├── .gitignore ├── .travis.settings.xml ├── .travis.yml ├── README.md ├── application-metadata-impl ├── pom.xml └── src │ └── main │ └── resources │ └── org │ └── cytoscape │ └── application │ └── internal │ └── config.properties ├── assembly ├── pom.xml └── src │ └── main │ ├── bin │ ├── cytoscape.bat │ ├── cytoscape.sh │ ├── gen_vmoptions.bat │ └── gen_vmoptions.sh │ ├── descriptors │ ├── config-dev.xml │ ├── config-unix.xml │ └── config-windows.xml │ ├── filtered-resources │ └── etc │ │ ├── org.apache.karaf.features.cfg │ │ └── system.properties │ ├── resources │ ├── cytoscape_logo_512.png │ ├── etc │ │ ├── custom.properties │ │ ├── jetty.xml │ │ ├── org.cytoscape.cfg │ │ ├── org.ops4j.pax.logging.cfg │ │ └── org.ops4j.pax.url.mvn.cfg │ └── sampleData │ │ ├── BINDhuman.sif │ │ ├── BINDyeast.sif │ │ ├── galExpData.csv │ │ ├── galFiltered.cys │ │ ├── galFiltered.sif │ │ ├── importNetworkFromFile.csv │ │ ├── sampleStyles.xml │ │ └── sessions │ │ ├── Affinity Purification.cys │ │ ├── Import & Save.cys │ │ ├── Ivacaftor Coauthor.cys │ │ ├── Styles Demo.cys │ │ ├── TCGA Colorectal Cancer.cys │ │ ├── The_Yeast_Interactome.cys │ │ ├── Yeast Gene Interactions.cys │ │ └── Yeast Perturbation.cys │ └── xsl │ └── template.xslt ├── branding ├── pom.xml └── src │ └── main │ ├── etc │ └── logo.txt │ └── resources │ └── org │ └── apache │ └── karaf │ └── branding │ └── branding.properties.template ├── cmdline-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── cmdline │ └── internal │ ├── CommandLineArgsImpl.java │ └── CyActivator.java ├── diagnostics ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── diagnostics │ ├── PerformanceDetails.java │ ├── SystemDetails.java │ └── internal │ ├── Activator.java │ ├── PerformanceDetailsBuilder.java │ ├── PerformanceTracker.java │ ├── SystemDetailsImpl.java │ ├── SystemInformation.java │ └── heuristics │ ├── AbstractHeuristic.java │ ├── Heuristic.java │ ├── ProcHeuristic.java │ ├── Sw_VersHeuristic.java │ ├── SysctlHeuristic.java │ ├── UnameHeuristic.java │ ├── Vm_StatHeuristic.java │ └── WmicHeuristic.java ├── features ├── pom.xml └── src │ └── main │ └── resources │ └── features.xml ├── integration-test ├── README-BundleExceptions.txt ├── pom.xml └── src │ └── test │ ├── java │ └── org │ │ └── cytoscape │ │ └── session │ │ ├── BasicIntegrationTest.java │ │ ├── Cy252SimpleSessionLodingTest.java │ │ ├── Cy263SimpleSessionLodingTest.java │ │ ├── Cy270SimpleSessionLodingTest.java │ │ ├── Cy283ComplexSessionLodingTest.java │ │ ├── Cy283GroupsSessionLoadingTest.java │ │ ├── Cy3CollapsedGroupsSessionLoadingTest.java │ │ ├── Cy3ExpandedGroupsSessionLoadingTest.java │ │ ├── Cy3GroupsSessionLoadingTest.java │ │ ├── Cy3SimpleSessionLodingTest.java │ │ ├── Cy3SubnetworksSessionLoadingTest.java │ │ └── Cy3VisualMappingsSessionLoadingTest.java │ └── resources │ └── testData │ ├── session2x │ ├── v252Session.cys │ ├── v263SessionLarge.cys │ ├── v270session.cys │ ├── v283Groups.cys │ └── v283Session1.cys │ └── session3x │ ├── groups.cys │ ├── nestedGroups_collapsed.cys │ ├── nestedGroups_expanded.cys │ ├── simpleSession.cys │ ├── subnetworks.cys │ └── visualMappings.cys ├── launcher ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── launcher │ └── internal │ ├── Launcher.java │ ├── MacHelper.java │ └── SplashPanel.java ├── packaging ├── README.txt ├── pom.xml ├── pom.xml.versionsBackup ├── sign-dmg.sh └── src │ └── main │ ├── images │ ├── cytoscape3-file-icon-trans-128x128.icns │ ├── cytoscape3-icon-trans-128x128.icns │ ├── cytoscape3-icon-trans-128x128.ico │ ├── cytoscape3-icon-trans-128x128.png │ ├── cytoscape3-icon-trans-16x16.png │ ├── cytoscape3-icon-trans-32x32.png │ ├── cytoscape3_logo.ico │ └── whatsnew │ │ ├── app_store.png │ │ ├── app_store@2x.png │ │ ├── edge_labels.png │ │ ├── edge_labels@2x.png │ │ ├── selection_lasso.png │ │ ├── selection_lasso@2x.png │ │ ├── table_style.png │ │ └── table_style@2x.png │ └── 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