├── StatisticsPathwayResult.java │ │ │ ├── StatisticsPlugin.java │ │ │ ├── StatisticsResult.java │ │ │ ├── StatisticsTableModel.java │ │ │ └── ZScoreCalculator.java │ └── test │ │ └── org │ │ └── pathvisio │ │ └── statistics │ │ └── ZScoreTest.java └── org.pathvisio.visualization │ ├── .classpath │ ├── .project │ ├── META-INF │ └── MANIFEST.MF │ ├── build.properties │ ├── build.xml │ └── src │ └── org │ └── pathvisio │ └── visualization │ ├── Activator.java │ ├── gui │ ├── ColorGradientCombo.java │ ├── ColorGradientPanel.java │ ├── ColorRulePanel.java │ ├── ColorSetChooser.java │ ├── ColorSetCombo.java │ ├── ColorSetDlg.java │ ├── ColorSetPanel.java │ ├── MethodPanel.java │ ├── VisualizationDialog.java │ └── VisualizationPanel.java │ └── plugins │ ├── ColorByExpression.java │ ├── ColorByExpressionPanel.java │ ├── DataNodeLabel.java │ ├── JCheckBoxList.java │ ├── LegendPanel.java │ ├── LegendVisualization.java │ ├── SampleCheckList.java │ ├── SortSampleCheckList.java │ ├── TextByExpression.java │ └── VisualizationPlugin.java ├── pathvisio.bat ├── pathvisio.iss ├── pathvisio.sh ├── plugin-common.xml ├── pv_checks.xml ├── pvicon.ico ├── readme.md ├── scripts ├── gpmldiff.sh └── gpmlpatch.sh ├── testData ├── 2008a-deprecation-test.gpml ├── 2010a │ ├── biopax-literaturexref-testcase.gpml │ ├── biopax-opencontrolledvocabulary-testcase.gpml │ ├── fail1.gpml │ ├── fail10.gpml │ ├── fail2.gpml │ ├── fail3.gpml │ ├── fail4.gpml │ ├── fail5.gpml │ ├── fail6.gpml │ ├── fail7.gpml │ ├── fail8.gpml │ ├── fail9.gpml │ ├── parsetest1.gpml │ ├── parsetest2.gpml │ ├── parsetest3.gpml │ ├── parsetest4.gpml │ ├── parsetest5.gpml │ ├── parsetest6.gpml │ ├── parsetest7.gpml │ └── parsetest8.gpml ├── WP248_2008a.gpml ├── WP248_2010a.gpml ├── deprecated-shapes.gpml ├── line_thickness_test │ ├── arrowhead-thickness-test.gpml │ ├── line-thickness.gpml │ └── linethickness.png ├── mpoint-test.gpml ├── nographics-test.gpml ├── shapes.gpml ├── shapes.png ├── test.gpml ├── test.mapp ├── test2.gpml └── zscore │ └── gpml │ ├── BLood Clotting Cascade.gpml │ ├── Complement activation.gpml │ ├── Eicosanoid Synthesis.gpml │ ├── Electron Transport.gpml │ ├── Focal Adhesion.gpml │ ├── G13 signaling.gpml │ ├── Glycogen Metabolism.gpml │ ├── MAPK Cascade.gpml │ ├── Oxidative stress.gpml │ ├── S1P signaling.gpml │ ├── Steriod Biosynthesis.gpml │ ├── Translation Factors.gpml │ ├── Wnt signaling.gpml │ └── testAlternative.gpml ├── webstart └── pathvisio.jnlp └── www ├── bigcateye.jpg └── bigcateye_135x135.png /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PathVisio/pathvisio/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/ant.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PathVisio/pathvisio/HEAD/.github/workflows/ant.yml -------------------------------------------------------------------------------- /.gitignore: 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