├── .github └── workflows │ └── annual_copyright_update.yml ├── .gitignore ├── .travis.settings.xml ├── .travis.yml ├── LICENSE ├── README.md ├── app-impl ├── README.md ├── api-notes.txt ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── app │ │ │ └── internal │ │ │ ├── CyActivator.java │ │ │ ├── CyAppAdapterImpl.java │ │ │ ├── action │ │ │ ├── CitationsAction.java │ │ │ ├── UpdateNotificationAction.java │ │ │ └── YFilesAction.java │ │ │ ├── event │ │ │ ├── AppsChangedEvent.java │ │ │ ├── AppsChangedListener.java │ │ │ ├── UpdatesChangedEvent.java │ │ │ └── UpdatesChangedListener.java │ │ │ ├── exception │ │ │ ├── AppDisableException.java │ │ │ ├── AppDownloadException.java │ │ │ ├── AppInstallException.java │ │ │ ├── AppLoadingException.java │ │ │ ├── AppParsingException.java │ │ │ ├── AppStartupException.java │ │ │ ├── AppStoppingException.java │ │ │ ├── AppUninstallException.java │ │ │ ├── AppUnloadingException.java │ │ │ └── AppUpdateException.java │ │ │ ├── manager │ │ │ ├── App.java │ │ │ ├── AppDependencyNode.java │ │ │ ├── AppManager.java │ │ │ ├── AppParser.java │ │ │ ├── BundleApp.java │ │ │ ├── LaunchManager.java │ │ │ ├── ParseAppDependencies.java │ │ │ ├── Range.java │ │ │ ├── SimpleApp.java │ │ │ └── Version.java │ │ │ ├── net │ │ │ ├── DownloadStatus.java │ │ │ ├── ResultsFilterer.java │ │ │ ├── Update.java │ │ │ ├── UpdateManager.java │ │ │ ├── WebApp.java │ │ │ └── WebQuerier.java │ │ │ ├── task │ │ │ ├── AbstractAppTask.java │ │ │ ├── AppManagerTask.java │ │ │ ├── AppManagerTaskFactory.java │ │ │ ├── AppStoreTask.java │ │ │ ├── AppStoreTaskFactory.java │ │ │ ├── ChangeTabTask.java │ │ │ ├── ChangeTabTaskFactory.java │ │ │ ├── DisableTask.java │ │ │ ├── DisableTaskFactory.java │ │ │ ├── EnableTask.java │ │ │ ├── EnableTaskFactory.java │ │ │ ├── InformationTask.java │ │ │ ├── InformationTaskFactory.java │ │ │ ├── InstallAppsFromFileTask.java │ │ │ ├── InstallAppsFromWebAppTask.java │ │ │ ├── InstallAppsTask.java │ │ │ ├── InstallTask.java │ │ │ ├── InstallTaskFactory.java │ │ │ ├── InstallUpdatesTask.java │ │ │ ├── ListAppsTask.java │ │ │ ├── ListAppsTaskFactory.java │ │ │ ├── ListAvailableTask.java │ │ │ ├── ListAvailableTaskFactory.java │ │ │ ├── ListUpdatesTask.java │ │ │ ├── ListUpdatesTaskFactory.java │ │ │ ├── ManagerInstallAppsFromFileTask.java │ │ │ ├── ManagerInstallAppsFromFileTaskFactory.java │ │ │ ├── ResolveAppConflictTask.java │ │ │ ├── ResolveAppDependenciesTask.java │ │ │ ├── ShowInstalledAppsTask.java │ │ │ ├── StatusTask.java │ │ │ ├── StatusTaskFactory.java │ │ │ ├── UninstallTask.java │ │ │ ├── UninstallTaskFactory.java │ │ │ ├── UpdateTask.java │ │ │ └── UpdateTaskFactory.java │ │ │ ├── tunable │ │ │ ├── AppConflictHandler.java │ │ │ └── AppConflictHandlerFactory.java │ │ │ ├── ui │ │ │ ├── AppManagerDialog.java │ │ │ ├── AppManagerMediator.java │ │ │ ├── CitationsDialog.java │ │ │ └── downloadsites │ │ │ │ ├── DownloadSite.java │ │ │ │ ├── DownloadSitesManager.java │ │ │ │ └── ManageDownloadSitesDialog.java │ │ │ └── util │ │ │ ├── AppHelper.java │ │ │ ├── AppUtil.java │ │ │ ├── DebugHelper.java │ │ │ └── MiniTest.java │ └── resources │ │ └── AppManager │ │ ├── AppManager.html │ │ └── img │ │ ├── adn-brands.png │ │ ├── adn-brands.svg │ │ ├── hamburger.ai │ │ ├── hamburger.png │ │ ├── logo.png │ │ ├── logo_mgr.ai │ │ ├── logo_mgr_large.png │ │ ├── search.png │ │ ├── tab.png │ │ ├── trash.png │ │ ├── trash2.png │ │ ├── update1.png │ │ ├── update2.png │ │ └── update_og.png │ └── test │ └── java │ └── org │ └── cytoscape │ └── app │ └── internal │ ├── CyAppAdapterImplTest.java │ ├── net │ └── WebQuerierTest.java │ ├── ui │ └── downloadsites │ │ └── DownloadSitesManagerTest.java │ └── util │ └── AppUtilTest.java ├── application-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── application │ │ └── internal │ │ ├── CyActivator.java │ │ ├── CyApplicationConfigurationImpl.java │ │ ├── CyApplicationManagerImpl.java │ │ ├── CyVersionImpl.java │ │ ├── DefaultNetworkViewFactory.java │ │ └── ShutdownHandler.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── application │ └── internal │ └── CyApplicationManagerImplTest.java ├── command-executor-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── command │ │ └── internal │ │ ├── CommandExecutorImpl.java │ │ ├── CommandExecutorTask.java │ │ ├── CommandExecutorTaskFactoryImpl.java │ │ ├── CommandFileExecutorTask.java │ │ ├── CommandStringsExecutorTask.java │ │ ├── CyActivator.java │ │ ├── Executor.java │ │ ├── StringToModelImpl.java │ │ ├── TFExecutor.java │ │ ├── available │ │ ├── ArgHandler.java │ │ ├── ArgHandlerFactory.java │ │ ├── ArgRecorder.java │ │ ├── AvailableCommandsImpl.java │ │ ├── BasicArgHandler.java │ │ ├── BasicArgHandlerFactory.java │ │ └── dummies │ │ │ ├── DummyNetwork.java │ │ │ ├── DummyNetworkView.java │ │ │ └── DummyTable.java │ │ ├── tasks │ │ ├── EchoCommandTask.java │ │ ├── EchoCommandTaskFactory.java │ │ ├── QuitTask.java │ │ ├── QuitTaskFactory.java │ │ ├── RunCommandsTask.java │ │ ├── RunCommandsTaskFactory.java │ │ ├── SleepCommandTask.java │ │ └── SleepCommandTaskFactory.java │ │ └── tunables │ │ ├── BooleanTunableHandler.java │ │ ├── BoundedDoubleTunableHandler.java │ │ ├── BoundedFloatTunableHandler.java │ │ ├── BoundedIntTunableHandler.java │ │ ├── BoundedLongTunableHandler.java │ │ ├── CharTunableHandlerImpl.java │ │ ├── CommandTunableInterceptorImpl.java │ │ ├── CyIdentifiableStringTunableHandlerFactory.java │ │ ├── CyIdentifiableTunableHandler.java │ │ ├── CyNetworkTunableHandler.java │ │ ├── CyNetworkViewTunableHandler.java │ │ ├── CyTableTunableHandler.java │ │ ├── DoubleTunableHandler.java │ │ ├── EdgeListTunableHandler.java │ │ ├── FileTunableHandler.java │ │ ├── FloatTunableHandler.java │ │ ├── IntTunableHandler.java │ │ ├── ListMultipleTunableHandler.java │ │ ├── ListSingleTunableHandler.java │ │ ├── LongTunableHandler.java │ │ ├── NodeListTunableHandler.java │ │ ├── RowListTunableHandler.java │ │ ├── SimpleStringTunableHandlerFactory.java │ │ ├── StringTunableHandlerImpl.java │ │ └── URLTunableHandler.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── command │ └── internal │ ├── CommandParseTest.java │ └── StringToModelTest.java ├── core-task-impl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── task │ │ │ └── internal │ │ │ ├── CyActivator.java │ │ │ ├── DynamicTaskFactoryProvisionerImpl.java │ │ │ ├── edit │ │ │ ├── ConnectSelectedNodesEdit.java │ │ │ ├── ConnectSelectedNodesTask.java │ │ │ └── ConnectSelectedNodesTaskFactoryImpl.java │ │ │ ├── export │ │ │ ├── AbstractCyWriter.java │ │ │ ├── DelegatingOutputStream.java │ │ │ ├── TunableAbstractCyWriter.java │ │ │ ├── ViewWriter.java │ │ │ ├── graphics │ │ │ │ └── ExportNetworkImageTaskFactoryImpl.java │ │ │ ├── network │ │ │ │ ├── AbstractLoadNetworkTask.java │ │ │ │ ├── CyNetworkViewWriter.java │ │ │ │ ├── CyNetworkWriter.java │ │ │ │ ├── ExportNetworkTaskFactoryImpl.java │ │ │ │ ├── ExportNetworkViewTaskFactoryImpl.java │ │ │ │ ├── ExportSelectedNetworkTaskFactoryImpl.java │ │ │ │ ├── GenerateNetworkViewsTask.java │ │ │ │ ├── LoadMultipleNetworkFilesTaskFactoryImpl.java │ │ │ │ ├── LoadMultipleNetworksTask.java │ │ │ │ ├── LoadNetworkFileTask.java │ │ │ │ ├── LoadNetworkFileTaskFactoryImpl.java │ │ │ │ ├── LoadNetworkTask.java │ │ │ │ ├── LoadNetworkURLTask.java │ │ │ │ └── LoadNetworkURLTaskFactoryImpl.java │ │ │ ├── table │ │ │ │ ├── CyTableWriter.java │ │ │ │ ├── ExportNoGuiSelectedTableTaskFactoryImpl.java │ │ │ │ ├── ExportSelectedTableTaskFactoryImpl.java │ │ │ │ ├── ExportTableTaskFactoryImpl.java │ │ │ │ ├── NoGuiSelectExportTableTask.java │ │ │ │ └── SelectExportTableTask.java │ │ │ └── web │ │ │ │ ├── ExportAsWebArchiveTask.java │ │ │ │ ├── ExportAsWebArchiveTaskFactory.java │ │ │ │ └── ShowWarningTask.java │ │ │ ├── filter │ │ │ ├── ApplyFilterTask.java │ │ │ ├── ApplyFilterTaskFactory.java │ │ │ ├── ContainerTunable.java │ │ │ ├── CreateFilterTask.java │ │ │ ├── CreateFilterTaskFactory.java │ │ │ ├── DeleteFilterTask.java │ │ │ ├── DeleteFilterTaskFactory.java │ │ │ ├── GetFilterTask.java │ │ │ ├── GetFilterTaskFactory.java │ │ │ ├── ListFiltersTask.java │ │ │ ├── ListFiltersTaskFactory.java │ │ │ ├── RenameFilterTask.java │ │ │ ├── RenameFilterTaskFactory.java │ │ │ ├── SelectFilterTask.java │ │ │ ├── SelectFilterTaskFactory.java │ │ │ ├── SelectTunable.java │ │ │ ├── Sink.java │ │ │ └── TransformerJsonTunable.java │ │ │ ├── group │ │ │ ├── AbstractGroupTask.java │ │ │ ├── AddToGroupTask.java │ │ │ ├── AddToGroupTaskFactory.java │ │ │ ├── CollapseGroupTask.java │ │ │ ├── GetGroupTask.java │ │ │ ├── GetGroupTaskFactory.java │ │ │ ├── GroupEdit.java │ │ │ ├── GroupNodeContextTaskFactoryImpl.java │ │ │ ├── GroupNodesTask.java │ │ │ ├── GroupNodesTaskFactoryImpl.java │ │ │ ├── ListGroupsTask.java │ │ │ ├── ListGroupsTaskFactory.java │ │ │ ├── RemoveFromGroupTask.java │ │ │ ├── RemoveFromGroupTaskFactory.java │ │ │ ├── RenameGroupTask.java │ │ │ ├── RenameGroupTaskFactory.java │ │ │ ├── UnGroupNodesTask.java │ │ │ └── UnGroupNodesTaskFactoryImpl.java │ │ │ ├── help │ │ │ ├── HelpTask.java │ │ │ └── HelpTaskFactory.java │ │ │ ├── hide │ │ │ ├── AbstractHideFromSelectionTaskFactory.java │ │ │ ├── AbstractUnHideTaskFactory.java │ │ │ ├── HideCommandTask.java │ │ │ ├── HideCommandTaskFactory.java │ │ │ ├── HideEdit.java │ │ │ ├── HideFromSelectionTask.java │ │ │ ├── HideSelectedEdgesTaskFactoryImpl.java │ │ │ ├── HideSelectedNodesTaskFactoryImpl.java │ │ │ ├── HideSelectedTaskFactoryImpl.java │ │ │ ├── HideTask.java │ │ │ ├── HideTaskFactoryImpl.java │ │ │ ├── HideUnselectedEdgesTaskFactoryImpl.java │ │ │ ├── HideUnselectedNodesTaskFactoryImpl.java │ │ │ ├── HideUnselectedTaskFactoryImpl.java │ │ │ ├── HideUtils.java │ │ │ ├── UnHideAllEdgesTaskFactoryImpl.java │ │ │ ├── UnHideAllNodesTaskFactoryImpl.java │ │ │ ├── UnHideAllTaskFactoryImpl.java │ │ │ ├── UnHideCommandTask.java │ │ │ ├── UnHideCommandTaskFactory.java │ │ │ ├── UnHideFromSelectionTask.java │ │ │ ├── UnHideSelectedEdgesTaskFactoryImpl.java │ │ │ ├── UnHideSelectedNodesTaskFactoryImpl.java │ │ │ ├── UnHideTask.java │ │ │ └── UnHideTaskFactoryImpl.java │ │ │ ├── layout │ │ │ ├── ApplyPreferredLayoutTask.java │ │ │ ├── ApplyPreferredLayoutTaskFactoryImpl.java │ │ │ ├── GetPreferredLayoutTask.java │ │ │ ├── GetPreferredLayoutTaskFactory.java │ │ │ ├── SetPreferredLayoutTask.java │ │ │ └── SetPreferredLayoutTaskFactory.java │ │ │ ├── network │ │ │ ├── AbstractCreationTask.java │ │ │ ├── AbstractNetworkFromSelectionTask.java │ │ │ ├── CloneNetworkTask.java │ │ │ ├── CloneNetworkTaskFactoryImpl.java │ │ │ ├── DestroyNetworkTask.java │ │ │ ├── DestroyNetworkTaskFactoryImpl.java │ │ │ ├── GroupUtils.java │ │ │ ├── NewEmptyNetworkTask.java │ │ │ ├── NewEmptyNetworkTaskFactoryImpl.java │ │ │ ├── NewNetworkCommandTask.java │ │ │ ├── NewNetworkCommandTaskFactory.java │ │ │ ├── NewNetworkSelectedNodesEdgesTask.java │ │ │ ├── NewNetworkSelectedNodesEdgesTaskFactoryImpl.java │ │ │ ├── NewNetworkSelectedNodesOnlyTask.java │ │ │ ├── NewNetworkSelectedNodesOnlyTaskFactoryImpl.java │ │ │ └── RegisterNetworkTask.java │ │ │ ├── networkobjects │ │ │ ├── AbstractGetTask.java │ │ │ ├── AbstractPropertyTask.java │ │ │ ├── AddEdgeTask.java │ │ │ ├── AddEdgeTaskFactory.java │ │ │ ├── AddNodeTask.java │ │ │ ├── AddNodeTaskFactory.java │ │ │ ├── AddTask.java │ │ │ ├── AddTaskFactory.java │ │ │ ├── DeleteEdit.java │ │ │ ├── DeleteSelectedNodesAndEdgesTask.java │ │ │ ├── DeleteSelectedNodesAndEdgesTaskFactoryImpl.java │ │ │ ├── GetEdgePropertiesTask.java │ │ │ ├── GetEdgeTask.java │ │ │ ├── GetEdgeTaskFactory.java │ │ │ ├── GetNetworkPropertiesTask.java │ │ │ ├── GetNetworkTask.java │ │ │ ├── GetNetworkTaskFactory.java │ │ │ ├── GetNodePropertiesTask.java │ │ │ ├── GetNodeTask.java │ │ │ ├── GetNodeTaskFactory.java │ │ │ ├── GetPropertiesTaskFactory.java │ │ │ ├── ListEdgesTask.java │ │ │ ├── ListEdgesTaskFactory.java │ │ │ ├── ListNetworksTask.java │ │ │ ├── ListNetworksTaskFactory.java │ │ │ ├── ListNodesTask.java │ │ │ ├── ListNodesTaskFactory.java │ │ │ ├── ListPropertiesTask.java │ │ │ ├── ListPropertiesTaskFactory.java │ │ │ ├── RenameEdgeTask.java │ │ │ ├── RenameEdgeTaskFactory.java │ │ │ ├── RenameNodeTask.java │ │ │ ├── RenameNodeTaskFactory.java │ │ │ ├── SetCurrentNetworkTask.java │ │ │ ├── SetCurrentNetworkTaskFactory.java │ │ │ ├── SetEdgePropertiesTask.java │ │ │ ├── SetNetworkPropertiesTask.java │ │ │ ├── SetNodePropertiesTask.java │ │ │ └── SetPropertiesTaskFactory.java │ │ │ ├── proxysettings │ │ │ ├── ProxySettingsTask.java │ │ │ ├── ProxySettingsTask2.java │ │ │ └── ProxySettingsTaskFactoryImpl.java │ │ │ ├── select │ │ │ ├── AbstractSelectTask.java │ │ │ ├── DeselectAllEdgesTask.java │ │ │ ├── DeselectAllEdgesTaskFactoryImpl.java │ │ │ ├── DeselectAllNodesTask.java │ │ │ ├── DeselectAllNodesTaskFactoryImpl.java │ │ │ ├── DeselectAllTask.java │ │ │ ├── DeselectAllTaskFactoryImpl.java │ │ │ ├── DeselectEdgesTask.java │ │ │ ├── DeselectEdgesTaskFactoryImpl.java │ │ │ ├── DeselectNodesTask.java │ │ │ ├── DeselectNodesTaskFactoryImpl.java │ │ │ ├── DeselectTask.java │ │ │ ├── DeselectTaskFactory.java │ │ │ ├── InvertSelectedEdgesTask.java │ │ │ ├── InvertSelectedEdgesTaskFactoryImpl.java │ │ │ ├── InvertSelectedNodesTask.java │ │ │ ├── InvertSelectedNodesTaskFactoryImpl.java │ │ │ ├── SelectAdjacentEdgesTask.java │ │ │ ├── SelectAdjacentEdgesTaskFactoryImpl.java │ │ │ ├── SelectAllEdgesTask.java │ │ │ ├── SelectAllEdgesTaskFactoryImpl.java │ │ │ ├── SelectAllNodesTask.java │ │ │ ├── SelectAllNodesTaskFactoryImpl.java │ │ │ ├── SelectAllTask.java │ │ │ ├── SelectAllTaskFactoryImpl.java │ │ │ ├── SelectConnectedNodesTask.java │ │ │ ├── SelectConnectedNodesTaskFactoryImpl.java │ │ │ ├── SelectEdgesBetweenSelectedNodesTask.java │ │ │ ├── SelectEdgesBetweenSelectedNodesTaskFactoryImpl.java │ │ │ ├── SelectFirstNeighborsNodeViewTask.java │ │ │ ├── SelectFirstNeighborsNodeViewTaskFactoryImpl.java │ │ │ ├── SelectFirstNeighborsTask.java │ │ │ ├── SelectFirstNeighborsTaskFactoryImpl.java │ │ │ ├── SelectFromFileListTask.java │ │ │ ├── SelectFromFileListTaskFactoryImpl.java │ │ │ ├── SelectTask.java │ │ │ ├── SelectTaskFactory.java │ │ │ ├── SelectUtils.java │ │ │ └── SelectionEdit.java │ │ │ ├── session │ │ │ ├── AbstractOpenSessionTask.java │ │ │ ├── CySessionWriter.java │ │ │ ├── NewSessionTask.java │ │ │ ├── NewSessionTaskFactoryImpl.java │ │ │ ├── OpenSessionCommandTask.java │ │ │ ├── OpenSessionCommandTaskFactory.java │ │ │ ├── OpenSessionTask.java │ │ │ ├── OpenSessionTaskFactoryImpl.java │ │ │ ├── SaveSessionAsTask.java │ │ │ ├── SaveSessionAsTaskFactoryImpl.java │ │ │ ├── SaveSessionTask.java │ │ │ └── SaveSessionTaskFactoryImpl.java │ │ │ ├── setcurrent │ │ │ ├── SetCurrentNetworkTask.java │ │ │ └── SetCurrentNetworkTaskFactoryImpl.java │ │ │ ├── table │ │ │ ├── AbstractTableDataTask.java │ │ │ ├── AddRowTask.java │ │ │ ├── AddRowTaskFactory.java │ │ │ ├── CopyValueToColumnEdit.java │ │ │ ├── CopyValueToColumnTask.java │ │ │ ├── CopyValueToColumnTaskFactoryImpl.java │ │ │ ├── CreateColumnTask.java │ │ │ ├── CreateColumnTaskFactory.java │ │ │ ├── CreateEdgeAttributeTask.java │ │ │ ├── CreateNetworkAttributeTask.java │ │ │ ├── CreateNetworkAttributeTaskFactory.java │ │ │ ├── CreateNodeAttributeTask.java │ │ │ ├── CreateTableTask.java │ │ │ ├── CreateTableTaskFactory.java │ │ │ ├── DeleteColumnCommandTask.java │ │ │ ├── DeleteColumnCommandTaskFactory.java │ │ │ ├── DeleteColumnEdit.java │ │ │ ├── DeleteColumnTask.java │ │ │ ├── DeleteColumnTaskFactoryImpl.java │ │ │ ├── DeleteRowTask.java │ │ │ ├── DeleteRowTaskFactory.java │ │ │ ├── DeleteTableEdit.java │ │ │ ├── DeleteTableTask.java │ │ │ ├── DeleteTableTaskFactoryImpl.java │ │ │ ├── DestroyTableTask.java │ │ │ ├── DestroyTableTaskFactory.java │ │ │ ├── GetColumnTask.java │ │ │ ├── GetColumnTaskFactory.java │ │ │ ├── GetEdgeAttributeTask.java │ │ │ ├── GetNetworkAttributeTask.java │ │ │ ├── GetNetworkAttributeTaskFactory.java │ │ │ ├── GetNodeAttributeTask.java │ │ │ ├── GetRowTask.java │ │ │ ├── GetRowTaskFactory.java │ │ │ ├── GetValueTask.java │ │ │ ├── GetValueTaskFactory.java │ │ │ ├── JoinTablesTask.java │ │ │ ├── JoinTablesTaskTaskFactoryImpl.java │ │ │ ├── ListColumnsTask.java │ │ │ ├── ListColumnsTaskFactory.java │ │ │ ├── ListEdgeAttributesTask.java │ │ │ ├── ListNetworkAttributesTask.java │ │ │ ├── ListNetworkAttributesTaskFactory.java │ │ │ ├── ListNodeAttributesTask.java │ │ │ ├── ListRowsTask.java │ │ │ ├── ListRowsTaskFactory.java │ │ │ ├── ListTablesTask.java │ │ │ ├── ListTablesTaskFactory.java │ │ │ ├── MapGlobalToLocalTableTask.java │ │ │ ├── MapGlobalToLocalTableTaskFactoryImpl.java │ │ │ ├── MapTableToNetworkTablesTask.java │ │ │ ├── MapTableToNetworkTablesTaskFactoryImpl.java │ │ │ ├── MergeTablesTask.java │ │ │ ├── MergeTablesTaskFactoryImpl.java │ │ │ ├── RenameColumnCommandTask.java │ │ │ ├── RenameColumnEdit.java │ │ │ ├── RenameColumnTask.java │ │ │ ├── RenameColumnTaskFactoryImpl.java │ │ │ ├── SaveColumn.java │ │ │ ├── SetEdgeAttributeTask.java │ │ │ ├── SetNetworkAttributeTask.java │ │ │ ├── SetNetworkAttributeTaskFactory.java │ │ │ ├── SetNodeAttributeTask.java │ │ │ ├── SetTableTitleTask.java │ │ │ ├── SetTableTitleTaskFactory.java │ │ │ ├── SetValuesTask.java │ │ │ └── SetValuesTaskFactory.java │ │ │ ├── title │ │ │ ├── EditNetworkTitleTask.java │ │ │ ├── EditNetworkTitleTaskFactoryImpl.java │ │ │ └── NetworkTitleEdit.java │ │ │ ├── utils │ │ │ ├── ColumnListTunable.java │ │ │ ├── ColumnTunable.java │ │ │ ├── ColumnTypeTunable.java │ │ │ ├── ColumnValueTunable.java │ │ │ ├── CoreImplDocumentationConstants.java │ │ │ ├── DataUtils.java │ │ │ ├── EdgeTunable.java │ │ │ ├── IconUtil.java │ │ │ ├── NodeAndEdgeTunable.java │ │ │ ├── NodeTunable.java │ │ │ ├── RowTunable.java │ │ │ └── TableTunable.java │ │ │ ├── view │ │ │ ├── CopyExistingViewTask.java │ │ │ ├── CreateNetworkViewEdit.java │ │ │ ├── CreateNetworkViewTask.java │ │ │ ├── CreateNetworkViewTaskFactoryImpl.java │ │ │ ├── DestroyNetworkViewTask.java │ │ │ ├── DestroyNetworkViewTaskFactoryImpl.java │ │ │ ├── GetCurrentNetworkViewTask.java │ │ │ ├── GetCurrentNetworkViewTaskFactory.java │ │ │ ├── ListNetworkViewsTask.java │ │ │ ├── ListNetworkViewsTaskFactory.java │ │ │ ├── SetCurrentNetworkViewTask.java │ │ │ ├── SetCurrentNetworkViewTaskFactory.java │ │ │ ├── UpdateNetworkViewTask.java │ │ │ └── UpdateNetworkViewTaskFactory.java │ │ │ ├── vizmap │ │ │ ├── ApplyVisualStyleTask.java │ │ │ ├── ApplyVisualStyleTaskFactoryimpl.java │ │ │ ├── ClearAllEdgeBendsFactory.java │ │ │ ├── ClearAllEdgeBendsTask.java │ │ │ ├── ExportVizmapTaskFactoryImpl.java │ │ │ ├── LoadVizmapFileTask.java │ │ │ ├── LoadVizmapFileTaskFactoryImpl.java │ │ │ └── VizmapWriter.java │ │ │ └── zoom │ │ │ ├── AbstractZoomTask.java │ │ │ ├── FitContentEdit.java │ │ │ ├── FitContentTask.java │ │ │ ├── FitContentTaskFactory.java │ │ │ ├── FitSelectedTask.java │ │ │ ├── FitSelectedTaskFactory.java │ │ │ ├── ZoomEdit.java │ │ │ ├── ZoomInTask.java │ │ │ ├── ZoomInTaskFactory.java │ │ │ ├── ZoomOutTask.java │ │ │ └── ZoomOutTaskFactory.java │ └── resources │ │ ├── images │ │ ├── icons │ │ │ ├── apply-layout-32.png │ │ │ ├── export-img-32.png │ │ │ ├── export-net-32.png │ │ │ ├── export-table-32.png │ │ │ ├── first-neighbors-32.png │ │ │ ├── help-32.png │ │ │ ├── hide-selected-32.png │ │ │ ├── import-net-32.png │ │ │ ├── import-net-url-32.png │ │ │ ├── import-table-32.png │ │ │ ├── import-table-url-32.png │ │ │ ├── new-from-selected-32.png │ │ │ ├── open-file-32.png │ │ │ ├── save-32.png │ │ │ ├── show-all-32.png │ │ │ ├── zoom-fit-32.png │ │ │ ├── zoom-in-32.png │ │ │ ├── zoom-out-32.png │ │ │ └── zoom-selected-32.png │ │ ├── logo.png │ │ └── tooltips │ │ │ ├── apply-preferred-layout.gif │ │ │ ├── first-neighbors.gif │ │ │ ├── fit-content.gif │ │ │ ├── fit-selected.gif │ │ │ ├── show-hide.gif │ │ │ ├── zoom-in.gif │ │ │ └── zoom-out.gif │ │ └── org │ │ └── cytoscape │ │ └── task │ │ └── internal │ │ └── create_filter_long_description.md │ └── test │ ├── java │ └── org │ │ └── cytoscape │ │ └── task │ │ └── internal │ │ ├── export │ │ ├── AbstractCyWriterTest.java │ │ ├── graphics │ │ │ └── ExportNetworkImageTaskFactoryTest.java │ │ └── network │ │ │ └── CyNetworkViewWriterTest.java │ │ ├── filter │ │ └── CreateFilterTaskTest.java │ │ ├── group │ │ └── AbstractGroupTaskTest.java │ │ ├── hide │ │ ├── HideSelectedEdgesTaskFactoryTest.java │ │ ├── HideSelectedNodesTaskFactoryTest.java │ │ ├── HideSelectedTaskFactoryTest.java │ │ ├── HideUtilsTest.java │ │ ├── UnHideAllEdgesTaskFactoryTest.java │ │ ├── UnHideAllNodesTaskFactoryTest.java │ │ └── UnHideAllTaskFactoryTest.java │ │ ├── io │ │ └── ViewWriterTest.java │ │ ├── loadnetwork │ │ ├── AbstractLoadNetworkTaskTester.java │ │ ├── LoadNetworkFileTaskFactoryTest.java │ │ ├── LoadNetworkFileTaskTest.java │ │ ├── LoadNetworkURLTaskFactoryTest.java │ │ └── LoadNetworkURLTaskTest.java │ │ ├── network │ │ ├── CloneNetworkTaskFactoryTest.java │ │ ├── CloneNetworkTaskTest.java │ │ ├── DestroyNetworkTaskTest.java │ │ ├── NewEmptyNetworkTaskTest.java │ │ ├── NewNetworkSelectedNodesEdgesTaskFactoryTest.java │ │ ├── NewNetworkSelectedNodesEdgesTaskTest.java │ │ ├── NewNetworkSelectedNodesOnlyTaskFactoryTest.java │ │ └── NewNetworkSelectedNodesOnlyTaskTest.java │ │ ├── proxysettings │ │ ├── ProxySettingTaskTest.java │ │ └── ProxySettingsTaskFactoryTest.java │ │ ├── select │ │ ├── AbstractSelectTaskTester.java │ │ ├── AllFactoryTest.java │ │ ├── DeselectAllEdgesTaskTest.java │ │ ├── DeselectAllNodesTaskTest.java │ │ ├── DeselectAllTaskTest.java │ │ ├── InvertSelectedEdgesTaskTest.java │ │ ├── InvertSelectedNodesTaskTest.java │ │ ├── SelectAdjacentEdgesTaskTest.java │ │ ├── SelectAllEdgesTaskTest.java │ │ ├── SelectAllNodesTaskTest.java │ │ ├── SelectAllTaskTest.java │ │ ├── SelectConnectedNodesTaskTest.java │ │ ├── SelectFirstNeighborsNodeViewTaskTest.java │ │ ├── SelectFirstNeighborsTaskTest.java │ │ └── SelectFromFileListTaskTest.java │ │ ├── session │ │ ├── NewSessionTaskFactoryTest.java │ │ ├── NewSessionTaskTest.java │ │ ├── OpenSessionTaskFactoryTest.java │ │ ├── OpenSessionTaskTest.java │ │ ├── SaveSessionAsTaskFactoryTest.java │ │ ├── SaveSessionAsTaskTest.java │ │ ├── SaveSessionTaskFactoryTest.java │ │ └── SaveSessionTaskTest.java │ │ ├── setcurren │ │ ├── SetCurrentNetworkTaskFactoryImplTest.java │ │ └── SetCurrentNetworkTaskTest.java │ │ ├── table │ │ ├── JoinTablesTaskTest.java │ │ ├── MapTableToNetworkTableTaskTest.java │ │ ├── MappingIntegrationTest.java │ │ ├── MergeDataTableTaskTest.java │ │ └── RenameColumnEditTest.java │ │ ├── title │ │ ├── EditNetworkTitleTaskFactoryTest.java │ │ ├── EditNetworkTitleTaskTest.java │ │ └── NetworkTitleEditTest.java │ │ ├── view │ │ ├── CreateNetworkViewTaskTest.java │ │ └── DestroyNetworkViewTaskTest.java │ │ ├── vizmap │ │ ├── ApplyVisualStyleTaskTest.java │ │ └── LoadVizmapFileTaskFactoryTest.java │ │ └── zoom │ │ ├── FitContentEditTest.java │ │ ├── FitContentTaskFactoryTest.java │ │ ├── FitContentTaskTest.java │ │ ├── FitSelectedTaskFactoryTest.java │ │ ├── FitSelectedTaskTest.java │ │ ├── ZoomEditTest.java │ │ ├── ZoomInTaskFactoryTest.java │ │ ├── ZoomInTaskTest.java │ │ ├── ZoomOutTaskFactoryTest.java │ │ └── ZoomOutTaskTest.java │ └── resources │ ├── BIOGRID-ORGANISM-3.1.74.mitab.zip │ ├── bad_names.txt │ ├── empty.txt │ ├── node_names.txt │ └── test_session1.cys ├── custom-graphics-internal ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── cytoscape │ │ └── cg │ │ ├── event │ │ ├── CustomGraphicsLibraryUpdatedEvent.java │ │ ├── CustomGraphicsLibraryUpdatedListener.java │ │ ├── CustomGraphicsReadyToBeLoadedEvent.java │ │ └── CustomGraphicsReadyToBeLoadedListener.java │ │ ├── internal │ │ ├── CyActivator.java │ │ ├── action │ │ │ └── CustomGraphicsManagerAction.java │ │ ├── charts │ │ │ ├── AbstractChart.java │ │ │ ├── AbstractChartEditor.java │ │ │ ├── AbstractChartFactory.java │ │ │ ├── AbstractChartLayer.java │ │ │ ├── ColorSchemeEditor.java │ │ │ ├── CustomCategoryItemLabelGenerator.java │ │ │ ├── CustomPieSectionLabelGenerator.java │ │ │ ├── LabelPosition.java │ │ │ ├── bar │ │ │ │ ├── BarChart.java │ │ │ │ ├── BarChartEditor.java │ │ │ │ ├── BarChartFactory.java │ │ │ │ ├── BarChartTypeJsonDeserializer.java │ │ │ │ └── BarLayer.java │ │ │ ├── box │ │ │ │ ├── BoxChart.java │ │ │ │ ├── BoxChartEditor.java │ │ │ │ ├── BoxChartFactory.java │ │ │ │ └── BoxLayer.java │ │ │ ├── heatmap │ │ │ │ ├── HeatMapChart.java │ │ │ │ ├── HeatMapChartEditor.java │ │ │ │ ├── HeatMapChartFactory.java │ │ │ │ └── HeatMapLayer.java │ │ │ ├── line │ │ │ │ ├── LineChart.java │ │ │ │ ├── LineChartEditor.java │ │ │ │ ├── LineChartFactory.java │ │ │ │ └── LineLayer.java │ │ │ ├── pie │ │ │ │ ├── PieChart.java │ │ │ │ ├── PieChartEditor.java │ │ │ │ ├── PieChartFactory.java │ │ │ │ └── PieLayer.java │ │ │ ├── ring │ │ │ │ ├── RingChart.java │ │ │ │ ├── RingChartEditor.java │ │ │ │ ├── RingChartFactory.java │ │ │ │ └── RingLayer.java │ │ │ └── util │ │ │ │ ├── ColorGradient.java │ │ │ │ └── ColorScale.java │ │ ├── editor │ │ │ ├── CustomGraphicsVisualPropertyEditor.java │ │ │ ├── CyCustomGraphicsCellRenderer.java │ │ │ ├── CyCustomGraphicsPropertyEditor.java │ │ │ └── CyCustomGraphicsValueEditor.java │ │ ├── gradient │ │ │ ├── AbstractGradient.java │ │ │ ├── AbstractGradientEditor.java │ │ │ ├── AbstractGradientLayer.java │ │ │ ├── linear │ │ │ │ ├── LinearGradient.java │ │ │ │ ├── LinearGradientEditor.java │ │ │ │ ├── LinearGradientFactory.java │ │ │ │ └── LinearGradientLayer.java │ │ │ └── radial │ │ │ │ ├── RadialGradient.java │ │ │ │ ├── RadialGradientEditor.java │ │ │ │ ├── RadialGradientFactory.java │ │ │ │ └── RadialGradientLayer.java │ │ ├── image │ │ │ ├── AbstractURLImageCustomGraphicsFactory.java │ │ │ ├── BitmapCustomGraphicsFactory.java │ │ │ ├── MissingBitmapCustomGraphics.java │ │ │ ├── MissingImageCustomGraphics.java │ │ │ ├── MissingSVGCustomGraphics.java │ │ │ └── SVGCustomGraphicsFactory.java │ │ ├── json │ │ │ ├── ColorJsonDeserializer.java │ │ │ ├── ColorJsonSerializer.java │ │ │ ├── ColorSchemeJsonDeserializer.java │ │ │ ├── ColorSchemeJsonSerializer.java │ │ │ ├── CyColumnIdentifierJsonDeserializer.java │ │ │ ├── CyColumnIdentifierJsonSerializer.java │ │ │ ├── Point2DJsonDeserializer.java │ │ │ ├── Point2DJsonSerializer.java │ │ │ ├── PropertiesJsonDeserializer.java │ │ │ ├── PropertiesJsonSerializer.java │ │ │ ├── Rectangle2DJsonDeserializer.java │ │ │ └── Rectangle2DJsonSerializer.java │ │ ├── model │ │ │ ├── CustomGraphics2ManagerImpl.java │ │ │ └── CustomGraphicsManagerImpl.java │ │ ├── paint │ │ │ ├── ColorPaintFactory.java │ │ │ ├── GradientPaintFactory.java │ │ │ ├── LinearGradientPaintFactory.java │ │ │ ├── RadialGradientPaintFactory.java │ │ │ └── TexturePaintFactory.java │ │ ├── task │ │ │ ├── RestoreImagesTask.java │ │ │ ├── SaveGraphicsToSessionTask.java │ │ │ ├── SaveGraphicsToSessionTaskFactory.java │ │ │ └── SaveUserImagesTask.java │ │ ├── ui │ │ │ ├── CustomGraphicsListModel.java │ │ │ └── CustomGraphicsManagerDialog.java │ │ ├── util │ │ │ ├── AnglePicker.java │ │ │ ├── ColorKeyword.java │ │ │ ├── ColorUtil.java │ │ │ ├── EqualDashStroke.java │ │ │ ├── GradientEditor.java │ │ │ ├── IconUtil.java │ │ │ ├── ImageUtil.java │ │ │ ├── MathUtil.java │ │ │ ├── PaintFactory.java │ │ │ ├── PointPicker.java │ │ │ ├── SortedListModel.java │ │ │ ├── TextIcon.java │ │ │ ├── ViewUtil.java │ │ │ ├── VisualPropertyIcon.java │ │ │ └── VisualPropertyIconFactory.java │ │ └── vector │ │ │ ├── CustomGraphicsProperty.java │ │ │ ├── GradientLayerCustomGraphics.java │ │ │ ├── GradientOvalFactory.java │ │ │ ├── GradientOvalLayer.java │ │ │ ├── GradientRoundRectangleFactory.java │ │ │ ├── GradientRoundRectangleLayer.java │ │ │ ├── PaintCustomGraphics.java │ │ │ └── VectorCustomGraphics.java │ │ ├── model │ │ ├── AbstractCustomGraphics2.java │ │ ├── AbstractDCustomGraphics.java │ │ ├── AbstractURLImageCustomGraphics.java │ │ ├── BitmapCustomGraphics.java │ │ ├── BitmapLayer.java │ │ ├── CGComparator.java │ │ ├── ColorScheme.java │ │ ├── CustomGraphics2Manager.java │ │ ├── CustomGraphicsManager.java │ │ ├── CustomGraphicsPropertyImpl.java │ │ ├── CustomGraphicsRange.java │ │ ├── CustomGraphicsTranslator.java │ │ ├── CustomGraphicsVisualProperty.java │ │ ├── DummyCustomGraphics.java │ │ ├── IDGenerator.java │ │ ├── NullCustomGraphics.java │ │ ├── Orientation.java │ │ ├── RenderingContext.java │ │ ├── Rotation.java │ │ ├── SVGCustomGraphics.java │ │ ├── SVGLayer.java │ │ └── Taggable.java │ │ └── util │ │ ├── CustomGraphicsIcon.java │ │ ├── CustomGraphicsUtil.java │ │ ├── ImageCustomGraphicsSelector.java │ │ ├── LoadImageDialog.java │ │ ├── SimpleToolBarToggleButton.java │ │ └── URLImportPanel.java │ └── resources │ └── images │ ├── charts │ ├── bar-chart.png │ ├── box-chart.png │ ├── heatmap-chart.png │ ├── line-chart.png │ ├── pie-chart.png │ └── ring-chart.png │ ├── drop-img-file-56.png │ ├── no_image.png │ └── no_image.svg ├── cycl-impl ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── cytoscape │ │ └── cycl │ │ └── internal │ │ ├── CyActivator.java │ │ ├── CyCL.java │ │ ├── CyCLBufferImpl.java │ │ ├── CyCLContextImpl.java │ │ ├── CyCLDeviceImpl.java │ │ ├── CyCLFactoryImpl.java │ │ ├── CyCLKernelImpl.java │ │ ├── CyCLLocalSizeImpl.java │ │ ├── CyCLPlatformImpl.java │ │ ├── CyCLProgramImpl.java │ │ ├── CyCLSettingsTask.java │ │ ├── CyCLSettingsTaskFactory.java │ │ └── CyCLUtils.java │ └── resources │ └── Benchmark.cl ├── datasource-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── io │ └── datasource │ └── internal │ ├── CyActivator.java │ ├── DataSourceManagerImpl.java │ └── bookmarks │ └── BookmarkDataSourceBuilder.java ├── ding-impl ├── ding-presentation-impl │ ├── pom.xml │ └── src │ │ ├── main │ │ ├── java │ │ │ └── org │ │ │ │ └── cytoscape │ │ │ │ ├── ding │ │ │ │ ├── CyActivator.java │ │ │ │ ├── CyObjectPositionPropertyEditor.java │ │ │ │ ├── DArrowShape.java │ │ │ │ ├── DNodeShape.java │ │ │ │ ├── DVisualLexicon.java │ │ │ │ ├── Label.java │ │ │ │ ├── ObjectPlacerControl.java │ │ │ │ ├── ObjectPlacerGraphic.java │ │ │ │ ├── ObjectPositionCellRenderer.java │ │ │ │ ├── ObjectPositionValueEditor.java │ │ │ │ ├── PrintLOD.java │ │ │ │ ├── SelectModeAction.java │ │ │ │ ├── ShowGraphicsDetailsTask.java │ │ │ │ ├── ShowGraphicsDetailsTaskFactory.java │ │ │ │ ├── action │ │ │ │ │ └── GraphicsDetailAction.java │ │ │ │ ├── debug │ │ │ │ │ ├── DebugFrameInfo.java │ │ │ │ │ ├── DebugFrameType.java │ │ │ │ │ ├── DebugProgressMonitor.java │ │ │ │ │ ├── DebugProgressMonitorCallback.java │ │ │ │ │ ├── DebugProgressMonitorFactory.java │ │ │ │ │ ├── DebugRootFrameInfo.java │ │ │ │ │ ├── DebugRootProgressMonitor.java │ │ │ │ │ ├── DebugSubProgressMonitor.java │ │ │ │ │ ├── DebugUtil.java │ │ │ │ │ ├── DingDebugMediator.java │ │ │ │ │ ├── DingDebugPanel.java │ │ │ │ │ ├── FrameListPanel.java │ │ │ │ │ ├── FrameListTablePanel.java │ │ │ │ │ ├── FrameRatePanel.java │ │ │ │ │ ├── NetworkInfoPanel.java │ │ │ │ │ ├── NetworkViewportPanel.java │ │ │ │ │ ├── SettingsPanel.java │ │ │ │ │ └── ThumbnailPanel.java │ │ │ │ ├── dependency │ │ │ │ │ ├── CustomGraphicsSizeDependencyFactory.java │ │ │ │ │ ├── EdgeColorDependencyFactory.java │ │ │ │ │ └── NodeSizeDependencyFactory.java │ │ │ │ ├── icon │ │ │ │ │ ├── ArrowIcon.java │ │ │ │ │ ├── ColorIcon.java │ │ │ │ │ ├── EdgeBendIcon.java │ │ │ │ │ ├── EdgeStackingIcon.java │ │ │ │ │ ├── FontFaceIcon.java │ │ │ │ │ ├── NodeIcon.java │ │ │ │ │ ├── ObjectPositionIcon.java │ │ │ │ │ ├── StrokeIcon.java │ │ │ │ │ ├── TextIcon.java │ │ │ │ │ ├── VisualPropertyIcon.java │ │ │ │ │ └── VisualPropertyIconFactory.java │ │ │ │ ├── impl │ │ │ │ │ ├── AddEdgeBeginTask.java │ │ │ │ │ ├── AddEdgeNodeViewTaskFactoryImpl.java │ │ │ │ │ ├── AddEdgeTask.java │ │ │ │ │ ├── BendFactoryImpl.java │ │ │ │ │ ├── BendImpl.java │ │ │ │ │ ├── BendStore.java │ │ │ │ │ ├── BirdsEyeView.java │ │ │ │ │ ├── BirdsEyeViewLOD.java │ │ │ │ │ ├── ContentChangeListener.java │ │ │ │ │ ├── DEdgeDetails.java │ │ │ │ │ ├── DLineType.java │ │ │ │ │ ├── DNodeDetails.java │ │ │ │ │ ├── DRenderingEngine.java │ │ │ │ │ ├── DingGraphLOD.java │ │ │ │ │ ├── DingGraphLODAll.java │ │ │ │ │ ├── DingLock.java │ │ │ │ │ ├── DingNavigationRenderingEngineFactory.java │ │ │ │ │ ├── DingNetworkViewFactory.java │ │ │ │ │ ├── DingRenderer.java │ │ │ │ │ ├── DingRenderingEngineFactory.java │ │ │ │ │ ├── DingThumbnailRenderingEngineFactory.java │ │ │ │ │ ├── DingVisualStyleRenderingEngineFactory.java │ │ │ │ │ ├── HandleFactoryImpl.java │ │ │ │ │ ├── HandleImpl.java │ │ │ │ │ ├── HandleInfo.java │ │ │ │ │ ├── InputHandlerGlassPane.java │ │ │ │ │ ├── LabelSelection.java │ │ │ │ │ ├── LabelSelectionManager.java │ │ │ │ │ ├── NVLTFActionSupport.java │ │ │ │ │ ├── NamedTaskFactory.java │ │ │ │ │ ├── NetworkPicker.java │ │ │ │ │ ├── PopupMenuHelper.java │ │ │ │ │ ├── StaticTaskFactoryProvisioner.java │ │ │ │ │ ├── ThumbnailChangeListener.java │ │ │ │ │ ├── ThumbnailView.java │ │ │ │ │ ├── TransformChangeListener.java │ │ │ │ │ ├── ViewTaskFactoryListener.java │ │ │ │ │ ├── canvas │ │ │ │ │ │ ├── AnnotationCanvas.java │ │ │ │ │ │ ├── AnnotationThumbnailCanvas.java │ │ │ │ │ │ ├── BirdsEyeViewRenderComponent.java │ │ │ │ │ │ ├── CompositeGraphicsCanvas.java │ │ │ │ │ │ ├── CompositeImageCanvas.java │ │ │ │ │ │ ├── DingCanvas.java │ │ │ │ │ │ ├── EdgeCanvas.java │ │ │ │ │ │ ├── EdgeThumbnailCanvas.java │ │ │ │ │ │ ├── GraphicsProvider.java │ │ │ │ │ │ ├── ImageFuture.java │ │ │ │ │ │ ├── ImageGraphicsProvider.java │ │ │ │ │ │ ├── MainRenderComponent.java │ │ │ │ │ │ ├── NetworkImageBuffer.java │ │ │ │ │ │ ├── NetworkImageFactoryImpl.java │ │ │ │ │ │ ├── NetworkTransform.java │ │ │ │ │ │ ├── NodeCanvas.java │ │ │ │ │ │ ├── NodeThumbnailCanvas.java │ │ │ │ │ │ ├── NullGraphicsProvider.java │ │ │ │ │ │ ├── RenderComponent.java │ │ │ │ │ │ ├── SelectionCanvas.java │ │ │ │ │ │ └── SimpleGraphicsProvider.java │ │ │ │ │ ├── cyannotator │ │ │ │ │ │ ├── AnnotationClipboard.java │ │ │ │ │ │ ├── AnnotationFactoryManager.java │ │ │ │ │ │ ├── AnnotationManagerImpl.java │ │ │ │ │ │ ├── AnnotationNode.java │ │ │ │ │ │ ├── AnnotationTree.java │ │ │ │ │ │ ├── CyAnnotator.java │ │ │ │ │ │ ├── IllegalAnnotationStructureException.java │ │ │ │ │ │ ├── annotations │ │ │ │ │ │ │ ├── AbstractAnnotation.java │ │ │ │ │ │ │ ├── AnchorLocation.java │ │ │ │ │ │ │ ├── AnnotationSelection.java │ │ │ │ │ │ │ ├── ArrowAnnotationImpl.java │ │ │ │ │ │ │ ├── BoundedTextAnnotationImpl.java │ │ │ │ │ │ │ ├── DingAnnotation.java │ │ │ │ │ │ │ ├── GraphicsUtilities.java │ │ │ │ │ │ │ ├── GroupAnnotationImpl.java │ │ │ │ │ │ │ ├── ImageAnnotationImpl.java │ │ │ │ │ │ │ ├── ShapeAnnotationImpl.java │ │ │ │ │ │ │ └── TextAnnotationImpl.java │ │ │ │ │ │ ├── create │ │ │ │ │ │ │ ├── AbstractDingAnnotationFactory.java │ │ │ │ │ │ │ ├── ArrowAnnotationFactory.java │ │ │ │ │ │ │ ├── BoundedTextAnnotationFactory.java │ │ │ │ │ │ │ ├── GroupAnnotationFactory.java │ │ │ │ │ │ │ ├── ImageAnnotationFactory.java │ │ │ │ │ │ │ ├── ShapeAnnotationFactory.java │ │ │ │ │ │ │ └── TextAnnotationFactory.java │ │ │ │ │ │ ├── dialogs │ │ │ │ │ │ │ ├── AbstractAnnotationDialog.java │ │ │ │ │ │ │ ├── AbstractAnnotationEditor.java │ │ │ │ │ │ │ ├── ArrowAnnotationEditor.java │ │ │ │ │ │ │ ├── BoundedTextAnnotationEditor.java │ │ │ │ │ │ │ ├── ImageAnnotationEditor.java │ │ │ │ │ │ │ ├── LoadImageDialog.java │ │ │ │ │ │ │ ├── ShapeAnnotationEditor.java │ │ │ │ │ │ │ └── TextAnnotationEditor.java │ │ │ │ │ │ ├── tasks │ │ │ │ │ │ │ ├── AbstractAnnotationTunables.java │ │ │ │ │ │ │ ├── AddAnnotationCommandTask.java │ │ │ │ │ │ │ ├── AddAnnotationTask.java │ │ │ │ │ │ │ ├── AddAnnotationTaskFactory.java │ │ │ │ │ │ │ ├── AnnotationJsonConverter.java │ │ │ │ │ │ │ ├── CopyAnnotationStyleTask.java │ │ │ │ │ │ │ ├── CopyAnnotationStyleTaskFactory.java │ │ │ │ │ │ │ ├── DuplicateAnnotationsTask.java │ │ │ │ │ │ │ ├── DuplicateAnnotationsTaskFactory.java │ │ │ │ │ │ │ ├── EditAnnotationTask.java │ │ │ │ │ │ │ ├── EditAnnotationTaskFactory.java │ │ │ │ │ │ │ ├── GroupAnnotationsTask.java │ │ │ │ │ │ │ ├── GroupAnnotationsTaskFactory.java │ │ │ │ │ │ │ ├── ImageAnnotationTunables.java │ │ │ │ │ │ │ ├── ListAnnotationsTask.java │ │ │ │ │ │ │ ├── ListAnnotationsTaskFactory.java │ │ │ │ │ │ │ ├── PasteAnnotationStyleTask.java │ │ │ │ │ │ │ ├── PasteAnnotationStyleTaskFactory.java │ │ │ │ │ │ │ ├── ReloadImagesTask.java │ │ │ │ │ │ │ ├── RemoveAnnotationCommandTask.java │ │ │ │ │ │ │ ├── RemoveAnnotationTask.java │ │ │ │ │ │ │ ├── RemoveAnnotationTaskFactory.java │ │ │ │ │ │ │ ├── RemoveSelectedAnnotationsTask.java │ │ │ │ │ │ │ ├── RemoveSelectedAnnotationsTaskFactory.java │ │ │ │ │ │ │ ├── ReorderAnnotationsTask.java │ │ │ │ │ │ │ ├── ReorderSelectedAnnotationsTaskFactory.java │ │ │ │ │ │ │ ├── ShapeAnnotationTunables.java │ │ │ │ │ │ │ ├── StandardAnnotationTunables.java │ │ │ │ │ │ │ ├── TextAnnotationTunables.java │ │ │ │ │ │ │ ├── UngroupAnnotationsTask.java │ │ │ │ │ │ │ ├── UngroupAnnotationsTaskFactory.java │ │ │ │ │ │ │ ├── UpdateAnnotationTask.java │ │ │ │ │ │ │ └── UpdateAnnotationTaskFactory.java │ │ │ │ │ │ ├── ui │ │ │ │ │ │ │ ├── AnnotationMainPanel.java │ │ │ │ │ │ │ └── AnnotationMediator.java │ │ │ │ │ │ └── utils │ │ │ │ │ │ │ ├── AnglePicker.java │ │ │ │ │ │ │ ├── DoubleInputVerifier.java │ │ │ │ │ │ │ ├── EnhancedSlider.java │ │ │ │ │ │ │ ├── GradientEditor.java │ │ │ │ │ │ │ ├── MultipleGradientEditor.java │ │ │ │ │ │ │ ├── PointPicker.java │ │ │ │ │ │ │ ├── ShapeIcon.java │ │ │ │ │ │ │ └── ViewUtils.java │ │ │ │ │ ├── editor │ │ │ │ │ │ ├── DiscreteValueList.java │ │ │ │ │ │ ├── EdgeBendCellRenderer.java │ │ │ │ │ │ ├── EdgeBendEditor.java │ │ │ │ │ │ ├── EdgeBendPropertyEditor.java │ │ │ │ │ │ ├── EdgeBendValueEditor.java │ │ │ │ │ │ ├── EdgeBendValueEditorDialog.java │ │ │ │ │ │ ├── ObjectPositionVisualPropertyEditor.java │ │ │ │ │ │ └── SimpleRootPaneContainer.java │ │ │ │ │ ├── strokes │ │ │ │ │ │ ├── AnimatedDashDotStroke.java │ │ │ │ │ │ ├── AnimatedEqualDashStroke.java │ │ │ │ │ │ ├── AnimatedLongDashStroke.java │ │ │ │ │ │ ├── AnimatedStroke.java │ │ │ │ │ │ ├── BackwardSlashStroke.java │ │ │ │ │ │ ├── ContiguousArrowStroke.java │ │ │ │ │ │ ├── DAnimatedStroke.java │ │ │ │ │ │ ├── DashDotStroke.java │ │ │ │ │ │ ├── DotStroke.java │ │ │ │ │ │ ├── EqualDashStroke.java │ │ │ │ │ │ ├── ForwardSlashStroke.java │ │ │ │ │ │ ├── LongDashStroke.java │ │ │ │ │ │ ├── ParallelStroke.java │ │ │ │ │ │ ├── PipeStroke.java │ │ │ │ │ │ ├── SeparateArrowStroke.java │ │ │ │ │ │ ├── ShapeStroke.java │ │ │ │ │ │ ├── SineWaveStroke.java │ │ │ │ │ │ ├── SolidStroke.java │ │ │ │ │ │ ├── VerticalSlashStroke.java │ │ │ │ │ │ ├── WidthStroke.java │ │ │ │ │ │ ├── ZeroStroke.java │ │ │ │ │ │ └── ZigzagStroke.java │ │ │ │ │ ├── undo │ │ │ │ │ │ ├── AddEdgeEdit.java │ │ │ │ │ │ ├── AnnotationEdit.java │ │ │ │ │ │ ├── CompositeCyEdit.java │ │ │ │ │ │ ├── LabelEdit.java │ │ │ │ │ │ ├── ViewChangeEdit.java │ │ │ │ │ │ └── ViewState.java │ │ │ │ │ └── work │ │ │ │ │ │ ├── ConsoleProgressMonitor.java │ │ │ │ │ │ ├── DiscreteProgressMonitor.java │ │ │ │ │ │ ├── NoOutputProgressMonitor.java │ │ │ │ │ │ ├── ProgressMonitor.java │ │ │ │ │ │ ├── ProgressMonitorCloseable.java │ │ │ │ │ │ └── SubProgressMonitor.java │ │ │ │ └── internal │ │ │ │ │ └── util │ │ │ │ │ ├── ColorKeyword.java │ │ │ │ │ ├── ColorUtil.java │ │ │ │ │ ├── CustomGraphicsPositionCalculator.java │ │ │ │ │ ├── IconUtil.java │ │ │ │ │ ├── ImageUtil.java │ │ │ │ │ ├── MathUtil.java │ │ │ │ │ ├── MurmurHash3.java │ │ │ │ │ ├── OrderedMouseAdapter.java │ │ │ │ │ ├── SVGIcon.java │ │ │ │ │ ├── SortedListModel.java │ │ │ │ │ └── ViewUtil.java │ │ │ │ ├── graph │ │ │ │ └── render │ │ │ │ │ ├── immed │ │ │ │ │ ├── EdgeAnchors.java │ │ │ │ │ ├── GraphGraphics.java │ │ │ │ │ ├── arrow │ │ │ │ │ │ ├── AbstractArrow.java │ │ │ │ │ │ ├── Arrow.java │ │ │ │ │ │ ├── ArrowheadArrow.java │ │ │ │ │ │ ├── ArrowheadArrowShort.java │ │ │ │ │ │ ├── CrossDeltaArrow.java │ │ │ │ │ │ ├── DeltaArrow.java │ │ │ │ │ │ ├── DeltaArrowShort1.java │ │ │ │ │ │ ├── DeltaArrowShort2.java │ │ │ │ │ │ ├── DiamondArrow.java │ │ │ │ │ │ ├── DiamondArrowShort1.java │ │ │ │ │ │ ├── DiamondArrowShort2.java │ │ │ │ │ │ ├── DiscArrow.java │ │ │ │ │ │ ├── HalfBottomArrow.java │ │ │ │ │ │ ├── HalfCircleArrow.java │ │ │ │ │ │ ├── HalfTopArrow.java │ │ │ │ │ │ ├── NoArrow.java │ │ │ │ │ │ ├── SquareArrow.java │ │ │ │ │ │ └── TeeArrow.java │ │ │ │ │ └── nodeshape │ │ │ │ │ │ ├── AbstractNodeShape.java │ │ │ │ │ │ ├── DiamondNodeShape.java │ │ │ │ │ │ ├── EllipseNodeShape.java │ │ │ │ │ │ ├── HexagonNodeShape.java │ │ │ │ │ │ ├── LegacyCustomNodeShape.java │ │ │ │ │ │ ├── NodeShape.java │ │ │ │ │ │ ├── OctagonNodeShape.java │ │ │ │ │ │ ├── ParallelogramNodeShape.java │ │ │ │ │ │ ├── RectangleNodeShape.java │ │ │ │ │ │ ├── RoundedRectangleNodeShape.java │ │ │ │ │ │ ├── TriangleNodeShape.java │ │ │ │ │ │ └── VeeNodeShape.java │ │ │ │ │ └── stateful │ │ │ │ │ ├── CustomGraphicsInfo.java │ │ │ │ │ ├── EdgeDetails.java │ │ │ │ │ ├── GraphLOD.java │ │ │ │ │ ├── GraphRenderer.java │ │ │ │ │ ├── LabelInfo.java │ │ │ │ │ ├── LabelInfoCache.java │ │ │ │ │ ├── LabelInfoProvider.java │ │ │ │ │ ├── LabelLineInfo.java │ │ │ │ │ ├── NodeDetails.java │ │ │ │ │ └── RenderDetailFlags.java │ │ │ │ └── util │ │ │ │ └── intr │ │ │ │ ├── ArrayIntEnumerator.java │ │ │ │ ├── ArrayIntIterator.java │ │ │ │ ├── IntArray.java │ │ │ │ ├── IntBTree.java │ │ │ │ ├── IntEnumerator.java │ │ │ │ ├── IntHash.java │ │ │ │ ├── IntIntHash.java │ │ │ │ ├── IntIterator.java │ │ │ │ ├── IntObjHash.java │ │ │ │ ├── IntQueue.java │ │ │ │ ├── IntStack.java │ │ │ │ ├── IntTHash.java │ │ │ │ ├── LongBTree.java │ │ │ │ ├── LongEnumerator.java │ │ │ │ ├── LongHash.java │ │ │ │ ├── LongLongHash.java │ │ │ │ ├── LongObjHash.java │ │ │ │ ├── LongStack.java │ │ │ │ ├── MinIntHeap.java │ │ │ │ └── MinLongHeap.java │ │ └── resources │ │ │ └── images │ │ │ ├── about_icons.txt │ │ │ ├── arrowIcon.png │ │ │ ├── boundedIcon.png │ │ │ ├── default_network.png │ │ │ ├── editor_icons_original.pdf │ │ │ ├── imageIcon.png │ │ │ ├── no_image.png │ │ │ ├── no_image.svg │ │ │ ├── recursive_network.png │ │ │ ├── shapeIcon.png │ │ │ ├── stock_dialog-warning-32.png │ │ │ └── textIcon.png │ │ └── test │ │ └── java │ │ └── org │ │ └── cytoscape │ │ ├── ding │ │ ├── EdgeBendTest.java │ │ ├── NetworkViewTestSupport.java │ │ ├── customgraphics │ │ │ ├── AbstractCustomGraphics2Test.java │ │ │ └── impl │ │ │ │ └── readme.txt │ │ ├── impl │ │ │ ├── DGraphViewApplyTest.java │ │ │ ├── cyannotator │ │ │ │ ├── AbstractAnnotationTest.java │ │ │ │ ├── AnnotationTreeTest.java │ │ │ │ └── AnnotatorStructureTest.java │ │ │ └── work │ │ │ │ └── ProgressMonitorTest.java │ │ └── internal │ │ │ ├── charts │ │ │ ├── BarChartTest.java │ │ │ ├── BoxChartTest.java │ │ │ ├── DummyCyColumnIdentifierFactory.java │ │ │ ├── HeatMapChartTest.java │ │ │ ├── LineChartTest.java │ │ │ ├── PieChartTest.java │ │ │ └── RingChartTest.java │ │ │ ├── gradients │ │ │ ├── LinearGradientTest.java │ │ │ └── RadialGradientTest.java │ │ │ └── util │ │ │ └── MathUtilTest.java │ │ ├── graph │ │ └── render │ │ │ ├── immed │ │ │ ├── GraphGraphicsTest.java │ │ │ └── OldGraphGraphics.java │ │ │ └── stateful │ │ │ ├── GraphRendererTest.java │ │ │ └── MeasuredLineCreatorTest.java │ │ ├── util │ │ └── intr │ │ │ ├── BitSetPerformance.java │ │ │ ├── IntBTreeConstructionTuner.java │ │ │ ├── IntBTreePerformance.java │ │ │ ├── IntBTreeQueryTuner.java │ │ │ ├── IntHashPerformance.java │ │ │ ├── MinIntHeapPerformance.java │ │ │ └── PrimesGenerator.java │ │ └── view │ │ ├── CytoscapeViewTest.java.asdf │ │ ├── DVisualLexiconTest.java │ │ └── impl │ │ └── FlagAndSelectionHandlerTest.java.asdf ├── performance-debug │ ├── pom.xml │ └── src │ │ └── main │ │ └── resources │ │ └── testData │ │ └── sif │ │ ├── A200-200.sif │ │ ├── A50-100.sif │ │ └── A50-50.sif └── pom.xml ├── edge-bundler-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── edge │ └── bundler │ └── internal │ ├── CyActivator.java │ ├── EdgeBundlerRunner.java │ ├── EdgeBundlerTask.java │ ├── EdgeBundlerTaskFactory.java │ └── EdgeCompatabilityRunner.java ├── editor-impl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── editor │ │ │ └── internal │ │ │ ├── AddNestedNetworkTask.java │ │ │ ├── AddNestedNetworkTaskFactory.java │ │ │ ├── AddNodeEdit.java │ │ │ ├── AddNodeTask.java │ │ │ ├── AddNodeTaskFactory.java │ │ │ ├── ClipboardImpl.java │ │ │ ├── ClipboardManagerImpl.java │ │ │ ├── CopyEdgeTaskFactory.java │ │ │ ├── CopyNodeTaskFactory.java │ │ │ ├── CopyTask.java │ │ │ ├── CopyTaskFactory.java │ │ │ ├── CutEdgeTaskFactory.java │ │ │ ├── CutNodeTaskFactory.java │ │ │ ├── CutTask.java │ │ │ ├── CutTaskFactory.java │ │ │ ├── CyActivator.java │ │ │ ├── DeleteNestedNetworkTask.java │ │ │ ├── DeleteNestedNetworkTaskFactory.java │ │ │ ├── GoToNestedNetworkTask.java │ │ │ ├── GoToNestedNetworkTaskFactory.java │ │ │ ├── PasteEdit.java │ │ │ ├── PasteTask.java │ │ │ ├── PasteTaskFactory.java │ │ │ ├── RenameNodeEdit.java │ │ │ ├── RenameNodeTask.java │ │ │ ├── RenameNodeTaskFactory.java │ │ │ ├── SIFInterpreterEdgeEdit.java │ │ │ ├── SIFInterpreterNodeEdit.java │ │ │ ├── SIFInterpreterTask.java │ │ │ └── SIFInterpreterTaskFactory.java │ └── resources │ │ └── images │ │ ├── edge.png │ │ ├── network.png │ │ └── node.png │ └── test │ └── java │ └── org │ └── cytoscape │ └── editor │ └── internal │ └── ClipboardImplTest.java ├── equations-functions-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── equations │ │ └── internal │ │ ├── CyActivator.java │ │ └── functions │ │ ├── Degree.java │ │ ├── GetTableCell.java │ │ ├── InDegree.java │ │ ├── IsDirected.java │ │ ├── OutDegree.java │ │ ├── SourceID.java │ │ ├── SuidSearchUtil.java │ │ └── TargetID.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── equations │ └── internal │ └── functions │ ├── DegreeTest.java │ ├── InDegreeTest.java │ ├── OutDegreeTest.java │ ├── SourceIDTest.java │ └── TargetIDTest.java ├── equations-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── equations │ │ └── internal │ │ ├── BooleanList.java │ │ ├── Categories.java │ │ ├── CyActivator.java │ │ ├── DoubleList.java │ │ ├── EquationCompilerImpl.java │ │ ├── EquationParserImpl.java │ │ ├── EquationTokeniserImpl.java │ │ ├── LongList.java │ │ ├── ParseException.java │ │ ├── StringList.java │ │ ├── Token.java │ │ ├── Tokeniser.java │ │ ├── builtins │ │ ├── ACos.java │ │ ├── ASin.java │ │ ├── ATan2.java │ │ ├── Abs.java │ │ ├── And.java │ │ ├── Average.java │ │ ├── BList.java │ │ ├── Combin.java │ │ ├── Concatenate.java │ │ ├── Cos.java │ │ ├── Cosh.java │ │ ├── Count.java │ │ ├── Degrees.java │ │ ├── Error.java │ │ ├── Exp.java │ │ ├── FList.java │ │ ├── First.java │ │ ├── GeoMean.java │ │ ├── HarMean.java │ │ ├── IList.java │ │ ├── If.java │ │ ├── Largest.java │ │ ├── Last.java │ │ ├── Left.java │ │ ├── Len.java │ │ ├── ListToString.java │ │ ├── Ln.java │ │ ├── Log.java │ │ ├── Lower.java │ │ ├── Max.java │ │ ├── Median.java │ │ ├── Mid.java │ │ ├── Min.java │ │ ├── Mod.java │ │ ├── Mode.java │ │ ├── NormDist.java │ │ ├── Not.java │ │ ├── Now.java │ │ ├── Nth.java │ │ ├── Or.java │ │ ├── Permut.java │ │ ├── Pi.java │ │ ├── Product.java │ │ ├── Radians.java │ │ ├── Right.java │ │ ├── Round.java │ │ ├── SList.java │ │ ├── Sign.java │ │ ├── Sin.java │ │ ├── Sinh.java │ │ ├── Split.java │ │ ├── Sqrt.java │ │ ├── StDev.java │ │ ├── Substitute.java │ │ ├── Sum.java │ │ ├── Tan.java │ │ ├── Tanh.java │ │ ├── Text.java │ │ ├── Today.java │ │ ├── Trunc.java │ │ ├── Upper.java │ │ ├── Value.java │ │ └── Var.java │ │ ├── interpreter │ │ ├── Instruction.java │ │ └── InterpreterImpl.java │ │ └── parse_tree │ │ ├── BinOpNode.java │ │ ├── BooleanConstantNode.java │ │ ├── FConvNode.java │ │ ├── FloatConstantNode.java │ │ ├── FuncCallNode.java │ │ ├── IdentNode.java │ │ ├── SConvNode.java │ │ ├── StringConstantNode.java │ │ └── UnaryOpNode.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── equations │ └── internal │ ├── AttribParserTest.java │ ├── BooleanListTest.java │ ├── DoubleListTest.java │ ├── EquationTokenizerTest.java │ ├── EquationUpgradeTest.java │ ├── EquationUtilTest.java │ ├── LongListTest.java │ ├── StringListTest.java │ ├── TokeniserTest.java │ ├── builtins │ ├── ACosTest.java │ ├── ASinTest.java │ ├── ATan2Test.java │ ├── AbsTest.java │ ├── AndTest.java │ ├── AverageTest.java │ ├── BListTest.java │ ├── CombinTest.java │ ├── ConcatenateTest.java │ ├── CosTest.java │ ├── CoshTest.java │ ├── CountTest.java │ ├── ErrorTest.java │ ├── ExpTest.java │ ├── FListTest.java │ ├── FirstTest.java │ ├── Framework.java │ ├── GeoMeanTest.java │ ├── HarMeanTest.java │ ├── IListTest.java │ ├── IfTest.java │ ├── LargestTest.java │ ├── LastTest.java │ ├── LeftTest.java │ ├── LenTest.java │ ├── ListToStringTest.java │ ├── LnTest.java │ ├── LowerTest.java │ ├── MaxTest.java │ ├── MedianTest.java │ ├── MidTest.java │ ├── MinTest.java │ ├── ModTest.java │ ├── ModeTest.java │ ├── NormDistTest.java │ ├── NotTest.java │ ├── NowTest.java │ ├── NthTest.java │ ├── OrTest.java │ ├── PermutTest.java │ ├── ProductTest.java │ ├── RadiansTest.java │ ├── RightTest.java │ ├── RoundTest.java │ ├── SListTest.java │ ├── SignTest.java │ ├── SinTest.java │ ├── SinhTest.java │ ├── SqrtTest.java │ ├── StDevTest.java │ ├── SubstituteTest.java │ ├── SumTest.java │ ├── TanTest.java │ ├── TanhTest.java │ ├── TextTest.java │ ├── TodayTest.java │ ├── TruncTest.java │ ├── UpperTest.java │ ├── ValueTest.java │ └── VarTest.java │ └── interpreter │ └── InterpreterTest.java ├── event-impl ├── impl │ ├── pom.xml │ └── src │ │ ├── main │ │ ├── java │ │ │ └── org │ │ │ │ └── cytoscape │ │ │ │ └── event │ │ │ │ └── internal │ │ │ │ ├── CyActivator.java │ │ │ │ ├── CyEventHelperImpl.java │ │ │ │ ├── CyListenerAdapter.java │ │ │ │ ├── PayloadAccumulator.java │ │ │ │ └── ServiceComparator.java │ │ └── resources │ │ │ └── readme.txt │ │ └── test │ │ └── java │ │ └── org │ │ └── cytoscape │ │ └── event │ │ └── internal │ │ └── CyEventHelperTest.java ├── it │ ├── pom.xml │ └── src │ │ └── test │ │ └── java │ │ └── org │ │ └── cytoscape │ │ └── event │ │ └── ServiceConfigurationTest.java └── pom.xml ├── filter-impl ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── cytoscape │ │ └── filter │ │ └── internal │ │ ├── CyActivator.java │ │ ├── filters │ │ ├── FilterApp.java │ │ ├── FilterMenuItemAction.java │ │ ├── event │ │ │ ├── FiltersChangedEvent.java │ │ │ └── FiltersChangedListener.java │ │ ├── model │ │ │ ├── AdvancedSetting.java │ │ │ ├── AtomicFilter.java │ │ │ ├── CompositeFilter.java │ │ │ ├── CyFilter.java │ │ │ ├── EdgeInteractionFilter.java │ │ │ ├── FilterModelLocator.java │ │ │ ├── InteractionFilter.java │ │ │ ├── NodeInteractionFilter.java │ │ │ ├── NumericFilter.java │ │ │ ├── Relation.java │ │ │ ├── StringFilter.java │ │ │ └── TopologyFilter.java │ │ ├── util │ │ │ ├── ApplyFilterThread.java │ │ │ ├── FilterUtil.java │ │ │ ├── SelectUtil.java │ │ │ ├── ServicesUtil.java │ │ │ ├── VisualPropertyUtil.java │ │ │ ├── WidestStringComboBoxModel.java │ │ │ ├── WidestStringComboBoxPopupMenuListener.java │ │ │ └── WidestStringProvider.java │ │ └── view │ │ │ ├── EditNameDialog.java │ │ │ ├── EditRangeDialog.java │ │ │ ├── FilterIndexingTask.java │ │ │ ├── FilterIndexingTaskFactory.java │ │ │ ├── FilterMainPanel.java │ │ │ ├── FilterSettingPanel.java │ │ │ ├── InteractionFilterPanel.java │ │ │ ├── PassFilterWidestStringComboBoxModel.java │ │ │ └── TopoFilterPanel.java │ │ ├── gui │ │ └── FilterCytoPanelComponent.java │ │ ├── prefuse │ │ ├── data │ │ │ └── query │ │ │ │ └── NumberRangeModel.java │ │ └── util │ │ │ ├── TypeLib.java │ │ │ └── ui │ │ │ ├── JRangeSlider.java │ │ │ └── ValuedRangeModel.java │ │ ├── quickfind │ │ ├── app │ │ │ ├── QuickFindApp.java │ │ │ └── package.html │ │ ├── util │ │ │ ├── CyAttributesUtil.java │ │ │ ├── IndexType.java │ │ │ ├── QuickFind.java │ │ │ ├── QuickFindImpl.java │ │ │ ├── QuickFindListener.java │ │ │ ├── TaskMonitorBase.java │ │ │ └── package.html │ │ └── view │ │ │ ├── QuickFindConfigDialog.java │ │ │ └── package.html │ │ ├── read │ │ └── filter │ │ │ └── FilterReader.java │ │ ├── widgets │ │ ├── autocomplete │ │ │ ├── index │ │ │ │ ├── GenericIndex.java │ │ │ │ ├── GenericIndexImpl.java │ │ │ │ ├── Hit.java │ │ │ │ ├── IndexFactory.java │ │ │ │ ├── IndexListener.java │ │ │ │ ├── NumberIndex.java │ │ │ │ ├── NumberIndexImpl.java │ │ │ │ ├── TextIndex.java │ │ │ │ ├── TextIndexImpl.java │ │ │ │ ├── Trie.java │ │ │ │ └── package.html │ │ │ └── view │ │ │ │ ├── AutoCompleteDocument.java │ │ │ │ ├── ComboBoxFactory.java │ │ │ │ ├── TextBoxRenderer.java │ │ │ │ ├── TextIndexComboBox.java │ │ │ │ └── package.html │ │ └── slider │ │ │ ├── JRangeSliderExtended.java │ │ │ └── package.html │ │ └── write │ │ └── filter │ │ └── FilterWriter.java │ └── resources │ ├── default_filters.props │ └── images │ ├── add.png │ ├── config.png │ ├── delete.png │ ├── duplicate.png │ ├── filter-small.png │ ├── filter.png │ ├── minus.gif │ ├── plus.gif │ ├── properties.png │ └── rename.png ├── filter2-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── filter │ │ └── internal │ │ ├── AbstractMemoizableTransformer.java │ │ ├── ApplyCheck.java │ │ ├── CyActivator.java │ │ ├── CyNetworkSource.java │ │ ├── FilterCytoPanelComponent.java │ │ ├── FilterIO.java │ │ ├── FilterSettingsManager.java │ │ ├── MemoizableTransformer.java │ │ ├── ModelMonitor.java │ │ ├── ModelUtil.java │ │ ├── filters │ │ ├── column │ │ │ ├── ColumnChooser.java │ │ │ ├── ColumnElement.java │ │ │ ├── ColumnFilter.java │ │ │ ├── ColumnFilterController.java │ │ │ ├── ColumnFilterFactory.java │ │ │ ├── ColumnFilterView.java │ │ │ └── ColumnFilterViewFactory.java │ │ ├── composite │ │ │ ├── CompositeFilterController.java │ │ │ ├── CompositeFilterFactory.java │ │ │ ├── CompositeFilterImpl.java │ │ │ ├── CompositeFilterPanel.java │ │ │ ├── CompositeSeparator.java │ │ │ └── CompositeTransformerPanel.java │ │ ├── degree │ │ │ ├── DegreeFilter.java │ │ │ ├── DegreeFilterController.java │ │ │ ├── DegreeFilterFactory.java │ │ │ ├── DegreeFilterView.java │ │ │ ├── DegreeFilterViewFactory.java │ │ │ └── DegreeRange.java │ │ └── topology │ │ │ ├── TopologyFilter.java │ │ │ ├── TopologyFilterController.java │ │ │ ├── TopologyFilterFactory.java │ │ │ ├── TopologyFilterView.java │ │ │ └── TopologyFilterViewFactory.java │ │ ├── predicates │ │ ├── NumericPredicateDelegate.java │ │ ├── PredicateDelegate.java │ │ ├── PredicateDelegates.java │ │ └── StringPredicateDelegate.java │ │ ├── range │ │ ├── DoubleSliderModel.java │ │ ├── IntegerSliderModel.java │ │ ├── JRangeSlider.java │ │ ├── RangeChooser.java │ │ ├── RangeChooserController.java │ │ ├── RangeListener.java │ │ └── SliderModel.java │ │ ├── tasks │ │ ├── ExportNamedTransformersTask.java │ │ ├── ExportNamedTransformersTaskFactory.java │ │ ├── ImportNamedTransformersTask.java │ │ └── ImportNamedTransformersTaskFactory.java │ │ ├── transformers │ │ ├── adjacency │ │ │ ├── AdjacencyTransformer.java │ │ │ ├── AdjacencyTransformerFactory.java │ │ │ └── AdjacencyTransformerViewFactory.java │ │ └── interaction │ │ │ ├── InteractionTransformer.java │ │ │ ├── InteractionTransformerFactory.java │ │ │ └── InteractionTransformerViewFactory.java │ │ ├── view │ │ ├── AbstractComboBoxModel.java │ │ ├── AbstractPanel.java │ │ ├── AbstractPanelController.java │ │ ├── BooleanComboBox.java │ │ ├── ComboItem.java │ │ ├── CompositeFilterLayoutUpdator.java │ │ ├── CompositePanelComponent.java │ │ ├── DocumentListenerAdapter.java │ │ ├── DragHandler.java │ │ ├── DynamicComboBoxModel.java │ │ ├── FilterElement.java │ │ ├── FilterPanel.java │ │ ├── FilterPanelController.java │ │ ├── Handle.java │ │ ├── Matcher.java │ │ ├── NamedElement.java │ │ ├── NamedElementListener.java │ │ ├── PathDataFlavor.java │ │ ├── SelectPanel.java │ │ ├── SelectPanelComponent.java │ │ ├── TransformerElement.java │ │ ├── TransformerElementViewModel.java │ │ ├── TransformerPanel.java │ │ ├── TransformerPanelController.java │ │ ├── TransformerViewManager.java │ │ ├── ViewUtil.java │ │ └── look │ │ │ ├── FilterPanelStyle.java │ │ │ ├── FlatStyle.java │ │ │ └── StandardStyle.java │ │ └── work │ │ ├── AbstractWorker.java │ │ ├── DefaultBuffer.java │ │ ├── DiscreteProgressMonitor.java │ │ ├── FilterWorker.java │ │ ├── LazyWorkQueue.java │ │ ├── LazyWorker.java │ │ ├── ProgressMonitor.java │ │ ├── SubProgressMonitor.java │ │ ├── TransformerBuffer.java │ │ ├── TransformerExecutionStrategy.java │ │ ├── TransformerManagerImpl.java │ │ ├── TransformerWorker.java │ │ ├── ValidationManager.java │ │ └── ValidationViewListener.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── filter │ └── internal │ ├── ColumnFilterTest.java │ ├── CompositeFilterTest.java │ ├── DegreeFilterTest.java │ ├── PerformanceMonitorTest.java │ ├── PerformanceScaffold.java │ ├── TopologyFilterTest.java │ └── UiScaffold.java ├── graphml-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── io │ │ └── internal │ │ ├── CyActivator.java │ │ ├── read │ │ └── graphml │ │ │ ├── GraphMLFileFilter.java │ │ │ ├── GraphMLParser.java │ │ │ ├── GraphMLReader.java │ │ │ ├── GraphMLReaderFactory.java │ │ │ └── GraphMLToken.java │ │ └── write │ │ └── graphml │ │ ├── GraphMLAttributeDataTypes.java │ │ ├── GraphMLNetworkWriterFactory.java │ │ └── GraphMLWriter.java │ └── test │ ├── java │ └── org │ │ └── cytoscape │ │ └── data │ │ ├── reader │ │ └── graphml │ │ │ └── GraphMLReaderTest.java │ │ └── writer │ │ └── graphml │ │ └── GraphMLWriterTest.java │ └── resources │ ├── atted.graphml │ ├── desc.graphml │ ├── exptest.graphml │ ├── igraph_sample.graphml │ ├── nested.xml │ ├── nested2.xml │ ├── simple.graphml │ ├── simpleWithAttributes.xml │ ├── testGraph1.xml │ └── yFilesSample.xml ├── group-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── group │ │ └── internal │ │ ├── CyActivator.java │ │ ├── CyGroupFactoryImpl.java │ │ ├── CyGroupImpl.java │ │ ├── CyGroupManagerImpl.java │ │ ├── GroupIO.java │ │ ├── GroupUtil.java │ │ ├── LockedVisualPropertiesManager.java │ │ ├── ModelUtils.java │ │ ├── data │ │ ├── CyGroupAggregationManagerImpl.java │ │ ├── CyGroupAggregationSettings.java │ │ ├── CyGroupNodeSettingsTaskFactory.java │ │ ├── CyGroupSettingsImpl.java │ │ ├── CyGroupSettingsTask.java │ │ ├── CyGroupSettingsTaskFactory.java │ │ ├── CyGroupViewSettings.java │ │ ├── GroupDataCollapseHandler.java │ │ ├── GroupViewTypeChangedEvent.java │ │ ├── GroupViewTypeChangedListener.java │ │ └── aggregators │ │ │ ├── AbstractAggregator.java │ │ │ ├── BooleanAggregator.java │ │ │ ├── DoubleAggregator.java │ │ │ ├── DoubleListAggregator.java │ │ │ ├── IntegerAggregator.java │ │ │ ├── IntegerListAggregator.java │ │ │ ├── ListAggregator.java │ │ │ ├── LongAggregator.java │ │ │ ├── LongListAggregator.java │ │ │ ├── NoneAggregator.java │ │ │ ├── StringAggregator.java │ │ │ └── StringListAggregator.java │ │ └── view │ │ ├── GroupViewCollapseHandler.java │ │ ├── GroupViewDoubleClickListener.java │ │ ├── NodeChangeListener.java │ │ └── ViewUtils.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── group │ ├── CyGroupTest.java │ ├── GroupTestSupport.java │ └── TestCyGroupFactory.java ├── gui-cmdline-parser-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── cmdline │ └── gui │ └── internal │ ├── CyActivator.java │ ├── Parser.java │ ├── SessionLoadHandler.java │ └── StartupConfig.java ├── headless-application-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── internal │ ├── CyActivator.java │ └── NetworkAddedSetCurrent.java ├── headless-cmdline-parser-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── cmdline │ └── headless │ └── internal │ ├── CyActivator.java │ ├── Parser.java │ └── StartupConfig.java ├── hotfix_create.sh ├── io-impl ├── impl │ ├── pom.xml │ └── src │ │ ├── main │ │ ├── java │ │ │ └── org │ │ │ │ └── cytoscape │ │ │ │ └── io │ │ │ │ └── internal │ │ │ │ ├── CyActivator.java │ │ │ │ ├── read │ │ │ │ ├── AbstractNetworkReaderFactory.java │ │ │ │ ├── AbstractPropertyReader.java │ │ │ │ ├── AbstractTableReader.java │ │ │ │ ├── AbstractTableReaderFactory.java │ │ │ │ ├── AbstractVizmapReader.java │ │ │ │ ├── CopyInputStream.java │ │ │ │ ├── CyNetworkReaderManagerImpl.java │ │ │ │ ├── CyPropertyReaderManagerImpl.java │ │ │ │ ├── CySessionReaderManagerImpl.java │ │ │ │ ├── CyTableReaderManagerImpl.java │ │ │ │ ├── GenericReaderManager.java │ │ │ │ ├── MarkSupportedInputStream.java │ │ │ │ ├── VizmapReaderManagerImpl.java │ │ │ │ ├── ZipInputStreamWrapper.java │ │ │ │ ├── bookmarks │ │ │ │ │ ├── BookmarkFileFilter.java │ │ │ │ │ ├── BookmarkReader.java │ │ │ │ │ └── BookmarkReaderFactory.java │ │ │ │ ├── cysession │ │ │ │ │ ├── CysessionFileFilter.java │ │ │ │ │ ├── CysessionReader.java │ │ │ │ │ └── CysessionReaderFactory.java │ │ │ │ ├── datatable │ │ │ │ │ ├── CSVCyReader.java │ │ │ │ │ ├── CSVCyReaderFactory.java │ │ │ │ │ ├── ColumnInfo.java │ │ │ │ │ ├── CyAttributesReader.java │ │ │ │ │ ├── CyAttributesReaderFactory.java │ │ │ │ │ ├── CyTablesXMLReader.java │ │ │ │ │ ├── SessionTableFileFilter.java │ │ │ │ │ └── TableInfo.java │ │ │ │ ├── expression │ │ │ │ │ ├── ExpressionReader.java │ │ │ │ │ ├── ExpressionReaderFactory.java │ │ │ │ │ └── mRNAMeasurement.java │ │ │ │ ├── gml │ │ │ │ │ ├── GMLFileFilter.java │ │ │ │ │ ├── GMLNetworkReader.java │ │ │ │ │ ├── GMLNetworkReaderFactory.java │ │ │ │ │ ├── GMLParser.java │ │ │ │ │ └── KeyValue.java │ │ │ │ ├── properties │ │ │ │ │ ├── PropertiesFileFilter.java │ │ │ │ │ ├── PropertiesReader.java │ │ │ │ │ └── PropertiesReaderFactory.java │ │ │ │ ├── session │ │ │ │ │ ├── AbstractSessionReader.java │ │ │ │ │ ├── Cy2SessionReaderFactoryImpl.java │ │ │ │ │ ├── Cy2SessionReaderImpl.java │ │ │ │ │ ├── Cy3SessionReaderFactoryImpl.java │ │ │ │ │ ├── Cy3SessionReaderImpl.java │ │ │ │ │ ├── CyTableMetadataImpl.java │ │ │ │ │ └── SessionFileFilter.java │ │ │ │ ├── sif │ │ │ │ │ ├── Interaction.java │ │ │ │ │ ├── SIFNetworkReader.java │ │ │ │ │ └── SIFNetworkReaderFactory.java │ │ │ │ ├── transformer │ │ │ │ │ └── CyTransformerReaderImpl.java │ │ │ │ ├── vizmap │ │ │ │ │ ├── VizmapPropertiesFileFilter.java │ │ │ │ │ ├── VizmapPropertiesReader.java │ │ │ │ │ ├── VizmapPropertiesReaderFactory.java │ │ │ │ │ ├── VizmapXMLFileFilter.java │ │ │ │ │ ├── VizmapXMLReader.java │ │ │ │ │ └── VizmapXMLReaderFactory.java │ │ │ │ └── xgmml │ │ │ │ │ ├── GenericXGMMLFileFilter.java │ │ │ │ │ ├── GenericXGMMLReader.java │ │ │ │ │ ├── GenericXGMMLReaderFactory.java │ │ │ │ │ ├── Handler.java │ │ │ │ │ ├── HandlerFactory.java │ │ │ │ │ ├── MetadataEntries.java │ │ │ │ │ ├── MetadataParser.java │ │ │ │ │ ├── ObjectTypeMap.java │ │ │ │ │ ├── ParseState.java │ │ │ │ │ ├── RDFTags.java │ │ │ │ │ ├── SAXState.java │ │ │ │ │ ├── SessionXGMMLFileFilter.java │ │ │ │ │ ├── SessionXGMMLNetworkFileFilter.java │ │ │ │ │ ├── SessionXGMMLNetworkReader.java │ │ │ │ │ ├── SessionXGMMLNetworkReaderFactory.java │ │ │ │ │ ├── SessionXGMMLNetworkViewFileFilter.java │ │ │ │ │ ├── SessionXGMMLNetworkViewReader.java │ │ │ │ │ ├── SessionXGMMLNetworkViewReaderFactory.java │ │ │ │ │ ├── XGMMLParser.java │ │ │ │ │ └── handler │ │ │ │ │ ├── AbstractHandler.java │ │ │ │ │ ├── AttributeValueUtil.java │ │ │ │ │ ├── HandleEdge.java │ │ │ │ │ ├── HandleEdgeAttribute.java │ │ │ │ │ ├── HandleEdgeGraphics.java │ │ │ │ │ ├── HandleEdgeHandle.java │ │ │ │ │ ├── HandleEdgeHandleDone.java │ │ │ │ │ ├── HandleEdgeHandleList.java │ │ │ │ │ ├── HandleGraph.java │ │ │ │ │ ├── HandleGraphAttribute.java │ │ │ │ │ ├── HandleGraphDone.java │ │ │ │ │ ├── HandleGraphGraphics.java │ │ │ │ │ ├── HandleListAttribute.java │ │ │ │ │ ├── HandleListAttributeDone.java │ │ │ │ │ ├── HandleNode.java │ │ │ │ │ ├── HandleNodeAttribute.java │ │ │ │ │ ├── HandleNodeGraph.java │ │ │ │ │ ├── HandleNodeGraphDone.java │ │ │ │ │ ├── HandleNodeGraphics.java │ │ │ │ │ ├── HandleRDF.java │ │ │ │ │ ├── HandleRDFDate.java │ │ │ │ │ ├── HandleRDFDescription.java │ │ │ │ │ ├── HandleRDFFormat.java │ │ │ │ │ ├── HandleRDFIdentifier.java │ │ │ │ │ ├── HandleRDFSource.java │ │ │ │ │ ├── HandleRDFTitle.java │ │ │ │ │ ├── HandleRDFType.java │ │ │ │ │ ├── HandleViewEdge.java │ │ │ │ │ ├── HandleViewEdgeGraphics.java │ │ │ │ │ ├── HandleViewGraph.java │ │ │ │ │ ├── HandleViewGraphGraphics.java │ │ │ │ │ ├── HandleViewLockedVisualPropAttribute.java │ │ │ │ │ ├── HandleViewNode.java │ │ │ │ │ ├── HandleViewNodeGraphics.java │ │ │ │ │ ├── ReadDataManager.java │ │ │ │ │ └── XGMMLParseUtil.java │ │ │ │ ├── ui │ │ │ │ └── ExportBitmapOptionsPanel.java │ │ │ │ ├── util │ │ │ │ ├── FilterIO.java │ │ │ │ ├── GroupUtil.java │ │ │ │ ├── ReadCache.java │ │ │ │ ├── ReadUtils.java │ │ │ │ ├── RecentlyOpenedTrackerImpl.java │ │ │ │ ├── SUIDUpdater.java │ │ │ │ ├── StreamUtilImpl.java │ │ │ │ ├── UnrecognizedVisualPropertyManager.java │ │ │ │ ├── session │ │ │ │ │ └── SessionUtil.java │ │ │ │ ├── vizmap │ │ │ │ │ ├── CalculatorConverter.java │ │ │ │ │ ├── CalculatorConverterFactory.java │ │ │ │ │ ├── ColStyleIdMap.java │ │ │ │ │ └── VisualStyleSerializer.java │ │ │ │ └── xgmml │ │ │ │ │ └── ObjectType.java │ │ │ │ └── write │ │ │ │ ├── AbstractCyWriterFactory.java │ │ │ │ ├── AbstractWriterManager.java │ │ │ │ ├── CyNetworkViewWriterManagerImpl.java │ │ │ │ ├── CyTableWriterManagerImpl.java │ │ │ │ ├── PresentationWriterManagerImpl.java │ │ │ │ ├── PropertyWriterManagerImpl.java │ │ │ │ ├── SessionWriterManagerImpl.java │ │ │ │ ├── VizmapWriterManagerImpl.java │ │ │ │ ├── bookmarks │ │ │ │ ├── BookmarksWriterFactoryImpl.java │ │ │ │ └── BookmarksWriterImpl.java │ │ │ │ ├── cysession │ │ │ │ ├── CysessionWriterFactoryImpl.java │ │ │ │ └── CysessionWriterImpl.java │ │ │ │ ├── datatable │ │ │ │ ├── CyTablesXMLWriter.java │ │ │ │ └── csv │ │ │ │ │ ├── CSVCyWriter.java │ │ │ │ │ └── CSVTableWriterFactory.java │ │ │ │ ├── gml │ │ │ │ └── GMLWriter.javax │ │ │ │ ├── graphics │ │ │ │ ├── BitmapWriter.java │ │ │ │ ├── BitmapWriterFactory.java │ │ │ │ ├── PDFWriter.java │ │ │ │ ├── PDFWriterFactory.java │ │ │ │ ├── PNGWriter.java │ │ │ │ ├── PSWriter.java │ │ │ │ ├── PSWriterFactory.java │ │ │ │ ├── SVGWriter.java │ │ │ │ ├── SVGWriterFactory.java │ │ │ │ └── command │ │ │ │ │ ├── AbstractExportNetworkImageTask.java │ │ │ │ │ ├── ExportNetworkJPGTask.java │ │ │ │ │ ├── ExportNetworkPDFTask.java │ │ │ │ │ ├── ExportNetworkPNGTask.java │ │ │ │ │ ├── ExportNetworkPSTask.java │ │ │ │ │ ├── ExportNetworkSVGTask.java │ │ │ │ │ ├── ExportNetworkTaskFactory.java │ │ │ │ │ └── ExportNetworkTunables.java │ │ │ │ ├── properties │ │ │ │ ├── PropertiesWriterFactoryImpl.java │ │ │ │ └── PropertiesWriterImpl.java │ │ │ │ ├── session │ │ │ │ ├── SessionWriterFactoryImpl.java │ │ │ │ └── SessionWriterImpl.java │ │ │ │ ├── sif │ │ │ │ ├── SifNetworkWriterFactory.java │ │ │ │ └── SifWriter.java │ │ │ │ ├── transformer │ │ │ │ └── CyTransformerWriterImpl.java │ │ │ │ ├── vizmap │ │ │ │ ├── VizmapWriterFactoryImpl.java │ │ │ │ └── VizmapWriterImpl.java │ │ │ │ └── xgmml │ │ │ │ ├── GenericXGMMLWriter.java │ │ │ │ ├── GenericXGMMLWriterFactory.java │ │ │ │ ├── GenericXGMMLWriterNoViewFactory.java │ │ │ │ ├── SessionXGMMLNetworkViewWriter.java │ │ │ │ ├── SessionXGMMLNetworkWriter.java │ │ │ │ └── SessionXGMMLWriterFactory.java │ │ └── resources │ │ │ └── xsd │ │ │ ├── cysession.xsd │ │ │ ├── cytables.xsd │ │ │ ├── vizmap.xsd │ │ │ └── xlinks-2001.xsd │ │ └── test │ │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── io │ │ │ └── internal │ │ │ ├── read │ │ │ ├── AbstractNetworkReaderTest.java │ │ │ ├── datatable │ │ │ │ ├── CSVCyReaderTest.java │ │ │ │ └── TextDataTableReaderTest.java.asdf │ │ │ ├── gml │ │ │ │ ├── GMLFileFilterTest.java │ │ │ │ └── GMLNetworkReaderTest.java │ │ │ ├── nnf │ │ │ │ └── NNFReaderTest.java │ │ │ ├── session │ │ │ │ ├── Cy3SessionReaderImplTest.java │ │ │ │ └── SessionFileFilterTest.java │ │ │ ├── sif │ │ │ │ ├── InteractionTest.java │ │ │ │ └── SIFNetworkViewReaderTest.java │ │ │ └── xgmml │ │ │ │ ├── GenericXGMMLFileFilterTest.java │ │ │ │ └── GenericXGMMLReaderTest.java │ │ │ ├── util │ │ │ ├── FilterIOTest.java │ │ │ ├── SUIDUpdaterTest.java │ │ │ ├── UnrecognizedVisualPropertyManagerTest.java │ │ │ └── vizmap │ │ │ │ ├── CalculatorConverterFactoryTest.java │ │ │ │ ├── CalculatorConverterTest.java │ │ │ │ └── VisualStyleSerializerTest.java │ │ │ └── write │ │ │ ├── graphics │ │ │ ├── BitmapWriterTest.java │ │ │ └── PDFWriterTest.java │ │ │ ├── sif │ │ │ └── SifWriterTest.java │ │ │ └── xgmml │ │ │ ├── AbstractXGMMLWriterTest.java │ │ │ ├── GenericXGMMLWriterTest.java │ │ │ ├── SessionXGMMLNetworkViewWriterTest.java │ │ │ └── SessionXGMMLNetworkWriterTest.java │ │ └── resources │ │ └── testData │ │ ├── NNFData │ │ ├── 1000SmallNetworks.nnf │ │ ├── 100SmallNetworks.nnf │ │ ├── 10LargeNetworks.nnf │ │ ├── 300SmallNetworks.nnf │ │ ├── 5Nested.nnf │ │ ├── bad1.nnf │ │ ├── bad2.nnf │ │ ├── calc_network_size │ │ ├── generate_multi_level_networks │ │ ├── generate_networks │ │ ├── good1.nnf │ │ ├── good2.nnf │ │ ├── good3.nnf │ │ ├── good4.nnf │ │ ├── good5.nnf │ │ ├── good6.nnf │ │ ├── intermediate.nnf │ │ ├── large.nnf │ │ ├── loop.nnf │ │ ├── loop1.nnf │ │ ├── small.nnf │ │ ├── t3.cys │ │ └── t4.cys │ │ ├── datatable │ │ ├── blank_delimiter.txt │ │ ├── table_comma.txt │ │ ├── table_space.txt │ │ └── table_tab.txt │ │ ├── filter │ │ └── topology-filter-3.2.json │ │ ├── gml │ │ ├── cy2_arrows.gml │ │ ├── example-directed1.gml │ │ ├── example-directed2.gml │ │ ├── example1.gml │ │ ├── example2.gml │ │ ├── galFiltered_old.gml │ │ └── yed_arrows.gml │ │ ├── sif │ │ ├── SIF-Japanese.sif │ │ ├── degenerate.sif │ │ ├── multiWordProteins.sif │ │ ├── multiWordProteinsFileTrailingSpaces.sif │ │ ├── orphanFirst.sif │ │ └── typical.sif │ │ ├── vizmap │ │ ├── v240_vizmap.props │ │ ├── v252_vizmap.props │ │ ├── v270_vizmap.props │ │ └── v283_vizmap.props │ │ └── xgmml │ │ ├── INVALID.xgmml │ │ ├── bare_ampersands.xgmml │ │ ├── empty.xgmml │ │ ├── empty_DTD.xgmml │ │ ├── galFiltered.xgmml │ │ ├── group_2x_collapsed.xgmml │ │ ├── group_2x_expanded.xgmml │ │ ├── hiddenAtt.xgmml │ │ ├── listAtt.xgmml │ │ ├── nested_groups_283.xgmml │ │ ├── simple.xgmml │ │ ├── simple_3.3.xgmml │ │ └── suid_metadata.xgmml ├── performance │ ├── pom.xml │ └── src │ │ └── main │ │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── io │ │ │ └── read │ │ │ └── sif │ │ │ └── PerfTest.java │ │ └── resources │ │ └── testData │ │ └── sif │ │ ├── A200-200.sif │ │ ├── A50-100.sif │ │ ├── A50-50.sif │ │ └── biogrid-fly.sif └── pom.xml ├── jobs-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── jobs │ └── internal │ ├── CyActivator.java │ ├── CyJobManagerImpl.java │ ├── GUICyJobMonitor.java │ ├── GUIJobDialog.java │ ├── JobStatusBar.java │ └── SimpleCyJobMonitor.java ├── layout-cytoscape-impl ├── pom.xml └── src │ ├── main │ └── java │ │ ├── csapps │ │ └── layout │ │ │ ├── CyActivator.java │ │ │ ├── Profile.java │ │ │ └── algorithms │ │ │ ├── GroupAttributesLayout.java │ │ │ ├── GroupAttributesLayout.java.broken │ │ │ ├── GroupAttributesLayoutContext.java │ │ │ ├── GroupAttributesLayoutTask.java │ │ │ ├── StackedNodeLayout.java │ │ │ ├── StackedNodeLayoutContext.java │ │ │ ├── StackedNodeLayoutTask.java │ │ │ ├── bioLayout │ │ │ ├── BioLayoutAlgorithm.java │ │ │ ├── BioLayoutAlgorithmTask.java │ │ │ ├── BioLayoutContext.java │ │ │ ├── BioLayoutFRAlgorithm.java │ │ │ ├── BioLayoutFRAlgorithmTask.java │ │ │ ├── BioLayoutFRContext.java │ │ │ ├── BioLayoutKKAlgorithm.java │ │ │ ├── BioLayoutKKAlgorithmTask.java │ │ │ └── BioLayoutKKContext.java │ │ │ ├── circularLayout │ │ │ ├── CircularLayoutAlgorithm.java │ │ │ ├── CircularLayoutAlgorithmTask.java │ │ │ └── CircularLayoutContext.java │ │ │ ├── cose │ │ │ ├── CoSELayoutAlgorithm.java │ │ │ ├── CoSELayoutAlgorithmTask.java │ │ │ └── CoSELayoutContext.java │ │ │ ├── graphPartition │ │ │ ├── AttributeCircleLayout.java │ │ │ ├── AttributeCircleLayoutContext.java │ │ │ ├── AttributeCircleLayoutTask.java │ │ │ ├── AttributeGridLayout.java │ │ │ ├── AttributeGridLayoutContext.java │ │ │ ├── AttributeGridLayoutTask.java │ │ │ ├── DegreeSortedCircleContext.java │ │ │ ├── DegreeSortedCircleLayout.java │ │ │ ├── DegreeSortedCircleLayoutTask.java │ │ │ ├── ISOMLayout.java │ │ │ ├── ISOMLayoutContext.java │ │ │ ├── ISOMLayoutTask.java │ │ │ └── Layout.java │ │ │ └── hierarchicalLayout │ │ │ ├── Edge.java │ │ │ ├── Graph.java │ │ │ ├── HierarchicalLayoutAlgorithm.java │ │ │ ├── HierarchicalLayoutAlgorithmTask.java │ │ │ └── HierarchicalLayoutContext.java │ │ └── org │ │ └── ivis │ │ ├── layout │ │ ├── Cluster.java │ │ ├── ClusterManager.java │ │ ├── Clustered.java │ │ ├── LEdge.java │ │ ├── LGraph.java │ │ ├── LGraphManager.java │ │ ├── LGraphObject.java │ │ ├── LNode.java │ │ ├── LNodeDegreeSort.java │ │ ├── Layout.java │ │ ├── LayoutConstants.java │ │ ├── LayoutOptionsPack.java │ │ ├── ProgressListener.java │ │ ├── Updatable.java │ │ ├── cose │ │ │ ├── CoSEConstants.java │ │ │ ├── CoSEEdge.java │ │ │ ├── CoSEGraph.java │ │ │ ├── CoSEGraphManager.java │ │ │ ├── CoSELayout.java │ │ │ ├── CoSENode.java │ │ │ ├── CoarseningEdge.java │ │ │ ├── CoarseningGraph.java │ │ │ └── CoarseningNode.java │ │ ├── fd │ │ │ ├── FDLayout.java │ │ │ ├── FDLayoutConstants.java │ │ │ ├── FDLayoutEdge.java │ │ │ └── FDLayoutNode.java │ │ ├── sbgn │ │ │ ├── Compaction.java │ │ │ ├── SbgnPDConstants.java │ │ │ ├── SbgnPDEdge.java │ │ │ ├── SbgnPDLayout.java │ │ │ ├── SbgnPDNode.java │ │ │ ├── SbgnProcessNode.java │ │ │ ├── VisibilityEdge.java │ │ │ └── VisibilityGraph.java │ │ └── util │ │ │ ├── ComparableNode.java │ │ │ ├── GraphMLWriter.java │ │ │ ├── MemberPack.java │ │ │ ├── Organization.java │ │ │ ├── Polyomino.java │ │ │ ├── PolyominoPacking.java │ │ │ ├── PolyominoQuickSort.java │ │ │ └── RectProc.java │ │ └── util │ │ ├── DimensionD.java │ │ ├── IGeometry.java │ │ ├── IMath.java │ │ ├── IndexedObjectSort.java │ │ ├── IntegerQuickSort.java │ │ ├── PointD.java │ │ ├── QuickSort.java │ │ ├── RectangleD.java │ │ └── Transform.java │ └── test │ └── resources │ └── circular-layout-tests │ ├── CircularLayout Tests Instructions.pdf │ ├── IL6Shubs_Cor_Signif.txt │ ├── LUAD_vest_v2.cys │ └── goTrees.cys ├── layout-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── view │ │ └── layout │ │ └── internal │ │ ├── CyActivator.java │ │ ├── CyLayoutAlgorithmManagerImpl.java │ │ ├── algorithms │ │ ├── GridNodeLayout.java │ │ ├── GridNodeLayout.java.edited │ │ ├── GridNodeLayoutContext.java │ │ └── GridNodeLayoutTask.java │ │ └── task │ │ ├── LayoutTaskFactoryWrapper.java │ │ └── LayoutWrapperTask.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── view │ └── layout │ ├── AbstractLayoutAlgorithmTest.java │ ├── AbstractLayoutTaskTest.java │ ├── AbstractPartitionLayoutTaskTest.java │ ├── LayoutAlgorithmTest.java │ ├── LayoutEdgeTest.java │ ├── LayoutNodeTest.java │ ├── LayoutPartitionTest.java │ ├── LayoutTaskTest.java │ └── PartitionUtilTest.java ├── layout-jgraph-impl ├── pom.xml └── src │ └── main │ └── java │ └── csapps │ └── layout │ ├── CyActivator.java │ ├── JGraphLayoutWrapper.java │ └── JGraphLayoutWrapperTask.java ├── layout-prefuse-impl ├── pom.xml └── src │ └── main │ └── java │ ├── org │ └── cytoscape │ │ └── prefuse │ │ └── layouts │ │ └── internal │ │ ├── CyActivator.java │ │ ├── ForceDirectedLayout.java │ │ ├── ForceDirectedLayoutContext.java │ │ └── ForceDirectedLayoutTask.java │ └── prefuse │ └── util │ └── force │ ├── AbstractForce.java │ ├── BackwardEulerIntegrator.java │ ├── CircularWallForce.java │ ├── DragForce.java │ ├── EulerIntegrator.java │ ├── Force.java │ ├── ForceItem.java │ ├── ForceSimulator.java │ ├── GravitationalForce.java │ ├── Integrator.java │ ├── NBodyForce.java │ ├── RungeKuttaIntegrator.java │ ├── Spring.java │ ├── SpringForce.java │ ├── StateMonitor.java │ └── WallForce.java ├── linkout-impl ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── cytoscape │ │ └── linkout │ │ └── internal │ │ ├── CyActivator.java │ │ ├── DynamicEdgeLinkoutMenuFactory.java │ │ ├── DynamicNodeLinkoutMenuFactory.java │ │ ├── DynamicSupport.java │ │ ├── EdgeLinkoutTaskFactory.java │ │ ├── LinkOut.java │ │ ├── LinkoutTask.java │ │ ├── NodeLinkoutTaskFactory.java │ │ └── PropsReader.java │ └── resources │ └── linkout.props ├── log-swing-impl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── log │ │ │ └── internal │ │ │ ├── AllLogMessagesProcesser.java │ │ │ ├── AppenderToQueue.java │ │ │ ├── ConsoleDialog.java │ │ │ ├── CyActivator.java │ │ │ ├── CyStatusBar.java │ │ │ ├── LogViewer.java │ │ │ ├── LowPriorityDaemonThreadFactory.java │ │ │ ├── QueueProcesser.java │ │ │ ├── UserMessagesDialog.java │ │ │ └── UserMessagesProcesser.java │ └── resources │ │ ├── LICENSE.txt │ │ ├── README-ICONS │ │ ├── console-debug.png │ │ ├── console-error.png │ │ ├── console-info.png │ │ ├── console-warn.png │ │ ├── console.png │ │ ├── consoledialogbase.html │ │ ├── logConsole.png │ │ ├── status-bar-debug.png │ │ ├── status-bar-error.png │ │ ├── status-bar-info.png │ │ └── status-bar-warn.png │ └── test │ └── java │ └── org │ └── cytoscape │ └── log │ └── internal │ └── LogViewerTest.java ├── manual-layout-impl ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── cytoscape │ │ ├── math │ │ └── xform │ │ │ ├── AffineTransform3D.java │ │ │ ├── AxisRotation3D.java │ │ │ ├── Matrix4x4.java │ │ │ ├── Point3D.java │ │ │ ├── Scale3D.java │ │ │ ├── Transformation3D.java │ │ │ └── Translation3D.java │ │ └── view │ │ └── manual │ │ └── internal │ │ ├── CyActivator.java │ │ ├── common │ │ ├── AbstractManualLayoutAction.java │ │ ├── CheckBoxTracker.java │ │ ├── GraphConverter2.java │ │ ├── PolymorphicSlider.java │ │ └── SliderStateTracker.java │ │ ├── control │ │ ├── actions │ │ │ ├── AbstractControlAction.java │ │ │ ├── ControlPanelAction.java │ │ │ ├── align │ │ │ │ ├── HAlignCenter.java │ │ │ │ ├── HAlignLeft.java │ │ │ │ ├── HAlignRight.java │ │ │ │ ├── VAlignBottom.java │ │ │ │ ├── VAlignCenter.java │ │ │ │ └── VAlignTop.java │ │ │ ├── dist │ │ │ │ ├── HDistCenter.java │ │ │ │ ├── HDistLeft.java │ │ │ │ ├── HDistRight.java │ │ │ │ ├── VDistBottom.java │ │ │ │ ├── VDistCenter.java │ │ │ │ └── VDistTop.java │ │ │ └── stack │ │ │ │ ├── HStackBottom.java │ │ │ │ ├── HStackCenter.java │ │ │ │ ├── HStackTop.java │ │ │ │ ├── VStackCenter.java │ │ │ │ ├── VStackLeft.java │ │ │ │ └── VStackRight.java │ │ └── view │ │ │ ├── AlignPanel.java │ │ │ ├── DistPanel.java │ │ │ ├── LayoutToolsPanel.java │ │ │ └── StackPanel.java │ │ ├── layout │ │ └── algorithm │ │ │ └── MutablePolyEdgeGraphLayout.java │ │ ├── rotate │ │ ├── RotatePanel.java │ │ └── RotationLayouter.java │ │ ├── scale │ │ ├── ScaleLayouter.java │ │ └── ScalePanel.java │ │ ├── tasks │ │ ├── RotateTask.java │ │ ├── RotateTaskFactory.java │ │ ├── ScaleTask.java │ │ └── ScaleTaskFactory.java │ │ └── util │ │ ├── IconUtil.java │ │ └── Util.java │ └── resources │ └── images │ ├── H_ALIGN_CENTER.gif │ ├── H_ALIGN_LEFT.gif │ ├── H_ALIGN_RIGHT.gif │ ├── H_DIST_CENTER.gif │ ├── H_DIST_LEFT.gif │ ├── H_DIST_RIGHT.gif │ ├── H_STACK_BOTTOM.gif │ ├── H_STACK_CENTER.gif │ ├── H_STACK_TOP.gif │ ├── V_ALIGN_BOTTOM.gif │ ├── V_ALIGN_CENTER.gif │ ├── V_ALIGN_TOP.gif │ ├── V_DIST_BOTTOM.gif │ ├── V_DIST_CENTER.gif │ ├── V_DIST_TOP.gif │ ├── V_STACK_CENTER.gif │ ├── V_STACK_LEFT.gif │ └── V_STACK_RIGHT.gif ├── model-impl ├── impl │ ├── pom.xml │ └── src │ │ ├── main │ │ ├── java │ │ │ └── org │ │ │ │ └── cytoscape │ │ │ │ └── model │ │ │ │ └── internal │ │ │ │ ├── AbstractTableFacade.java │ │ │ │ ├── AttribTopoGraphNode.java │ │ │ │ ├── ColumnSetListener.java │ │ │ │ ├── CyActivator.java │ │ │ │ ├── CyColumnImpl.java │ │ │ │ ├── CyEdgeImpl.java │ │ │ │ ├── CyListImpl.java │ │ │ │ ├── CyNetworkFactoryImpl.java │ │ │ │ ├── CyNetworkManagerImpl.java │ │ │ │ ├── CyNetworkTableManagerImpl.java │ │ │ │ ├── CyNodeImpl.java │ │ │ │ ├── CyRootNetworkImpl.java │ │ │ │ ├── CyRootNetworkManagerImpl.java │ │ │ │ ├── CySubNetworkImpl.java │ │ │ │ ├── CyTableEntryImpl.java │ │ │ │ ├── CyTableFactoryImpl.java │ │ │ │ ├── CyTableImpl.java │ │ │ │ ├── CyTableManagerImpl.java │ │ │ │ ├── CyTableMetadataImpl.java │ │ │ │ ├── DefaultTablesNetwork.java │ │ │ │ ├── EdgePointer.java │ │ │ │ ├── EqnSupport.java │ │ │ │ ├── InteractionSetListener.java │ │ │ │ ├── LocalTableFacade.java │ │ │ │ ├── LocalTableFacade.java.with_abstract │ │ │ │ ├── NameSetListener.java │ │ │ │ ├── NetworkNameSetListener.java │ │ │ │ ├── NodePointer.java │ │ │ │ ├── NonVirtualColumnInfo.java │ │ │ │ ├── RemovedAttributesCache.java │ │ │ │ ├── SelectionMediator.java │ │ │ │ ├── SharedTableFacade.java │ │ │ │ ├── SimpleNetwork.java │ │ │ │ ├── TableEventHelperFacade.java │ │ │ │ ├── VirtualColumn.java │ │ │ │ ├── VirtualColumnAdder.java │ │ │ │ ├── WeakMapList.java │ │ │ │ ├── column │ │ │ │ ├── CanonicalStringPool.java │ │ │ │ ├── CanonicalStringPoolFilter.java │ │ │ │ ├── ColumnData.java │ │ │ │ ├── ColumnDataFactory.java │ │ │ │ ├── ColumnDataFactoryFastUtil.java │ │ │ │ ├── ColumnDataFactoryHashMap.java │ │ │ │ ├── ColumnDataFactoryHashMapWithStringPool.java │ │ │ │ ├── EquationSupport.java │ │ │ │ ├── LongToBooleanColumn.java │ │ │ │ └── MapColumn.java │ │ │ │ └── tsort │ │ │ │ ├── TopoGraphNode.java │ │ │ │ └── TopologicalSort.java │ │ └── resources │ │ │ └── readme.txt │ │ └── test │ │ └── java │ │ └── org │ │ └── cytoscape │ │ └── model │ │ ├── CyColumnTest.java │ │ ├── CyEdgeTest.java │ │ ├── CyIdentifiableTest.java │ │ ├── CyNetworkAutoDeleteTest.java │ │ ├── CyNetworkTableManagerTest.java │ │ ├── CyNetworkTest.java │ │ ├── CyNodeTest.java │ │ ├── CyTableManagerTest.java │ │ ├── CyTableTest.java │ │ ├── CyTableUtilTest.java │ │ ├── EquationTest.java │ │ ├── GraphObjectTest.java │ │ ├── NamespaceTableTest.java │ │ ├── NetworkTestSupport.java │ │ ├── NetworkTestSupportTest.java │ │ ├── TableTestSupport.java │ │ ├── TableTestSupportTest.java │ │ ├── TestCyNetworkFactory.java │ │ ├── internal │ │ ├── column │ │ │ └── ColumnDataTest.java │ │ └── tsort │ │ │ └── TopologicalSortTest.java │ │ └── subnetwork │ │ ├── CyRootNetworkCyNetworkTest.java │ │ ├── CyRootNetworkTest.java │ │ ├── CySubNetworkCyNetworkTest.java │ │ ├── CySubNetworkCyTableManagerTest.java │ │ └── CySubNetworkTest.java ├── it │ ├── pom.xml │ └── src │ │ └── test │ │ └── java │ │ └── org │ │ └── cytoscape │ │ └── model │ │ └── ServiceConfigurationTest.java ├── performance-debug │ ├── pom.xml │ └── src │ │ └── main │ │ └── java │ │ └── org │ │ └── cytoscape │ │ └── model │ │ └── PerfTest.java ├── performance │ ├── baseline.xml │ ├── pom.xml │ └── src │ │ └── test │ │ └── java │ │ └── org │ │ └── cytoscape │ │ └── model │ │ └── ServiceConfigurationTest.java ├── pom.xml └── table-performance-debug │ ├── pom.xml │ └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── model │ └── PerfTest.java ├── pom.xml ├── presentation-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── view │ │ └── presentation │ │ └── internal │ │ ├── CyActivator.java │ │ ├── RenderingEngineManagerImpl.java │ │ └── property │ │ └── values │ │ ├── CyColumnIdentifierFactoryImpl.java │ │ └── CyColumnIdentifierImpl.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── view │ └── presentation │ └── RenderingEngineManagerTest.java ├── property-impl ├── .springBeans ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── cytoscape │ │ └── property │ │ └── internal │ │ ├── CyActivator.java │ │ ├── PropsReader.java │ │ └── bookmark │ │ ├── BookmarkReader.java │ │ └── BookmarksUtilImpl.java │ └── resources │ ├── bookmarks.xml │ └── cytoscape3.props ├── search2-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── search │ │ └── internal │ │ ├── CyActivator.java │ │ ├── index │ │ ├── AttributeFields.java │ │ ├── CaseInsensitiveWhitespaceAnalyzer.java │ │ ├── CustomMultiFieldQueryParser.java │ │ ├── Index.java │ │ ├── SearchManager.java │ │ ├── TableIndexer.java │ │ └── TableType.java │ │ ├── progress │ │ ├── CompositeProgressMonitor.java │ │ ├── DiscreteProgressMonitor.java │ │ ├── ProgressMonitor.java │ │ ├── ProgressViewer.java │ │ └── SubProgressMonitor.java │ │ ├── search │ │ ├── NetworkTableSearchTask.java │ │ ├── NodeAndEdgeSelectorTask.java │ │ ├── SearchResults.java │ │ ├── SearchTask.java │ │ ├── TableRowSelectorTask.java │ │ └── TableSearchTask.java │ │ └── ui │ │ ├── NetworkSearchBox.java │ │ ├── NetworkSearchToolbarComponent.java │ │ ├── NetworkTableSearchAction.java │ │ ├── NetworkTableSearchBox.java │ │ ├── SearchBox.java │ │ └── debug │ │ ├── DebugSearchProgressPanel.java │ │ └── ProgressPanel.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── search │ └── internal │ ├── AttributeFieldsTest.java │ ├── LogSilenceRule.java │ ├── NodeAndEdgeSelectorTaskTest.java │ └── index │ └── QueryTest.java ├── session-impl ├── impl │ └── pom.xml ├── integration-test │ └── pom.xml ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── session │ └── internal │ ├── CyActivator.java │ ├── CyNetworkNamingImpl.java │ ├── CySessionManagerImpl.java │ └── CyTableMetadataImpl.java ├── swing-application-impl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── internal │ │ │ ├── CyActivator.java │ │ │ ├── MacCyActivator.java │ │ │ ├── QuickStartStartup.java │ │ │ ├── SessionHandler.java │ │ │ ├── actions │ │ │ ├── AboutAction.java │ │ │ ├── BookmarkAction.java │ │ │ ├── CheckForUpdatesAction.java │ │ │ ├── CloseWindowAction.java │ │ │ ├── CommandListAction.java │ │ │ ├── CommandListUI.java │ │ │ ├── CreateNetworkViewsAction.java │ │ │ ├── CytoPanelAction.java │ │ │ ├── DestroyNetworkViewsAction.java │ │ │ ├── DestroyNetworksAction.java │ │ │ ├── DetachedViewToolBarAction.java │ │ │ ├── ExitAction.java │ │ │ ├── ExportImageAction.java │ │ │ ├── ExportNetworkAction.java │ │ │ ├── FullScreenAction.java │ │ │ ├── FullScreenMacAction.java │ │ │ ├── NewNetworkFromSelectionAction.java │ │ │ ├── PreferenceAction.java │ │ │ ├── PrintAction.java │ │ │ ├── RecentSessionManager.java │ │ │ └── StarterPanelAction.java │ │ │ ├── command │ │ │ ├── CommandTaskRunner.java │ │ │ ├── CommandToolPanel.java │ │ │ ├── ConsoleCommandHandler.java │ │ │ ├── HelpGenerator.java │ │ │ ├── JResultsPane.java │ │ │ ├── MessageHandler.java │ │ │ ├── PauseCommandTask.java │ │ │ └── PauseCommandTaskFactory.java │ │ │ ├── dialogs │ │ │ ├── BookmarkDialog.java │ │ │ ├── BookmarkDialogFactory.java │ │ │ ├── PreferenceTableModel.java │ │ │ ├── PreferenceValueDialog.java │ │ │ ├── PreferencesDialog.java │ │ │ └── PreferencesDialogFactory.java │ │ │ ├── io │ │ │ └── SessionIO.java │ │ │ ├── layout │ │ │ └── ui │ │ │ │ ├── DynamicLayoutMenu.java │ │ │ │ ├── LayoutMenuPopulator.java │ │ │ │ ├── LayoutSettingsDialog.java │ │ │ │ ├── LayoutSettingsManager.java │ │ │ │ ├── NetworkViewMenuListener.java │ │ │ │ ├── SettingsAction.java │ │ │ │ └── StaticLayoutMenu.java │ │ │ ├── model │ │ │ ├── RootNetworkManager.java │ │ │ └── SelectionMode.java │ │ │ ├── select │ │ │ ├── AbstractViewUpdater.java │ │ │ ├── RowViewTracker.java │ │ │ ├── RowsSetViewUpdater.java │ │ │ ├── SelectEdgeViewUpdater.java │ │ │ └── SelectNodeViewUpdater.java │ │ │ ├── shutdown │ │ │ └── ConfigDirPropertyWriter.java │ │ │ ├── task │ │ │ ├── CytoPanelTaskFactoryTunableAction.java │ │ │ ├── DynamicTaskFactory.java │ │ │ ├── DynamicTogglableTaskFactory.java │ │ │ ├── GetLatestVersionTask.java │ │ │ ├── LoadFileListTask.java │ │ │ └── TaskFactoryTunableAction.java │ │ │ ├── tunable │ │ │ ├── CyPropertyConfirmation.java │ │ │ └── CyPropertyConfirmationHandler.java │ │ │ ├── undo │ │ │ ├── RedoAction.java │ │ │ └── UndoAction.java │ │ │ ├── util │ │ │ ├── HSLColor.java │ │ │ ├── IconUtil.java │ │ │ ├── RandomImage.java │ │ │ ├── SimpleToolBarToggleButton.java │ │ │ ├── Util.java │ │ │ └── undo │ │ │ │ └── UndoMonitor.java │ │ │ └── view │ │ │ ├── AbstractNetworkPanel.java │ │ │ ├── AbstractNetworkPanelModel.java │ │ │ ├── BiModalJSplitPane.java │ │ │ ├── BirdsEyeViewPanel.java │ │ │ ├── CyColumnPresentationManagerImpl.java │ │ │ ├── CyDesktopManager.java │ │ │ ├── CyHelpBrokerImpl.java │ │ │ ├── CytoPanelImpl.java │ │ │ ├── CytoPanelNameInternal.java │ │ │ ├── CytoPanelStateInternal.java │ │ │ ├── CytoPanelUtil.java │ │ │ ├── CytoscapeDesktop.java │ │ │ ├── CytoscapeMenuBar.java │ │ │ ├── CytoscapeMenuPopulator.java │ │ │ ├── CytoscapeMenus.java │ │ │ ├── CytoscapeToolBar.java │ │ │ ├── ExpandCollapseButton.java │ │ │ ├── GridViewToggleModel.java │ │ │ ├── GridViewTogglePanel.java │ │ │ ├── MacFullScreenEnabler.java │ │ │ ├── MemStatusPanel.java │ │ │ ├── NetworkMainPanel.java │ │ │ ├── NetworkMediator.java │ │ │ ├── NetworkSearchBar.java │ │ │ ├── NetworkSearchMediator.java │ │ │ ├── NetworkSelectionMediator.java │ │ │ ├── NetworkViewComparisonPanel.java │ │ │ ├── NetworkViewContainer.java │ │ │ ├── NetworkViewFrame.java │ │ │ ├── NetworkViewGrid.java │ │ │ ├── NetworkViewMainPanel.java │ │ │ ├── NetworkViewMediator.java │ │ │ ├── NetworkViewPreviewDialog.java │ │ │ ├── NullNetworkViewPanel.java │ │ │ ├── RootNetworkPanel.java │ │ │ ├── RootNetworkPanelModel.java │ │ │ ├── SimpleRootPaneContainer.java │ │ │ ├── StarterPanel.java │ │ │ ├── SubNetworkPanel.java │ │ │ ├── SubNetworkPanelModel.java │ │ │ ├── ToolBarEnableUpdater.java │ │ │ ├── help │ │ │ ├── AboutDialog.java │ │ │ ├── ArrangeTask.java │ │ │ ├── ArrangeTaskFactory.java │ │ │ ├── HelpContactHelpDeskTask.java │ │ │ ├── HelpContactHelpDeskTaskFactory.java │ │ │ ├── HelpLinkTaskFactory.java │ │ │ ├── HelpReportABugTask.java │ │ │ ├── HelpReportABugTaskFactory.java │ │ │ ├── HelpTourTask.java │ │ │ ├── HelpTourTaskFactory.java │ │ │ ├── HelpTutorialsTask.java │ │ │ ├── HelpTutorialsTaskFactory.java │ │ │ ├── HelpUserManualTask.java │ │ │ ├── HelpUserManualTaskFactory.java │ │ │ ├── HelpVideosTask.java │ │ │ └── HelpVideosTaskFactory.java │ │ │ ├── updater │ │ │ └── UpdatesDialog.java │ │ │ └── util │ │ │ ├── CyToolBar.java │ │ │ ├── MenuScroller.java │ │ │ ├── SVGIcon.java │ │ │ ├── ToggleableButtonGroup.java │ │ │ ├── VerticalButtonUI.java │ │ │ └── ViewUtil.java │ └── resources │ │ ├── images │ │ ├── about.svg │ │ ├── drop-net-file-56.png │ │ ├── logo-light-96.png │ │ ├── logo.png │ │ ├── python-logo.svg │ │ ├── r-logo.svg │ │ └── tooltips │ │ │ ├── selection-mode-annotations.gif │ │ │ ├── selection-mode-edges.gif │ │ │ ├── selection-mode-node-label.gif │ │ │ └── selection-mode-nodes.gif │ │ ├── toolbar.stoplist │ │ └── xsd │ │ ├── networkList.xsd │ │ └── sessionState.xsd │ └── test │ └── java │ └── org │ └── cytoscape │ └── internal │ └── view │ ├── CytoscapeDesktopTest.java │ ├── SwingRunner.java │ └── util │ └── ViewUtilTest.java ├── swing-util-impl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── util │ │ │ └── swing │ │ │ └── internal │ │ │ ├── ColorBlindAwareColorChooserPanel.java │ │ │ ├── ColorIcon.java │ │ │ ├── ColorPaletteProviderPanel.java │ │ │ ├── ColorPaletteProviderPanel.java.save │ │ │ ├── ColorPanelSelectionModel.java │ │ │ ├── CyActivator.java │ │ │ ├── CyColorPaletteChooserFactoryImpl.java │ │ │ ├── CyColorPaletteChooserImpl.java │ │ │ ├── FileUtilImpl.java │ │ │ ├── Help.java │ │ │ ├── IconManagerImpl.java │ │ │ ├── OpenBrowserImpl.java │ │ │ └── PaletteIcon.java │ └── resources │ │ └── fonts │ │ ├── cytoscape-3.ttf │ │ └── fontawesome-webfont.ttf │ └── test │ └── java │ └── org │ └── cytoscape │ └── util │ └── swing │ └── internal │ ├── CyActivatorTest.java │ ├── FileUtilImplTest.java │ └── OpenBrowserImplTest.java ├── table-browser-impl ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── cytoscape │ │ └── browser │ │ └── internal │ │ ├── CyActivator.java │ │ ├── action │ │ ├── CreateColumnAction.java │ │ ├── DeleteColumnsAction.java │ │ ├── ShowColumnsAction.java │ │ ├── TableOptionsAction.java │ │ └── TaskFactoryTunableAction.java │ │ ├── format │ │ └── SetColumnFormatDialog.java │ │ ├── io │ │ ├── TableColumnStat.java │ │ └── TableColumnStatFileIO.java │ │ ├── task │ │ ├── ClearAllErrorsTask.java │ │ ├── ClearAllErrorsTaskFactory.java │ │ ├── DeleteTableTask.java │ │ ├── DeleteTableTaskFactoryImpl.java │ │ ├── DynamicTableTaskFactory.java │ │ ├── DynamicTogglableTableTaskFactory.java │ │ ├── HideColumnTask.java │ │ ├── HideColumnTaskFactory.java │ │ ├── SetColumnFormatTask.java │ │ ├── SetColumnFormatTaskFactory.java │ │ ├── ToggleTextWrapTask.java │ │ └── ToggleTextWrapTaskFactory.java │ │ ├── util │ │ ├── CyToolBar.java │ │ ├── IconUtil.java │ │ ├── TableBrowserUtil.java │ │ └── ViewUtil.java │ │ └── view │ │ ├── AbstractTableBrowser.java │ │ ├── DefaultTableBrowser.java │ │ ├── DeletionDialog.java │ │ ├── GlobalTableBrowser.java │ │ ├── MultiLineToolTip.java │ │ ├── OpenURLMenu.java │ │ ├── TableBrowserMediator.java │ │ ├── TableBrowserStyleMediator.java │ │ ├── TableChooserCellRenderer.java │ │ ├── TableRenderer.java │ │ ├── ToolBarEnableUpdater.java │ │ └── tools │ │ ├── AbstractToolBarControl.java │ │ ├── GeneralOptionsControl.java │ │ ├── RowHeightControl.java │ │ └── ViewModeControl.java │ └── resources │ └── images │ ├── about_icon.txt │ ├── datatype_boolean2_16.png │ ├── datatype_boolean_16.png │ ├── datatype_float_double_16.png │ ├── datatype_int_16.png │ ├── datatype_list_16.png │ ├── datatype_string_16.png │ ├── decimalDecrease.png │ ├── decimalIncrease.png │ ├── drop-table-file-56.png │ ├── fx.png │ ├── primary_key.png │ ├── select_all.png │ ├── stock_delete.png │ ├── stock_insert-columns.png │ ├── stock_new.png │ ├── stock_open.png │ ├── stock_select-row.png │ ├── table-gear-icon.png │ ├── table-select-column-icon.png │ ├── table_delete.png │ ├── table_map.png │ ├── table_selection_mode.png │ └── unselect_all.png ├── table-import-impl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── tableimport │ │ │ └── internal │ │ │ ├── CyActivator.java │ │ │ ├── io │ │ │ └── WildCardCyFileFilter.java │ │ │ ├── reader │ │ │ ├── AbstractGraphReader.java │ │ │ ├── AbstractLineParser.java │ │ │ ├── AbstractMappingParameters.java │ │ │ ├── AttributeLineParser.java │ │ │ ├── AttributeMappingParameters.java │ │ │ ├── DefaultAttributeTableReader.java │ │ │ ├── ExcelAttributeSheetReader.java │ │ │ ├── ExcelNetworkSheetReader.java │ │ │ ├── GraphReader.java │ │ │ ├── MappingParameter.java │ │ │ ├── NetworkLineParser.java │ │ │ ├── NetworkTableMappingParameters.java │ │ │ ├── NetworkTableReader.java │ │ │ ├── SupportedFileType.java │ │ │ ├── TextDelimiter.java │ │ │ ├── TextTableReader.java │ │ │ └── ontology │ │ │ │ ├── GeneAssociationReader.java │ │ │ │ ├── GeneAssociationTag.java │ │ │ │ ├── OBONetworkReaderFactory.java │ │ │ │ ├── OBOReader.java │ │ │ │ └── OBOTags.java │ │ │ ├── task │ │ │ ├── AbstractLoadTableTask.java │ │ │ ├── AbstractTableReaderFactory.java │ │ │ ├── AddImportedTableTask.java │ │ │ ├── CombineNetworkReaderAndMappingTask.java │ │ │ ├── CombineTableReaderAndMappingTask.java │ │ │ ├── DelimitersTunable.java │ │ │ ├── FinalStatusMessageUpdateTask.java │ │ │ ├── ImportAttributeTableReaderFactory.java │ │ │ ├── ImportAttributeTableReaderTask.java │ │ │ ├── ImportNetworkTableReaderFactory.java │ │ │ ├── ImportNetworkTableReaderTask.java │ │ │ ├── ImportNoGuiNetworkReaderFactory.java │ │ │ ├── ImportNoGuiTableReaderFactory.java │ │ │ ├── ImportOntologyAndAnnotationAction.java │ │ │ ├── ImportOntologyAndAnnotationTask.java │ │ │ ├── ImportOntologyAndAnnotationTaskFactory.java │ │ │ ├── ImportTableDataTask.java │ │ │ ├── ImportTableDataTaskFactoryImpl.java │ │ │ ├── LoadNetworkReaderTask.java │ │ │ ├── LoadTableFileTask.java │ │ │ ├── LoadTableFileTaskFactoryImpl.java │ │ │ ├── LoadTableReaderTask.java │ │ │ ├── LoadTableURLTask.java │ │ │ ├── LoadTableURLTaskFactoryImpl.java │ │ │ ├── MapGeneAssociationTask.java │ │ │ ├── NetworkCollectionHelper.java │ │ │ ├── ReaderTableTask.java │ │ │ ├── RegisterOntologyTask.java │ │ │ ├── SelectFileTableTask.java │ │ │ ├── SelectURLTableTask.java │ │ │ └── TableImportContext.java │ │ │ ├── tunable │ │ │ ├── AttributeMappingParametersHandler.java │ │ │ ├── AttributeMappingParametersHandlerFactory.java │ │ │ ├── NetworkTableMappingParametersHandler.java │ │ │ └── NetworkTableMappingParametersHandlerFactory.java │ │ │ ├── ui │ │ │ ├── AttributeEditorPanel.java │ │ │ ├── AttributeSettings.java │ │ │ ├── DataEvents.java │ │ │ ├── DataSourceSelectDialog.java │ │ │ ├── ImportTablePanel.java │ │ │ ├── OntologyPanelBuilder.java │ │ │ ├── PreviewTablePanel.java │ │ │ └── theme │ │ │ │ └── ImportDialogIcons.java │ │ │ └── util │ │ │ ├── AttributeDataType.java │ │ │ ├── DataUtils.java │ │ │ ├── FileType.java │ │ │ ├── IconUtil.java │ │ │ ├── ImportType.java │ │ │ ├── OntologyDAGManager.java │ │ │ ├── OntologyUtil.java │ │ │ ├── ProxyHandler.java │ │ │ ├── SourceColumnSemantic.java │ │ │ ├── TypeUtil.java │ │ │ └── URLUtil.java │ └── resources │ │ ├── images │ │ └── ximian │ │ │ ├── stock_3d-light-on-16.png │ │ │ ├── stock_data-sources-modified-16.png │ │ │ └── stock_internet-16.png │ │ └── tax_report.txt │ └── test │ ├── java │ └── org │ │ └── cytoscape │ │ └── tableimport │ │ └── internal │ │ ├── reader │ │ └── ontology │ │ │ ├── GeneAssociationReaderTest.java │ │ │ └── OBOReaderTest.java │ │ ├── task │ │ ├── LoadAttributesFileTaskFactoryImplTest.java │ │ └── LoadAttributesURLTaskFactoryImplTest.java │ │ └── util │ │ └── TypeUtilTest.java │ └── resources │ ├── dummy_obo.obo │ ├── gene_association.sgd │ ├── gene_ontology_ext.obo.obo │ ├── goslim_generic.obo.obo │ └── goslim_yeast.obo.obo ├── table-presentation-impl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── view │ │ │ └── table │ │ │ └── internal │ │ │ ├── BrowserTableVisualLexicon.java │ │ │ ├── CyActivator.java │ │ │ ├── TableRenderingEngineFactoryImpl.java │ │ │ ├── TableRenderingEngineImpl.java │ │ │ ├── TableViewRendererImpl.java │ │ │ ├── VisualPropertyChangeListener.java │ │ │ ├── equation │ │ │ ├── ApplyWorker.java │ │ │ ├── EquationEditorDialogFactory.java │ │ │ ├── EquationEditorMediator.java │ │ │ ├── EquationEditorPanel.java │ │ │ ├── EquationEditorTask.java │ │ │ ├── EquationEditorTaskFactory.java │ │ │ ├── EquationTokenMaker.java │ │ │ ├── FunctionInfo.java │ │ │ ├── InfoPanel.java │ │ │ ├── ItemListPanel.java │ │ │ ├── ItemPanel.java │ │ │ ├── ItemTreePanel.java │ │ │ ├── SyntaxAreaFactory.java │ │ │ ├── SyntaxAreaPanel.java │ │ │ └── TutorialItems.java │ │ │ ├── impl │ │ │ ├── BrowserTable.java │ │ │ ├── BrowserTableCellRenderer.java │ │ │ ├── BrowserTableColumnModel.java │ │ │ ├── BrowserTableColumnModelGravityEvent.java │ │ │ ├── BrowserTableColumnModelListener.java │ │ │ ├── BrowserTableHeaderRenderer.java │ │ │ ├── BrowserTableModel.java │ │ │ ├── BrowserTablePresentation.java │ │ │ ├── BrowserTableRowHeader.java │ │ │ ├── BrowserTableRowHeaderRenderer.java │ │ │ ├── MultiLineTableCellEditor.java │ │ │ ├── PopupMenuHelper.java │ │ │ └── icon │ │ │ │ ├── ColorIcon.java │ │ │ │ ├── FontFaceIcon.java │ │ │ │ ├── TextIcon.java │ │ │ │ ├── VisualPropertyIcon.java │ │ │ │ └── VisualPropertyIconFactory.java │ │ │ └── util │ │ │ ├── TableBrowserUtil.java │ │ │ ├── ValidatedObjectAndEditString.java │ │ │ ├── ValidatedObjectAndEditStringComparator.java │ │ │ └── ViewUtil.java │ └── resources │ │ ├── fonts │ │ └── jsMath-cmti10.ttf │ │ └── images │ │ └── sparklines │ │ ├── bar-chart.png │ │ ├── line-chart.png │ │ └── pie-chart.png │ └── test │ └── java │ └── org │ └── cytoscape │ └── view │ └── table │ ├── BrowserTableColumnModelTest.java │ ├── BrowserTableTest.java │ └── TableViewTestSupport.java ├── util-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── util │ └── internal │ ├── CyActivator.java │ └── color │ ├── AbstractDivergingPalette.java │ ├── AbstractPalette.java │ ├── BuiltinDivergentPaletteProvider.java │ ├── ColorBrewer.java │ ├── ColorBrewerPaletteProvider.java │ ├── PaletteProviderManagerImpl.java │ ├── RainbowOSCPaletteProvider.java │ ├── RainbowPaletteProvider.java │ ├── RandomPaletteProvider.java │ ├── Viridis.java │ └── ViridisPaletteProvider.java ├── viewmodel-impl ├── impl │ ├── pom.xml │ └── src │ │ ├── main │ │ ├── java │ │ │ └── org │ │ │ │ └── cytoscape │ │ │ │ └── view │ │ │ │ └── model │ │ │ │ └── internal │ │ │ │ ├── CyActivator.java │ │ │ │ ├── NullCyNetworkViewFactory.java │ │ │ │ ├── NullCyNetworkViewImpl.java │ │ │ │ ├── base │ │ │ │ ├── CyViewBase.java │ │ │ │ ├── NullViewConfigImpl.java │ │ │ │ ├── VPStore.java │ │ │ │ ├── VPStoreViewConfig.java │ │ │ │ └── ViewLock.java │ │ │ │ ├── network │ │ │ │ ├── CyEdgeViewImpl.java │ │ │ │ ├── CyNetworkViewFactoryConfigImpl.java │ │ │ │ ├── CyNetworkViewFactoryImpl.java │ │ │ │ ├── CyNetworkViewFactoryProviderImpl.java │ │ │ │ ├── CyNetworkViewImpl.java │ │ │ │ ├── CyNetworkViewManagerImpl.java │ │ │ │ ├── CyNodeViewImpl.java │ │ │ │ ├── NetworkModelListener.java │ │ │ │ ├── VPEdgeStore.java │ │ │ │ ├── VPNetworkStore.java │ │ │ │ ├── VPNodeStore.java │ │ │ │ ├── snapshot │ │ │ │ │ ├── CyEdgeViewSnapshotImpl.java │ │ │ │ │ ├── CyNetworkViewSnapshotImpl.java │ │ │ │ │ ├── CyNodeViewSnapshotImpl.java │ │ │ │ │ └── CyViewSnapshotBase.java │ │ │ │ └── spacial │ │ │ │ │ └── SimpleSpacialIndex2DSnapshotImpl.java │ │ │ │ └── table │ │ │ │ ├── CyColumnViewImpl.java │ │ │ │ ├── CyRowViewImpl.java │ │ │ │ ├── CyTableViewFactoryImpl.java │ │ │ │ ├── CyTableViewFactoryProviderImpl.java │ │ │ │ ├── CyTableViewImpl.java │ │ │ │ ├── CyTableViewManagerImpl.java │ │ │ │ └── TableModelListener.java │ │ └── javadoc │ │ │ └── org │ │ │ └── cytoscape │ │ │ └── viewmodel │ │ │ ├── events │ │ │ └── package.html │ │ │ └── package.html │ │ └── test │ │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── view │ │ │ └── model │ │ │ ├── network │ │ │ ├── CyNetworkViewManagerTest.java │ │ │ ├── NetworkViewBatchTest.java │ │ │ ├── NetworkViewFactoryTestSupport.java │ │ │ ├── NetworkViewImplTest.java │ │ │ ├── NetworkViewTestUtils.java │ │ │ └── SpacialIndex2DTest.java │ │ │ └── table │ │ │ ├── TableViewFactoryTestSupport.java │ │ │ ├── TableViewImplTest.java │ │ │ └── TableViewTestUtils.java │ │ └── resources │ │ └── log4j.properties ├── it │ ├── pom.xml │ └── src │ │ └── test │ │ └── java │ │ └── org │ │ └── cytoscape │ │ └── view │ │ └── model │ │ └── ServiceConfigurationTest.java └── pom.xml ├── vizmap-gui-core-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── view │ └── vizmap │ └── gui │ └── core │ └── internal │ ├── CyActivator.java │ └── cellrenderer │ ├── ContinuousMappingCellRenderer.java │ └── ContinuousMappingCellRendererFactoryImpl.java ├── vizmap-gui-impl ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── cytoscape │ │ └── view │ │ └── vizmap │ │ └── gui │ │ └── internal │ │ ├── ApplicationFacade.java │ │ ├── ColumnSpec.java │ │ ├── CyActivator.java │ │ ├── GraphObjectType.java │ │ ├── MappingFunctionFactoryManagerImpl.java │ │ ├── VisualStyleSet.java │ │ ├── VizMapperProperty.java │ │ ├── action │ │ ├── AbstractVizMapperAction.java │ │ ├── ApplyVisualStyleAction.java │ │ ├── EditSelectedDiscreteValuesAction.java │ │ ├── GenerateDiscreteValuesAction.java │ │ ├── ModifyBrightnessAction.java │ │ └── RemoveSelectedDiscreteValuesAction.java │ │ ├── controller │ │ ├── CopyContinuousMappingCommand.java │ │ ├── ImportDefaultVisualStylesCommand.java │ │ ├── LoadVisualStylesCommand.java │ │ ├── RemoveLockedValuesCommand.java │ │ ├── RemoveVisualMappingsCommand.java │ │ ├── SetLockedValuesCommand.java │ │ └── StartupCommand.java │ │ ├── event │ │ ├── CellEditorEventHandler.java │ │ ├── CellType.java │ │ └── VizMapEventHandlerManagerImpl.java │ │ ├── model │ │ ├── AttributeSet.java │ │ ├── AttributeSetProxy.java │ │ ├── LockedValueState.java │ │ ├── LockedValuesVO.java │ │ ├── MappingFunctionFactoryProxy.java │ │ ├── PropsProxy.java │ │ └── VizMapperProxy.java │ │ ├── task │ │ ├── ClearAllBendsForThisEdgeTask.java │ │ ├── ClearAllBendsForThisEdgeTaskFactory.java │ │ ├── CopyContinuousMappingTask.java │ │ ├── CopyVisualStyleTask.java │ │ ├── CopyVisualStyleTaskFactory.java │ │ ├── CreateLegendTask.java │ │ ├── CreateLegendTaskFactory.java │ │ ├── CreateNewVisualStyleTask.java │ │ ├── CreateNewVisualStyleTaskFactory.java │ │ ├── ImportDefaultVizmapTask.java │ │ ├── MakeVisualStylesDefaultTask.java │ │ ├── MakeVisualStylesDefaultTaskFactory.java │ │ ├── RefreshStyleTask.java │ │ ├── RefreshStyleTaskFactory.java │ │ ├── RemoveLockedValuesTask.java │ │ ├── RemoveVisualMappingsTask.java │ │ ├── RemoveVisualMappingsTaskFactory.java │ │ ├── RemoveVisualStylesTask.java │ │ ├── RemoveVisualStylesTaskFactory.java │ │ ├── RenameVisualStyleTask.java │ │ ├── RenameVisualStyleTaskFactory.java │ │ └── SetLockedValuesTask.java │ │ ├── util │ │ ├── MathUtil.java │ │ ├── NotificationNames.java │ │ ├── NumberConverter.java │ │ ├── ServicePropertiesUtil.java │ │ ├── ServicesUtil.java │ │ ├── VisualPropertyUtil.java │ │ └── mapgenerator │ │ │ ├── AbstractDiscreteMappingGenerator.java │ │ │ ├── FitLabelMappingGenerator.java │ │ │ ├── NumberSeriesMappingGenerator.java │ │ │ ├── PaletteMappingWrapper.java │ │ │ ├── RainbowColorMappingGenerator.java │ │ │ ├── RainbowOscColorMappingGenerator.java │ │ │ ├── RandomColorMappingGenerator.java │ │ │ └── RandomNumberMappingGenerator.java │ │ └── view │ │ ├── AbstractVizMapperModel.java │ │ ├── BiModalJSplitPane.java │ │ ├── ColumnStyleAddColumnPopup.java │ │ ├── ColumnStylePicker.java │ │ ├── DropDownMenuButton.java │ │ ├── OptionsButton.java │ │ ├── PropertySheetPanel.java │ │ ├── VisualPropertySheet.java │ │ ├── VisualPropertySheetContainer.java │ │ ├── VisualPropertySheetItem.java │ │ ├── VisualPropertySheetItemModel.java │ │ ├── VisualPropertySheetModel.java │ │ ├── VisualStylePanelProvider.java │ │ ├── VisualStyleSelector.java │ │ ├── VizMapPropertyBuilder.java │ │ ├── VizMapperMainPanel.java │ │ ├── VizMapperMediator.java │ │ ├── VizMapperMenuMediator.java │ │ ├── cellrenderer │ │ ├── CyColorCellRenderer.java │ │ ├── FontCellRenderer.java │ │ ├── IconCellRenderer.java │ │ └── NumberContinuousCellRenderer.java │ │ ├── editor │ │ ├── BasicVisualPropertyEditor.java │ │ ├── BooleanVisualPropertyEditor.java │ │ ├── ColorVisualPropertyEditor.java │ │ ├── DiscreteValueVisualPropertyEditor.java │ │ ├── EditorManagerImpl.java │ │ ├── FontVisualPropertyEditor.java │ │ ├── NumberVisualPropertyEditor.java │ │ ├── StringVisualPropertyEditor.java │ │ ├── mappingeditor │ │ │ ├── AbstractContinuousMappingEditor.java │ │ │ ├── BelowAndAbovePanel.java │ │ │ ├── C2CEditor.java │ │ │ ├── C2CMappingEditorPanel.java │ │ │ ├── C2DEditor.java │ │ │ ├── C2DMappingEditorPanel.java │ │ │ ├── ContinuousMappingEditorPanel.java │ │ │ ├── ContinuousTrackRenderer.java │ │ │ ├── CyGradientTrackRenderer.java │ │ │ ├── DiscreteTrackRenderer.java │ │ │ ├── EditorValueRangeTracer.java │ │ │ ├── GradientEditor.java │ │ │ ├── GradientEditorPanel.java │ │ │ ├── MinMaxDialog.java │ │ │ ├── TriangleThumbRenderer.java │ │ │ ├── VizMapTrackRenderer.java │ │ │ └── YValueLegendPanel.java │ │ ├── propertyeditor │ │ │ ├── AttributeComboBoxPropertyEditor.java │ │ │ ├── CyColorPropertyEditor.java │ │ │ ├── CyComboBoxPropertyEditor.java │ │ │ ├── CyDiscreteValuePropertyEditor.java │ │ │ ├── CyFontPropertyEditor.java │ │ │ ├── CyNumberPropertyEditor.java │ │ │ ├── CyStringPropertyEditor.java │ │ │ └── MappingTypeComboBoxPropertyEditor.java │ │ └── valueeditor │ │ │ ├── AbstractValueEditor.java │ │ │ ├── BooleanValueEditor.java │ │ │ ├── CyColorChooser.java │ │ │ ├── DiscreteValueEditor.java │ │ │ ├── FontValueEditor.java │ │ │ ├── NumericValueEditor.java │ │ │ └── StringValueEditor.java │ │ ├── legend │ │ ├── AbstractMappingLegendPanel.java │ │ ├── ContinuousLegendPanel.java │ │ ├── DiscreteLegendPanel.java │ │ ├── ExportLegendTask.java │ │ ├── LegendDialog.java │ │ ├── LegendTable.java │ │ └── PassthroughLegendPanel.java │ │ └── util │ │ ├── IconUtil.java │ │ ├── SimpleToolBarToggleButton.java │ │ └── ViewUtil.java │ └── resources │ ├── default_vizmap.xml │ ├── images │ ├── decimalDecrease.png │ └── decimalIncrease.png │ └── vizmapper.props ├── vizmap-impl ├── impl │ ├── pom.xml │ └── src │ │ ├── main │ │ ├── java │ │ │ └── org │ │ │ │ └── cytoscape │ │ │ │ └── view │ │ │ │ └── vizmap │ │ │ │ └── internal │ │ │ │ ├── AbstractApplyHandler.java │ │ │ │ ├── AbstractVisualMappingManager.java │ │ │ │ ├── ApplyHandler.java │ │ │ │ ├── ApplyToColumnHandler.java │ │ │ │ ├── ApplyToEdgeHandler.java │ │ │ │ ├── ApplyToNetworkHandler.java │ │ │ │ ├── ApplyToNodeHandler.java │ │ │ │ ├── CyActivator.java │ │ │ │ ├── NetworkVisualMappingManagerImpl.java │ │ │ │ ├── TableVisualMappingManagerImpl.java │ │ │ │ ├── VisualStyleFactoryImpl.java │ │ │ │ ├── VisualStyleImpl.java │ │ │ │ ├── mappings │ │ │ │ ├── ColorTranslator.java │ │ │ │ ├── ContinuousMappingFactory.java │ │ │ │ ├── ContinuousMappingImpl.java │ │ │ │ ├── DiscreteMappingFactory.java │ │ │ │ ├── DiscreteMappingImpl.java │ │ │ │ ├── NumberTranslator.java │ │ │ │ ├── PassthroughMappingFactory.java │ │ │ │ ├── PassthroughMappingImpl.java │ │ │ │ ├── StringTranslator.java │ │ │ │ └── interpolators │ │ │ │ │ ├── FlatInterpolator.java │ │ │ │ │ ├── Interpolator.java │ │ │ │ │ ├── LinearNumberInterpolator.java │ │ │ │ │ ├── LinearNumberToColorInterpolator.java │ │ │ │ │ ├── LinearNumberToNumberInterpolator.java │ │ │ │ │ └── NumberInterpolator.java │ │ │ │ └── util │ │ │ │ └── ColorUtil.java │ │ ├── javadoc │ │ │ └── org │ │ │ │ └── cytoscape │ │ │ │ └── vizmap │ │ │ │ ├── events │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ └── resources │ │ │ └── cross_browser_color_code.txt │ │ └── test │ │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── view │ │ │ └── vizmap │ │ │ └── internal │ │ │ ├── TableVisualMappingManagerTest.java │ │ │ ├── VisualMappingManagerTest.java │ │ │ ├── VisualStyleFactoryTest.java │ │ │ ├── VisualStyleTest.java │ │ │ └── mappings │ │ │ ├── ContinuousMappingTest.java │ │ │ └── DiscreteMappingTest.java │ │ └── resources │ │ └── log4j.properties ├── it │ ├── pom.xml │ └── src │ │ └── test │ │ └── java │ │ └── org │ │ └── cytoscape │ │ └── view │ │ └── vizmap │ │ └── ServiceConfigurationTest.java └── pom.xml ├── webservice-impl ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── cytoscape │ │ └── webservice │ │ └── internal │ │ ├── CyActivator.java │ │ ├── task │ │ ├── ShowImportDialogAction.java │ │ ├── WebServiceContextMenuTask.java │ │ ├── WebServiceEdgeContextMenuTaskFactory.java │ │ └── WebServiceNodeContextMenuTaskFactory.java │ │ └── ui │ │ ├── AboutDialog.java │ │ ├── WebServiceContextMenu.java │ │ ├── WebServiceContextMenuManager.java │ │ ├── WebServiceGUIImpl.java │ │ └── WebServiceImportDialog.java │ └── resources │ └── images │ └── icons │ └── import-net-db-32.png ├── work-headless-impl ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── cytoscape │ └── work │ └── internal │ ├── CyActivator.java │ └── task │ ├── HDialogTaskManager.java │ └── UndoSupportImpl.java ├── work-impl ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── cytoscape │ │ └── work │ │ └── internal │ │ ├── CyActivator.java │ │ ├── properties │ │ ├── BasicTypePropertyHandler.java │ │ ├── BoundedPropertyHandler.java │ │ ├── ListMultiplePropertyHandler.java │ │ ├── ListSinglePropertyHandler.java │ │ ├── ParameterizedTypePropertyHandler.java │ │ ├── SimpleTunablePropertyHandlerFactory.java │ │ ├── TunablePropertySerializerFactoryImpl.java │ │ └── TunablePropertySerializerImpl.java │ │ └── sync │ │ ├── DelegateTask.java │ │ ├── DelegatingTaskMonitor.java │ │ ├── LoggingTaskMonitor.java │ │ ├── SyncTaskManager.java │ │ ├── SyncTunableHandler.java │ │ ├── SyncTunableHandlerFactory.java │ │ ├── SyncTunableMutator.java │ │ ├── SyncTunableMutatorFactory.java │ │ ├── TunableRecorderManager.java │ │ └── TunableSetterImpl.java │ └── test │ └── java │ └── org │ └── cytoscape │ └── work │ └── internal │ ├── properties │ ├── Line.java │ ├── LotsOfTunables.java │ ├── Point.java │ ├── TunablePropertySerializerTest.java │ └── YesNoMaybe.java │ └── sync │ ├── DelegatingTaskMonitorTest.java │ ├── SyncTaskManagerTest.java │ ├── SyncTunableHandlerTest.java │ ├── SyncTunableMutatorTest.java │ ├── TunableHolder.java │ └── TunableSetterTest.java ├── work-swing-impl ├── impl │ ├── pom.xml │ └── src │ │ └── main │ │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── work │ │ │ └── internal │ │ │ ├── CyActivator.java │ │ │ ├── UndoSupportImpl.java │ │ │ ├── task │ │ │ ├── CyUserLogAppender.java │ │ │ ├── JDialogTaskManager.java │ │ │ ├── JPanelTaskManager.java │ │ │ ├── SwingTaskMonitor.java │ │ │ └── TaskHistory.java │ │ │ ├── tunables │ │ │ ├── AbstractNumberHandler.java │ │ │ ├── BooleanHandler.java │ │ │ ├── BoundedHandler.java │ │ │ ├── DoubleHandler.java │ │ │ ├── FileHandler.java │ │ │ ├── FileHandlerFactory.java │ │ │ ├── FloatHandler.java │ │ │ ├── IntegerHandler.java │ │ │ ├── JComboBoxDecorator.java │ │ │ ├── JDialogTunableMutator.java │ │ │ ├── JPanelTunableMutator.java │ │ │ ├── ListMultipleHandler.java │ │ │ ├── ListSingleHandler.java │ │ │ ├── LongHandler.java │ │ │ ├── StringHandler.java │ │ │ ├── URLHandler.java │ │ │ ├── URLHandlerFactory.java │ │ │ ├── UserActionHandler.java │ │ │ └── utils │ │ │ │ ├── CheckListCellRenderer.java │ │ │ │ ├── CheckListManager.java │ │ │ │ ├── ColorUtil.java │ │ │ │ ├── CyCardLayout.java │ │ │ │ ├── GUIDefaults.java │ │ │ │ ├── SimplePanel.java │ │ │ │ ├── StringUtil.java │ │ │ │ ├── SupportedFileTypesManager.java │ │ │ │ ├── TitledPanel.java │ │ │ │ ├── TunableBoundedField.java │ │ │ │ ├── TunableDialog.java │ │ │ │ ├── TunableSlider.java │ │ │ │ ├── ViewUtil.java │ │ │ │ └── XorPanel.java │ │ │ └── view │ │ │ ├── RoundedProgressBar.java │ │ │ ├── TaskDialog.java │ │ │ ├── TaskHistoryWindow.java │ │ │ ├── TaskMediator.java │ │ │ └── TaskStatusBar.java │ │ └── resources │ │ └── images │ │ └── open-file-24.png ├── it │ ├── pom.xml │ └── src │ │ └── test │ │ └── java │ │ └── org │ │ └── cytoscape │ │ └── work │ │ └── ServiceConfigurationTest.java └── pom.xml └── y-layouts.txt /.github/workflows/annual_copyright_update.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/.github/workflows/annual_copyright_update.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.settings.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/.travis.settings.xml -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/README.md -------------------------------------------------------------------------------- /app-impl/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/README.md -------------------------------------------------------------------------------- /app-impl/api-notes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/api-notes.txt -------------------------------------------------------------------------------- /app-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/pom.xml -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/action/CitationsAction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/action/CitationsAction.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/action/YFilesAction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/action/YFilesAction.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/event/AppsChangedEvent.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/event/AppsChangedEvent.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/manager/App.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/manager/App.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/manager/AppParser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppParser.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/manager/BundleApp.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/manager/BundleApp.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/manager/LaunchManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/manager/LaunchManager.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/manager/Range.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/manager/Range.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/manager/SimpleApp.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/manager/SimpleApp.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/manager/Version.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/manager/Version.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/net/DownloadStatus.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/net/DownloadStatus.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/net/ResultsFilterer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/net/ResultsFilterer.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/net/Update.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/net/Update.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/net/UpdateManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/net/UpdateManager.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/net/WebApp.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/net/WebApp.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/AbstractAppTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/AbstractAppTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/AppManagerTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/AppManagerTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/AppStoreTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/AppStoreTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/AppStoreTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/AppStoreTaskFactory.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/ChangeTabTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/ChangeTabTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/DisableTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/DisableTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/DisableTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/DisableTaskFactory.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/EnableTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/EnableTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/EnableTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/EnableTaskFactory.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/InformationTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/InformationTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/InstallAppsTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/InstallAppsTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/InstallTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/InstallTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/InstallTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/InstallTaskFactory.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/InstallUpdatesTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/InstallUpdatesTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/ListAppsTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/ListAppsTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/ListAppsTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/ListAppsTaskFactory.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/ListAvailableTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/ListAvailableTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/ListUpdatesTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/ListUpdatesTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/StatusTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/StatusTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/StatusTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/StatusTaskFactory.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/UninstallTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/UninstallTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/UpdateTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/UpdateTask.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/task/UpdateTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/task/UpdateTaskFactory.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerDialog.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerDialog.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerMediator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerMediator.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/ui/CitationsDialog.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/ui/CitationsDialog.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/util/AppHelper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/util/AppHelper.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/util/AppUtil.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/util/AppUtil.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/util/DebugHelper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/util/DebugHelper.java -------------------------------------------------------------------------------- /app-impl/src/main/java/org/cytoscape/app/internal/util/MiniTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/java/org/cytoscape/app/internal/util/MiniTest.java -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/AppManager.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/AppManager.html -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/adn-brands.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/adn-brands.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/adn-brands.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/adn-brands.svg -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/hamburger.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/hamburger.ai -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/hamburger.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/hamburger.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/logo.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/logo_mgr.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/logo_mgr.ai -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/logo_mgr_large.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/logo_mgr_large.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/search.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/search.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/tab.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/tab.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/trash.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/trash.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/trash2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/trash2.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/update1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/update1.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/update2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/update2.png -------------------------------------------------------------------------------- /app-impl/src/main/resources/AppManager/img/update_og.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/main/resources/AppManager/img/update_og.png -------------------------------------------------------------------------------- /app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java -------------------------------------------------------------------------------- /app-impl/src/test/java/org/cytoscape/app/internal/net/WebQuerierTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/test/java/org/cytoscape/app/internal/net/WebQuerierTest.java -------------------------------------------------------------------------------- /app-impl/src/test/java/org/cytoscape/app/internal/util/AppUtilTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/app-impl/src/test/java/org/cytoscape/app/internal/util/AppUtilTest.java -------------------------------------------------------------------------------- /application-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/application-impl/pom.xml -------------------------------------------------------------------------------- /command-executor-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/command-executor-impl/pom.xml -------------------------------------------------------------------------------- /core-task-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/pom.xml -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/export/ViewWriter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/export/ViewWriter.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/filter/Sink.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/filter/Sink.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupEdit.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupEdit.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/help/HelpTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/help/HelpTask.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/hide/HideEdit.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/hide/HideEdit.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/hide/HideTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/hide/HideTask.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/hide/HideUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/hide/HideUtils.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/hide/UnHideTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/hide/UnHideTask.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/select/SelectTask.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/table/AddRowTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/table/AddRowTask.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/table/GetRowTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/table/GetRowTask.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/table/SaveColumn.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/table/SaveColumn.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/utils/DataUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/utils/DataUtils.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/utils/EdgeTunable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/utils/EdgeTunable.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/utils/IconUtil.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/utils/IconUtil.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/utils/NodeTunable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/utils/NodeTunable.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/utils/RowTunable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/utils/RowTunable.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/zoom/ZoomEdit.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/zoom/ZoomEdit.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/zoom/ZoomInTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/zoom/ZoomInTask.java -------------------------------------------------------------------------------- /core-task-impl/src/main/java/org/cytoscape/task/internal/zoom/ZoomOutTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/java/org/cytoscape/task/internal/zoom/ZoomOutTask.java -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/apply-layout-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/apply-layout-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/export-img-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/export-img-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/export-net-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/export-net-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/export-table-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/export-table-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/first-neighbors-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/first-neighbors-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/help-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/help-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/hide-selected-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/hide-selected-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/import-net-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/import-net-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/import-net-url-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/import-net-url-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/import-table-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/import-table-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/import-table-url-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/import-table-url-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/new-from-selected-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/new-from-selected-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/open-file-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/open-file-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/save-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/save-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/show-all-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/show-all-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/zoom-fit-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/zoom-fit-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/zoom-in-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/zoom-in-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/zoom-out-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/zoom-out-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/icons/zoom-selected-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/icons/zoom-selected-32.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/logo.png -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/tooltips/apply-preferred-layout.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/tooltips/apply-preferred-layout.gif -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/tooltips/first-neighbors.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/tooltips/first-neighbors.gif -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/tooltips/fit-content.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/tooltips/fit-content.gif -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/tooltips/fit-selected.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/tooltips/fit-selected.gif -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/tooltips/show-hide.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/tooltips/show-hide.gif -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/tooltips/zoom-in.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/tooltips/zoom-in.gif -------------------------------------------------------------------------------- /core-task-impl/src/main/resources/images/tooltips/zoom-out.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/main/resources/images/tooltips/zoom-out.gif -------------------------------------------------------------------------------- /core-task-impl/src/test/java/org/cytoscape/task/internal/io/ViewWriterTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/test/java/org/cytoscape/task/internal/io/ViewWriterTest.java -------------------------------------------------------------------------------- /core-task-impl/src/test/java/org/cytoscape/task/internal/zoom/ZoomEditTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/test/java/org/cytoscape/task/internal/zoom/ZoomEditTest.java -------------------------------------------------------------------------------- /core-task-impl/src/test/resources/BIOGRID-ORGANISM-3.1.74.mitab.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/test/resources/BIOGRID-ORGANISM-3.1.74.mitab.zip -------------------------------------------------------------------------------- /core-task-impl/src/test/resources/bad_names.txt: -------------------------------------------------------------------------------- 1 | bart 2 | lisa 3 | maggie 4 | 5 | 6 | -------------------------------------------------------------------------------- /core-task-impl/src/test/resources/empty.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /core-task-impl/src/test/resources/node_names.txt: -------------------------------------------------------------------------------- 1 | homer 2 | marge 3 | -------------------------------------------------------------------------------- /core-task-impl/src/test/resources/test_session1.cys: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/core-task-impl/src/test/resources/test_session1.cys -------------------------------------------------------------------------------- /custom-graphics-internal/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/pom.xml -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/java/org/cytoscape/cg/model/BitmapLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/java/org/cytoscape/cg/model/BitmapLayer.java -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/java/org/cytoscape/cg/model/CGComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/java/org/cytoscape/cg/model/CGComparator.java -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/java/org/cytoscape/cg/model/ColorScheme.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/java/org/cytoscape/cg/model/ColorScheme.java -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/java/org/cytoscape/cg/model/IDGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/java/org/cytoscape/cg/model/IDGenerator.java -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/java/org/cytoscape/cg/model/Orientation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/java/org/cytoscape/cg/model/Orientation.java -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/java/org/cytoscape/cg/model/Rotation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/java/org/cytoscape/cg/model/Rotation.java -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/java/org/cytoscape/cg/model/SVGLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/java/org/cytoscape/cg/model/SVGLayer.java -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/java/org/cytoscape/cg/model/Taggable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/java/org/cytoscape/cg/model/Taggable.java -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/resources/images/charts/bar-chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/resources/images/charts/bar-chart.png -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/resources/images/charts/box-chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/resources/images/charts/box-chart.png -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/resources/images/charts/heatmap-chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/resources/images/charts/heatmap-chart.png -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/resources/images/charts/line-chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/resources/images/charts/line-chart.png -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/resources/images/charts/pie-chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/resources/images/charts/pie-chart.png -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/resources/images/charts/ring-chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/resources/images/charts/ring-chart.png -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/resources/images/drop-img-file-56.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/resources/images/drop-img-file-56.png -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/resources/images/no_image.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/resources/images/no_image.png -------------------------------------------------------------------------------- /custom-graphics-internal/src/main/resources/images/no_image.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/custom-graphics-internal/src/main/resources/images/no_image.svg -------------------------------------------------------------------------------- /cycl-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/pom.xml -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyActivator.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCL.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCL.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLBufferImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLBufferImpl.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLContextImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLContextImpl.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLDeviceImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLDeviceImpl.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLFactoryImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLFactoryImpl.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLKernelImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLKernelImpl.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLLocalSizeImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLLocalSizeImpl.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLPlatformImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLPlatformImpl.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLProgramImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLProgramImpl.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLSettingsTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLSettingsTask.java -------------------------------------------------------------------------------- /cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/java/org/cytoscape/cycl/internal/CyCLUtils.java -------------------------------------------------------------------------------- /cycl-impl/src/main/resources/Benchmark.cl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/cycl-impl/src/main/resources/Benchmark.cl -------------------------------------------------------------------------------- /datasource-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/datasource-impl/pom.xml -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/pom.xml -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/Label.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/Label.java -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/PrintLOD.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/PrintLOD.java -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/resources/images/about_icons.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/resources/images/about_icons.txt -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/resources/images/arrowIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/resources/images/arrowIcon.png -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/resources/images/boundedIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/resources/images/boundedIcon.png -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/resources/images/default_network.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/resources/images/default_network.png -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/resources/images/imageIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/resources/images/imageIcon.png -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/resources/images/no_image.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/resources/images/no_image.png -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/resources/images/no_image.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/resources/images/no_image.svg -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/resources/images/shapeIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/resources/images/shapeIcon.png -------------------------------------------------------------------------------- /ding-impl/ding-presentation-impl/src/main/resources/images/textIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/ding-presentation-impl/src/main/resources/images/textIcon.png -------------------------------------------------------------------------------- /ding-impl/performance-debug/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/performance-debug/pom.xml -------------------------------------------------------------------------------- /ding-impl/performance-debug/src/main/resources/testData/sif/A200-200.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/performance-debug/src/main/resources/testData/sif/A200-200.sif -------------------------------------------------------------------------------- /ding-impl/performance-debug/src/main/resources/testData/sif/A50-100.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/performance-debug/src/main/resources/testData/sif/A50-100.sif -------------------------------------------------------------------------------- /ding-impl/performance-debug/src/main/resources/testData/sif/A50-50.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/performance-debug/src/main/resources/testData/sif/A50-50.sif -------------------------------------------------------------------------------- /ding-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/ding-impl/pom.xml -------------------------------------------------------------------------------- /edge-bundler-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/edge-bundler-impl/pom.xml -------------------------------------------------------------------------------- /editor-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/pom.xml -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeEdit.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeEdit.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeTask.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNodeTaskFactory.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/ClipboardImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/ClipboardImpl.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/CopyTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/CopyTask.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/CopyTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/CopyTaskFactory.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/CutEdgeTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/CutEdgeTaskFactory.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/CutNodeTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/CutNodeTaskFactory.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/CutTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/CutTask.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/CutTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/CutTaskFactory.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/PasteEdit.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/PasteEdit.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/PasteTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/PasteTask.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/PasteTaskFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/PasteTaskFactory.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/RenameNodeEdit.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/RenameNodeEdit.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/RenameNodeTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/RenameNodeTask.java -------------------------------------------------------------------------------- /editor-impl/src/main/java/org/cytoscape/editor/internal/SIFInterpreterTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/java/org/cytoscape/editor/internal/SIFInterpreterTask.java -------------------------------------------------------------------------------- /editor-impl/src/main/resources/images/edge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/resources/images/edge.png -------------------------------------------------------------------------------- /editor-impl/src/main/resources/images/network.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/resources/images/network.png -------------------------------------------------------------------------------- /editor-impl/src/main/resources/images/node.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/main/resources/images/node.png -------------------------------------------------------------------------------- /editor-impl/src/test/java/org/cytoscape/editor/internal/ClipboardImplTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/editor-impl/src/test/java/org/cytoscape/editor/internal/ClipboardImplTest.java -------------------------------------------------------------------------------- /equations-functions-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-functions-impl/pom.xml -------------------------------------------------------------------------------- /equations-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/pom.xml -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/BooleanList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/BooleanList.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/Categories.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/Categories.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/CyActivator.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/DoubleList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/DoubleList.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/LongList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/LongList.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/StringList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/StringList.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/Token.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/Token.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/Tokeniser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/Tokeniser.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Abs.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Abs.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/And.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/And.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Cos.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Cos.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Exp.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Exp.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/If.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/If.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Len.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Len.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Ln.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Ln.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Log.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Log.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Max.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Max.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Mid.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Mid.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Min.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Min.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Mod.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Mod.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Not.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Not.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Now.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Now.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Nth.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Nth.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Or.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Or.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Pi.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Pi.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Sin.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Sin.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Sum.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Sum.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Tan.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Tan.java -------------------------------------------------------------------------------- /equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Var.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/Var.java -------------------------------------------------------------------------------- /equations-impl/src/test/java/org/cytoscape/equations/internal/LongListTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/equations-impl/src/test/java/org/cytoscape/equations/internal/LongListTest.java -------------------------------------------------------------------------------- /event-impl/impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/event-impl/impl/pom.xml -------------------------------------------------------------------------------- /event-impl/impl/src/main/java/org/cytoscape/event/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/event-impl/impl/src/main/java/org/cytoscape/event/internal/CyActivator.java -------------------------------------------------------------------------------- /event-impl/impl/src/main/resources/readme.txt: -------------------------------------------------------------------------------- 1 | Bundle resources go here 2 | -------------------------------------------------------------------------------- /event-impl/it/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/event-impl/it/pom.xml -------------------------------------------------------------------------------- /event-impl/it/src/test/java/org/cytoscape/event/ServiceConfigurationTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/event-impl/it/src/test/java/org/cytoscape/event/ServiceConfigurationTest.java -------------------------------------------------------------------------------- /event-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/event-impl/pom.xml -------------------------------------------------------------------------------- /filter-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/pom.xml -------------------------------------------------------------------------------- /filter-impl/src/main/java/org/cytoscape/filter/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/java/org/cytoscape/filter/internal/CyActivator.java -------------------------------------------------------------------------------- /filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterApp.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterApp.java -------------------------------------------------------------------------------- /filter-impl/src/main/resources/default_filters.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/default_filters.props -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/add.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/add.png -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/config.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/config.png -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/delete.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/delete.png -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/duplicate.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/duplicate.png -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/filter-small.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/filter-small.png -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/filter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/filter.png -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/minus.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/minus.gif -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/plus.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/plus.gif -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/properties.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/properties.png -------------------------------------------------------------------------------- /filter-impl/src/main/resources/images/rename.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter-impl/src/main/resources/images/rename.png -------------------------------------------------------------------------------- /filter2-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/pom.xml -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/ApplyCheck.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/ApplyCheck.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/CyActivator.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/CyNetworkSource.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/CyNetworkSource.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/FilterIO.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/FilterIO.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/ModelMonitor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/ModelMonitor.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/ModelUtil.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/ModelUtil.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/range/SliderModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/range/SliderModel.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/view/ComboItem.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/view/ComboItem.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/view/DragHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/view/DragHandler.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/view/FilterPanel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/view/FilterPanel.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/view/Handle.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/view/Handle.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/view/Matcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/view/Matcher.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/view/NamedElement.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/view/NamedElement.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/view/SelectPanel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/view/SelectPanel.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/view/ViewUtil.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/view/ViewUtil.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/work/FilterWorker.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/work/FilterWorker.java -------------------------------------------------------------------------------- /filter2-impl/src/main/java/org/cytoscape/filter/internal/work/LazyWorker.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/main/java/org/cytoscape/filter/internal/work/LazyWorker.java -------------------------------------------------------------------------------- /filter2-impl/src/test/java/org/cytoscape/filter/internal/ColumnFilterTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/test/java/org/cytoscape/filter/internal/ColumnFilterTest.java -------------------------------------------------------------------------------- /filter2-impl/src/test/java/org/cytoscape/filter/internal/DegreeFilterTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/test/java/org/cytoscape/filter/internal/DegreeFilterTest.java -------------------------------------------------------------------------------- /filter2-impl/src/test/java/org/cytoscape/filter/internal/UiScaffold.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/filter2-impl/src/test/java/org/cytoscape/filter/internal/UiScaffold.java -------------------------------------------------------------------------------- /graphml-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/pom.xml -------------------------------------------------------------------------------- /graphml-impl/src/main/java/org/cytoscape/io/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/main/java/org/cytoscape/io/internal/CyActivator.java -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/atted.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/atted.graphml -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/desc.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/desc.graphml -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/exptest.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/exptest.graphml -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/igraph_sample.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/igraph_sample.graphml -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/nested.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/nested.xml -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/nested2.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/nested2.xml -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/simple.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/simple.graphml -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/simpleWithAttributes.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/simpleWithAttributes.xml -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/testGraph1.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/testGraph1.xml -------------------------------------------------------------------------------- /graphml-impl/src/test/resources/yFilesSample.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/graphml-impl/src/test/resources/yFilesSample.xml -------------------------------------------------------------------------------- /group-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/pom.xml -------------------------------------------------------------------------------- /group-impl/src/main/java/org/cytoscape/group/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/main/java/org/cytoscape/group/internal/CyActivator.java -------------------------------------------------------------------------------- /group-impl/src/main/java/org/cytoscape/group/internal/CyGroupFactoryImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupFactoryImpl.java -------------------------------------------------------------------------------- /group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java -------------------------------------------------------------------------------- /group-impl/src/main/java/org/cytoscape/group/internal/CyGroupManagerImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupManagerImpl.java -------------------------------------------------------------------------------- /group-impl/src/main/java/org/cytoscape/group/internal/GroupIO.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/main/java/org/cytoscape/group/internal/GroupIO.java -------------------------------------------------------------------------------- /group-impl/src/main/java/org/cytoscape/group/internal/GroupUtil.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/main/java/org/cytoscape/group/internal/GroupUtil.java -------------------------------------------------------------------------------- /group-impl/src/main/java/org/cytoscape/group/internal/ModelUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/main/java/org/cytoscape/group/internal/ModelUtils.java -------------------------------------------------------------------------------- /group-impl/src/main/java/org/cytoscape/group/internal/view/ViewUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/main/java/org/cytoscape/group/internal/view/ViewUtils.java -------------------------------------------------------------------------------- /group-impl/src/test/java/org/cytoscape/group/CyGroupTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/test/java/org/cytoscape/group/CyGroupTest.java -------------------------------------------------------------------------------- /group-impl/src/test/java/org/cytoscape/group/GroupTestSupport.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/test/java/org/cytoscape/group/GroupTestSupport.java -------------------------------------------------------------------------------- /group-impl/src/test/java/org/cytoscape/group/TestCyGroupFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/group-impl/src/test/java/org/cytoscape/group/TestCyGroupFactory.java -------------------------------------------------------------------------------- /gui-cmdline-parser-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/gui-cmdline-parser-impl/pom.xml -------------------------------------------------------------------------------- /headless-application-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/headless-application-impl/pom.xml -------------------------------------------------------------------------------- /headless-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/headless-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java -------------------------------------------------------------------------------- /headless-cmdline-parser-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/headless-cmdline-parser-impl/pom.xml -------------------------------------------------------------------------------- /hotfix_create.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/hotfix_create.sh -------------------------------------------------------------------------------- /io-impl/impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/pom.xml -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CopyInputStream.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CopyInputStream.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLParser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLParser.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/KeyValue.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/KeyValue.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/Interaction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/Interaction.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/Handler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/Handler.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ParseState.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/ParseState.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/RDFTags.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/RDFTags.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SAXState.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SAXState.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/util/FilterIO.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/FilterIO.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadUtils.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/util/SUIDUpdater.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/SUIDUpdater.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/util/StreamUtilImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/StreamUtilImpl.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/util/xgmml/ObjectType.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/xgmml/ObjectType.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.javax: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.javax -------------------------------------------------------------------------------- /io-impl/impl/src/main/java/org/cytoscape/io/internal/write/sif/SifWriter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/sif/SifWriter.java -------------------------------------------------------------------------------- /io-impl/impl/src/main/resources/xsd/cysession.xsd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/resources/xsd/cysession.xsd -------------------------------------------------------------------------------- /io-impl/impl/src/main/resources/xsd/cytables.xsd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/resources/xsd/cytables.xsd -------------------------------------------------------------------------------- /io-impl/impl/src/main/resources/xsd/vizmap.xsd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/resources/xsd/vizmap.xsd -------------------------------------------------------------------------------- /io-impl/impl/src/main/resources/xsd/xlinks-2001.xsd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/main/resources/xsd/xlinks-2001.xsd -------------------------------------------------------------------------------- /io-impl/impl/src/test/java/org/cytoscape/io/internal/util/FilterIOTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/java/org/cytoscape/io/internal/util/FilterIOTest.java -------------------------------------------------------------------------------- /io-impl/impl/src/test/java/org/cytoscape/io/internal/util/SUIDUpdaterTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/java/org/cytoscape/io/internal/util/SUIDUpdaterTest.java -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/1000SmallNetworks.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/1000SmallNetworks.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/100SmallNetworks.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/100SmallNetworks.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/10LargeNetworks.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/10LargeNetworks.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/300SmallNetworks.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/300SmallNetworks.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/5Nested.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/5Nested.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/bad1.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/bad1.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/bad2.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/bad2.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/calc_network_size: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/calc_network_size -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/generate_multi_level_networks: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/generate_multi_level_networks -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/generate_networks: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/generate_networks -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/good1.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/good1.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/good2.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/good2.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/good3.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/good3.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/good4.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/good4.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/good5.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/good5.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/good6.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/good6.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/intermediate.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/intermediate.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/large.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/large.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/loop.nnf: -------------------------------------------------------------------------------- 1 | N1 N2 2 | N2 N1 3 | -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/loop1.nnf: -------------------------------------------------------------------------------- 1 | A B 2 | B A -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/small.nnf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/small.nnf -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/t3.cys: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/t3.cys -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/NNFData/t4.cys: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/NNFData/t4.cys -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/datatable/blank_delimiter.txt: -------------------------------------------------------------------------------- 1 | abc def ghi 2 | this won't parse 3 | nor will this 4 | -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/datatable/table_comma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/datatable/table_comma.txt -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/datatable/table_space.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/datatable/table_space.txt -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/datatable/table_tab.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/datatable/table_tab.txt -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/filter/topology-filter-3.2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/filter/topology-filter-3.2.json -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/gml/cy2_arrows.gml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/gml/cy2_arrows.gml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/gml/example-directed1.gml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/gml/example-directed1.gml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/gml/example-directed2.gml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/gml/example-directed2.gml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/gml/example1.gml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/gml/example1.gml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/gml/example2.gml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/gml/example2.gml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/gml/galFiltered_old.gml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/gml/galFiltered_old.gml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/gml/yed_arrows.gml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/gml/yed_arrows.gml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/sif/SIF-Japanese.sif: -------------------------------------------------------------------------------- 1 | これは 日本語の テストです 2 | 大野 test1 圭一朗 3 | mixed with English -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/sif/degenerate.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/sif/degenerate.sif -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/sif/multiWordProteins.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/sif/multiWordProteins.sif -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/sif/orphanFirst.sif: -------------------------------------------------------------------------------- 1 | YNL212W 2 | YNL314W pd YIR028W 3 | YPL111W 4 | -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/sif/typical.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/sif/typical.sif -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/vizmap/v240_vizmap.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/vizmap/v240_vizmap.props -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/vizmap/v252_vizmap.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/vizmap/v252_vizmap.props -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/vizmap/v270_vizmap.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/vizmap/v270_vizmap.props -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/vizmap/v283_vizmap.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/vizmap/v283_vizmap.props -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/INVALID.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/INVALID.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/bare_ampersands.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/bare_ampersands.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/empty.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/empty.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/empty_DTD.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/empty_DTD.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/galFiltered.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/galFiltered.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/group_2x_collapsed.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/group_2x_collapsed.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/group_2x_expanded.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/group_2x_expanded.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/hiddenAtt.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/hiddenAtt.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/listAtt.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/listAtt.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/nested_groups_283.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/nested_groups_283.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/simple.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/simple.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/simple_3.3.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/simple_3.3.xgmml -------------------------------------------------------------------------------- /io-impl/impl/src/test/resources/testData/xgmml/suid_metadata.xgmml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/impl/src/test/resources/testData/xgmml/suid_metadata.xgmml -------------------------------------------------------------------------------- /io-impl/performance/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/performance/pom.xml -------------------------------------------------------------------------------- /io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java -------------------------------------------------------------------------------- /io-impl/performance/src/main/resources/testData/sif/A200-200.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/performance/src/main/resources/testData/sif/A200-200.sif -------------------------------------------------------------------------------- /io-impl/performance/src/main/resources/testData/sif/A50-100.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/performance/src/main/resources/testData/sif/A50-100.sif -------------------------------------------------------------------------------- /io-impl/performance/src/main/resources/testData/sif/A50-50.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/performance/src/main/resources/testData/sif/A50-50.sif -------------------------------------------------------------------------------- /io-impl/performance/src/main/resources/testData/sif/biogrid-fly.sif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/performance/src/main/resources/testData/sif/biogrid-fly.sif -------------------------------------------------------------------------------- /io-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/io-impl/pom.xml -------------------------------------------------------------------------------- /jobs-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/jobs-impl/pom.xml -------------------------------------------------------------------------------- /jobs-impl/src/main/java/org/cytoscape/jobs/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/jobs-impl/src/main/java/org/cytoscape/jobs/internal/CyActivator.java -------------------------------------------------------------------------------- /jobs-impl/src/main/java/org/cytoscape/jobs/internal/CyJobManagerImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/jobs-impl/src/main/java/org/cytoscape/jobs/internal/CyJobManagerImpl.java -------------------------------------------------------------------------------- /jobs-impl/src/main/java/org/cytoscape/jobs/internal/GUICyJobMonitor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/jobs-impl/src/main/java/org/cytoscape/jobs/internal/GUICyJobMonitor.java -------------------------------------------------------------------------------- /jobs-impl/src/main/java/org/cytoscape/jobs/internal/GUIJobDialog.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/jobs-impl/src/main/java/org/cytoscape/jobs/internal/GUIJobDialog.java -------------------------------------------------------------------------------- /jobs-impl/src/main/java/org/cytoscape/jobs/internal/JobStatusBar.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/jobs-impl/src/main/java/org/cytoscape/jobs/internal/JobStatusBar.java -------------------------------------------------------------------------------- /jobs-impl/src/main/java/org/cytoscape/jobs/internal/SimpleCyJobMonitor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/jobs-impl/src/main/java/org/cytoscape/jobs/internal/SimpleCyJobMonitor.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/pom.xml -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/csapps/layout/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/csapps/layout/CyActivator.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/csapps/layout/Profile.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/csapps/layout/Profile.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/Cluster.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/Cluster.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/ClusterManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/ClusterManager.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/Clustered.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/Clustered.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/LEdge.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/LEdge.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/LGraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/LGraph.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/LGraphManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/LGraphManager.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/LGraphObject.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/LGraphObject.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/LNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/LNode.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/LNodeDegreeSort.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/LNodeDegreeSort.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/Layout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/Layout.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/LayoutConstants.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/LayoutConstants.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/LayoutOptionsPack.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/LayoutOptionsPack.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/ProgressListener.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/ProgressListener.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/Updatable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/Updatable.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSEConstants.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSEConstants.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSEEdge.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSEEdge.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSEGraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSEGraph.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSEGraphManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSEGraphManager.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSELayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSELayout.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSENode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoSENode.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoarseningEdge.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoarseningEdge.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoarseningGraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoarseningGraph.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoarseningNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/cose/CoarseningNode.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/fd/FDLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/fd/FDLayout.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/fd/FDLayoutConstants.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/fd/FDLayoutConstants.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/fd/FDLayoutEdge.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/fd/FDLayoutEdge.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/fd/FDLayoutNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/fd/FDLayoutNode.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/Compaction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/Compaction.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnPDConstants.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnPDConstants.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnPDEdge.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnPDEdge.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnPDLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnPDLayout.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnPDNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnPDNode.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnProcessNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/SbgnProcessNode.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/VisibilityEdge.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/VisibilityEdge.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/VisibilityGraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/sbgn/VisibilityGraph.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/util/ComparableNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/util/ComparableNode.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/util/GraphMLWriter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/util/GraphMLWriter.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/util/MemberPack.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/util/MemberPack.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/util/Organization.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/util/Organization.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/util/Polyomino.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/util/Polyomino.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/util/PolyominoPacking.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/util/PolyominoPacking.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/layout/util/RectProc.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/layout/util/RectProc.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/util/DimensionD.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/util/DimensionD.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/util/IGeometry.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/util/IGeometry.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/util/IMath.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/util/IMath.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/util/IndexedObjectSort.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/util/IndexedObjectSort.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/util/IntegerQuickSort.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/util/IntegerQuickSort.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/util/PointD.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/util/PointD.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/util/QuickSort.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/util/QuickSort.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/util/RectangleD.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/util/RectangleD.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/main/java/org/ivis/util/Transform.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/main/java/org/ivis/util/Transform.java -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/test/resources/circular-layout-tests/LUAD_vest_v2.cys: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/test/resources/circular-layout-tests/LUAD_vest_v2.cys -------------------------------------------------------------------------------- /layout-cytoscape-impl/src/test/resources/circular-layout-tests/goTrees.cys: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-cytoscape-impl/src/test/resources/circular-layout-tests/goTrees.cys -------------------------------------------------------------------------------- /layout-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-impl/pom.xml -------------------------------------------------------------------------------- /layout-impl/src/main/java/org/cytoscape/view/layout/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-impl/src/main/java/org/cytoscape/view/layout/internal/CyActivator.java -------------------------------------------------------------------------------- /layout-impl/src/test/java/org/cytoscape/view/layout/AbstractLayoutTaskTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-impl/src/test/java/org/cytoscape/view/layout/AbstractLayoutTaskTest.java -------------------------------------------------------------------------------- /layout-impl/src/test/java/org/cytoscape/view/layout/LayoutAlgorithmTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-impl/src/test/java/org/cytoscape/view/layout/LayoutAlgorithmTest.java -------------------------------------------------------------------------------- /layout-impl/src/test/java/org/cytoscape/view/layout/LayoutEdgeTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-impl/src/test/java/org/cytoscape/view/layout/LayoutEdgeTest.java -------------------------------------------------------------------------------- /layout-impl/src/test/java/org/cytoscape/view/layout/LayoutNodeTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-impl/src/test/java/org/cytoscape/view/layout/LayoutNodeTest.java -------------------------------------------------------------------------------- /layout-impl/src/test/java/org/cytoscape/view/layout/LayoutPartitionTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-impl/src/test/java/org/cytoscape/view/layout/LayoutPartitionTest.java -------------------------------------------------------------------------------- /layout-impl/src/test/java/org/cytoscape/view/layout/LayoutTaskTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-impl/src/test/java/org/cytoscape/view/layout/LayoutTaskTest.java -------------------------------------------------------------------------------- /layout-impl/src/test/java/org/cytoscape/view/layout/PartitionUtilTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-impl/src/test/java/org/cytoscape/view/layout/PartitionUtilTest.java -------------------------------------------------------------------------------- /layout-jgraph-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-jgraph-impl/pom.xml -------------------------------------------------------------------------------- /layout-jgraph-impl/src/main/java/csapps/layout/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-jgraph-impl/src/main/java/csapps/layout/CyActivator.java -------------------------------------------------------------------------------- /layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapper.java -------------------------------------------------------------------------------- /layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapperTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapperTask.java -------------------------------------------------------------------------------- /layout-prefuse-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/pom.xml -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/AbstractForce.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/AbstractForce.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/CircularWallForce.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/CircularWallForce.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/DragForce.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/DragForce.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/EulerIntegrator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/EulerIntegrator.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/Force.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/Force.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/ForceItem.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/ForceItem.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/ForceSimulator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/ForceSimulator.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/GravitationalForce.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/GravitationalForce.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/Integrator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/Integrator.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/NBodyForce.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/NBodyForce.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/RungeKuttaIntegrator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/RungeKuttaIntegrator.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/Spring.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/Spring.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/SpringForce.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/SpringForce.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/StateMonitor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/StateMonitor.java -------------------------------------------------------------------------------- /layout-prefuse-impl/src/main/java/prefuse/util/force/WallForce.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/layout-prefuse-impl/src/main/java/prefuse/util/force/WallForce.java -------------------------------------------------------------------------------- /linkout-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/linkout-impl/pom.xml -------------------------------------------------------------------------------- /linkout-impl/src/main/java/org/cytoscape/linkout/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/linkout-impl/src/main/java/org/cytoscape/linkout/internal/CyActivator.java -------------------------------------------------------------------------------- /linkout-impl/src/main/java/org/cytoscape/linkout/internal/DynamicSupport.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/linkout-impl/src/main/java/org/cytoscape/linkout/internal/DynamicSupport.java -------------------------------------------------------------------------------- /linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkOut.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkOut.java -------------------------------------------------------------------------------- /linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkoutTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkoutTask.java -------------------------------------------------------------------------------- /linkout-impl/src/main/java/org/cytoscape/linkout/internal/PropsReader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/linkout-impl/src/main/java/org/cytoscape/linkout/internal/PropsReader.java -------------------------------------------------------------------------------- /linkout-impl/src/main/resources/linkout.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/linkout-impl/src/main/resources/linkout.props -------------------------------------------------------------------------------- /log-swing-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/pom.xml -------------------------------------------------------------------------------- /log-swing-impl/src/main/java/org/cytoscape/log/internal/AppenderToQueue.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/java/org/cytoscape/log/internal/AppenderToQueue.java -------------------------------------------------------------------------------- /log-swing-impl/src/main/java/org/cytoscape/log/internal/ConsoleDialog.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/java/org/cytoscape/log/internal/ConsoleDialog.java -------------------------------------------------------------------------------- /log-swing-impl/src/main/java/org/cytoscape/log/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/java/org/cytoscape/log/internal/CyActivator.java -------------------------------------------------------------------------------- /log-swing-impl/src/main/java/org/cytoscape/log/internal/CyStatusBar.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/java/org/cytoscape/log/internal/CyStatusBar.java -------------------------------------------------------------------------------- /log-swing-impl/src/main/java/org/cytoscape/log/internal/LogViewer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/java/org/cytoscape/log/internal/LogViewer.java -------------------------------------------------------------------------------- /log-swing-impl/src/main/java/org/cytoscape/log/internal/QueueProcesser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/java/org/cytoscape/log/internal/QueueProcesser.java -------------------------------------------------------------------------------- /log-swing-impl/src/main/java/org/cytoscape/log/internal/UserMessagesDialog.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/java/org/cytoscape/log/internal/UserMessagesDialog.java -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/LICENSE.txt -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/README-ICONS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/README-ICONS -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/console-debug.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/console-debug.png -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/console-error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/console-error.png -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/console-info.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/console-info.png -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/console-warn.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/console-warn.png -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/console.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/console.png -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/consoledialogbase.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/consoledialogbase.html -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/logConsole.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/logConsole.png -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/status-bar-debug.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/status-bar-debug.png -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/status-bar-error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/status-bar-error.png -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/status-bar-info.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/status-bar-info.png -------------------------------------------------------------------------------- /log-swing-impl/src/main/resources/status-bar-warn.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/main/resources/status-bar-warn.png -------------------------------------------------------------------------------- /log-swing-impl/src/test/java/org/cytoscape/log/internal/LogViewerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/log-swing-impl/src/test/java/org/cytoscape/log/internal/LogViewerTest.java -------------------------------------------------------------------------------- /manual-layout-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/pom.xml -------------------------------------------------------------------------------- /manual-layout-impl/src/main/java/org/cytoscape/math/xform/AxisRotation3D.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/java/org/cytoscape/math/xform/AxisRotation3D.java -------------------------------------------------------------------------------- /manual-layout-impl/src/main/java/org/cytoscape/math/xform/Matrix4x4.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/java/org/cytoscape/math/xform/Matrix4x4.java -------------------------------------------------------------------------------- /manual-layout-impl/src/main/java/org/cytoscape/math/xform/Point3D.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/java/org/cytoscape/math/xform/Point3D.java -------------------------------------------------------------------------------- /manual-layout-impl/src/main/java/org/cytoscape/math/xform/Scale3D.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/java/org/cytoscape/math/xform/Scale3D.java -------------------------------------------------------------------------------- /manual-layout-impl/src/main/java/org/cytoscape/math/xform/Transformation3D.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/java/org/cytoscape/math/xform/Transformation3D.java -------------------------------------------------------------------------------- /manual-layout-impl/src/main/java/org/cytoscape/math/xform/Translation3D.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/java/org/cytoscape/math/xform/Translation3D.java -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/H_ALIGN_CENTER.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/H_ALIGN_CENTER.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/H_ALIGN_LEFT.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/H_ALIGN_LEFT.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/H_ALIGN_RIGHT.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/H_ALIGN_RIGHT.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/H_DIST_CENTER.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/H_DIST_CENTER.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/H_DIST_LEFT.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/H_DIST_LEFT.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/H_DIST_RIGHT.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/H_DIST_RIGHT.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/H_STACK_BOTTOM.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/H_STACK_BOTTOM.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/H_STACK_CENTER.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/H_STACK_CENTER.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/H_STACK_TOP.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/H_STACK_TOP.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/V_ALIGN_BOTTOM.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/V_ALIGN_BOTTOM.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/V_ALIGN_CENTER.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/V_ALIGN_CENTER.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/V_ALIGN_TOP.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/V_ALIGN_TOP.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/V_DIST_BOTTOM.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/V_DIST_BOTTOM.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/V_DIST_CENTER.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/V_DIST_CENTER.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/V_DIST_TOP.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/V_DIST_TOP.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/V_STACK_CENTER.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/V_STACK_CENTER.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/V_STACK_LEFT.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/V_STACK_LEFT.gif -------------------------------------------------------------------------------- /manual-layout-impl/src/main/resources/images/V_STACK_RIGHT.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/manual-layout-impl/src/main/resources/images/V_STACK_RIGHT.gif -------------------------------------------------------------------------------- /model-impl/impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/pom.xml -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyActivator.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/CyColumnImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyColumnImpl.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/CyEdgeImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyEdgeImpl.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/CyListImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyListImpl.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumn.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumn.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/java/org/cytoscape/model/internal/WeakMapList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/main/java/org/cytoscape/model/internal/WeakMapList.java -------------------------------------------------------------------------------- /model-impl/impl/src/main/resources/readme.txt: -------------------------------------------------------------------------------- 1 | Bundle resources go here 2 | -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/CyColumnTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/CyColumnTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/CyEdgeTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/CyEdgeTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/CyIdentifiableTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/CyIdentifiableTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkAutoDeleteTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkAutoDeleteTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/CyNetworkTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/CyNodeTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/CyNodeTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/CyTableUtilTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/CyTableUtilTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/EquationTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/EquationTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/GraphObjectTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/GraphObjectTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/NamespaceTableTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/NamespaceTableTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupportTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupportTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/TableTestSupport.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/TableTestSupport.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/TableTestSupportTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/TableTestSupportTest.java -------------------------------------------------------------------------------- /model-impl/impl/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/impl/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java -------------------------------------------------------------------------------- /model-impl/it/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/it/pom.xml -------------------------------------------------------------------------------- /model-impl/it/src/test/java/org/cytoscape/model/ServiceConfigurationTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/it/src/test/java/org/cytoscape/model/ServiceConfigurationTest.java -------------------------------------------------------------------------------- /model-impl/performance-debug/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/performance-debug/pom.xml -------------------------------------------------------------------------------- /model-impl/performance-debug/src/main/java/org/cytoscape/model/PerfTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/performance-debug/src/main/java/org/cytoscape/model/PerfTest.java -------------------------------------------------------------------------------- /model-impl/performance/baseline.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/performance/baseline.xml -------------------------------------------------------------------------------- /model-impl/performance/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/performance/pom.xml -------------------------------------------------------------------------------- /model-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/pom.xml -------------------------------------------------------------------------------- /model-impl/table-performance-debug/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/model-impl/table-performance-debug/pom.xml -------------------------------------------------------------------------------- /pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/pom.xml -------------------------------------------------------------------------------- /presentation-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/presentation-impl/pom.xml -------------------------------------------------------------------------------- /property-impl/.springBeans: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/property-impl/.springBeans -------------------------------------------------------------------------------- /property-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/property-impl/pom.xml -------------------------------------------------------------------------------- /property-impl/src/main/java/org/cytoscape/property/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/property-impl/src/main/java/org/cytoscape/property/internal/CyActivator.java -------------------------------------------------------------------------------- /property-impl/src/main/java/org/cytoscape/property/internal/PropsReader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/property-impl/src/main/java/org/cytoscape/property/internal/PropsReader.java -------------------------------------------------------------------------------- /property-impl/src/main/resources/bookmarks.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/property-impl/src/main/resources/bookmarks.xml -------------------------------------------------------------------------------- /property-impl/src/main/resources/cytoscape3.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/property-impl/src/main/resources/cytoscape3.props -------------------------------------------------------------------------------- /search2-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/search2-impl/pom.xml -------------------------------------------------------------------------------- /search2-impl/src/main/java/org/cytoscape/search/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/search2-impl/src/main/java/org/cytoscape/search/internal/CyActivator.java -------------------------------------------------------------------------------- /search2-impl/src/main/java/org/cytoscape/search/internal/index/Index.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/search2-impl/src/main/java/org/cytoscape/search/internal/index/Index.java -------------------------------------------------------------------------------- /search2-impl/src/main/java/org/cytoscape/search/internal/index/TableType.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/search2-impl/src/main/java/org/cytoscape/search/internal/index/TableType.java -------------------------------------------------------------------------------- /search2-impl/src/main/java/org/cytoscape/search/internal/search/SearchTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/search2-impl/src/main/java/org/cytoscape/search/internal/search/SearchTask.java -------------------------------------------------------------------------------- /search2-impl/src/main/java/org/cytoscape/search/internal/ui/SearchBox.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/search2-impl/src/main/java/org/cytoscape/search/internal/ui/SearchBox.java -------------------------------------------------------------------------------- /search2-impl/src/test/java/org/cytoscape/search/internal/LogSilenceRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/search2-impl/src/test/java/org/cytoscape/search/internal/LogSilenceRule.java -------------------------------------------------------------------------------- /search2-impl/src/test/java/org/cytoscape/search/internal/index/QueryTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/search2-impl/src/test/java/org/cytoscape/search/internal/index/QueryTest.java -------------------------------------------------------------------------------- /session-impl/impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/session-impl/impl/pom.xml -------------------------------------------------------------------------------- /session-impl/integration-test/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/session-impl/integration-test/pom.xml -------------------------------------------------------------------------------- /session-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/session-impl/pom.xml -------------------------------------------------------------------------------- /session-impl/src/main/java/org/cytoscape/session/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/session-impl/src/main/java/org/cytoscape/session/internal/CyActivator.java -------------------------------------------------------------------------------- /swing-application-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/pom.xml -------------------------------------------------------------------------------- /swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java -------------------------------------------------------------------------------- /swing-application-impl/src/main/java/org/cytoscape/internal/MacCyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/java/org/cytoscape/internal/MacCyActivator.java -------------------------------------------------------------------------------- /swing-application-impl/src/main/java/org/cytoscape/internal/SessionHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/java/org/cytoscape/internal/SessionHandler.java -------------------------------------------------------------------------------- /swing-application-impl/src/main/java/org/cytoscape/internal/util/Util.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/java/org/cytoscape/internal/util/Util.java -------------------------------------------------------------------------------- /swing-application-impl/src/main/resources/images/about.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/resources/images/about.svg -------------------------------------------------------------------------------- /swing-application-impl/src/main/resources/images/drop-net-file-56.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/resources/images/drop-net-file-56.png -------------------------------------------------------------------------------- /swing-application-impl/src/main/resources/images/logo-light-96.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/resources/images/logo-light-96.png -------------------------------------------------------------------------------- /swing-application-impl/src/main/resources/images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/resources/images/logo.png -------------------------------------------------------------------------------- /swing-application-impl/src/main/resources/images/python-logo.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/resources/images/python-logo.svg -------------------------------------------------------------------------------- /swing-application-impl/src/main/resources/images/r-logo.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/resources/images/r-logo.svg -------------------------------------------------------------------------------- /swing-application-impl/src/main/resources/toolbar.stoplist: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /swing-application-impl/src/main/resources/xsd/networkList.xsd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/resources/xsd/networkList.xsd -------------------------------------------------------------------------------- /swing-application-impl/src/main/resources/xsd/sessionState.xsd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-application-impl/src/main/resources/xsd/sessionState.xsd -------------------------------------------------------------------------------- /swing-util-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-util-impl/pom.xml -------------------------------------------------------------------------------- /swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/Help.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/Help.java -------------------------------------------------------------------------------- /swing-util-impl/src/main/resources/fonts/cytoscape-3.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-util-impl/src/main/resources/fonts/cytoscape-3.ttf -------------------------------------------------------------------------------- /swing-util-impl/src/main/resources/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/swing-util-impl/src/main/resources/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /table-browser-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/pom.xml -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/about_icon.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/about_icon.txt -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/datatype_boolean2_16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/datatype_boolean2_16.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/datatype_boolean_16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/datatype_boolean_16.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/datatype_float_double_16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/datatype_float_double_16.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/datatype_int_16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/datatype_int_16.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/datatype_list_16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/datatype_list_16.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/datatype_string_16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/datatype_string_16.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/decimalDecrease.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/decimalDecrease.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/decimalIncrease.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/decimalIncrease.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/drop-table-file-56.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/drop-table-file-56.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/fx.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/fx.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/primary_key.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/primary_key.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/select_all.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/select_all.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/stock_delete.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/stock_delete.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/stock_insert-columns.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/stock_insert-columns.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/stock_new.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/stock_new.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/stock_open.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/stock_open.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/stock_select-row.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/stock_select-row.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/table-gear-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/table-gear-icon.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/table-select-column-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/table-select-column-icon.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/table_delete.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/table_delete.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/table_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/table_map.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/table_selection_mode.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/table_selection_mode.png -------------------------------------------------------------------------------- /table-browser-impl/src/main/resources/images/unselect_all.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-browser-impl/src/main/resources/images/unselect_all.png -------------------------------------------------------------------------------- /table-import-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-import-impl/pom.xml -------------------------------------------------------------------------------- /table-import-impl/src/main/resources/images/ximian/stock_3d-light-on-16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-import-impl/src/main/resources/images/ximian/stock_3d-light-on-16.png -------------------------------------------------------------------------------- /table-import-impl/src/main/resources/images/ximian/stock_internet-16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-import-impl/src/main/resources/images/ximian/stock_internet-16.png -------------------------------------------------------------------------------- /table-import-impl/src/main/resources/tax_report.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-import-impl/src/main/resources/tax_report.txt -------------------------------------------------------------------------------- /table-import-impl/src/test/resources/dummy_obo.obo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-import-impl/src/test/resources/dummy_obo.obo -------------------------------------------------------------------------------- /table-import-impl/src/test/resources/gene_association.sgd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-import-impl/src/test/resources/gene_association.sgd -------------------------------------------------------------------------------- /table-import-impl/src/test/resources/gene_ontology_ext.obo.obo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-import-impl/src/test/resources/gene_ontology_ext.obo.obo -------------------------------------------------------------------------------- /table-import-impl/src/test/resources/goslim_generic.obo.obo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-import-impl/src/test/resources/goslim_generic.obo.obo -------------------------------------------------------------------------------- /table-import-impl/src/test/resources/goslim_yeast.obo.obo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-import-impl/src/test/resources/goslim_yeast.obo.obo -------------------------------------------------------------------------------- /table-presentation-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-presentation-impl/pom.xml -------------------------------------------------------------------------------- /table-presentation-impl/src/main/resources/fonts/jsMath-cmti10.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-presentation-impl/src/main/resources/fonts/jsMath-cmti10.ttf -------------------------------------------------------------------------------- /table-presentation-impl/src/main/resources/images/sparklines/bar-chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-presentation-impl/src/main/resources/images/sparklines/bar-chart.png -------------------------------------------------------------------------------- /table-presentation-impl/src/main/resources/images/sparklines/line-chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-presentation-impl/src/main/resources/images/sparklines/line-chart.png -------------------------------------------------------------------------------- /table-presentation-impl/src/main/resources/images/sparklines/pie-chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/table-presentation-impl/src/main/resources/images/sparklines/pie-chart.png -------------------------------------------------------------------------------- /util-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/util-impl/pom.xml -------------------------------------------------------------------------------- /util-impl/src/main/java/org/cytoscape/util/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/util-impl/src/main/java/org/cytoscape/util/internal/CyActivator.java -------------------------------------------------------------------------------- /util-impl/src/main/java/org/cytoscape/util/internal/color/ColorBrewer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/util-impl/src/main/java/org/cytoscape/util/internal/color/ColorBrewer.java -------------------------------------------------------------------------------- /util-impl/src/main/java/org/cytoscape/util/internal/color/Viridis.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/util-impl/src/main/java/org/cytoscape/util/internal/color/Viridis.java -------------------------------------------------------------------------------- /viewmodel-impl/impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/viewmodel-impl/impl/pom.xml -------------------------------------------------------------------------------- /viewmodel-impl/impl/src/main/javadoc/org/cytoscape/viewmodel/package.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/viewmodel-impl/impl/src/main/javadoc/org/cytoscape/viewmodel/package.html -------------------------------------------------------------------------------- /viewmodel-impl/impl/src/test/resources/log4j.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/viewmodel-impl/impl/src/test/resources/log4j.properties -------------------------------------------------------------------------------- /viewmodel-impl/it/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/viewmodel-impl/it/pom.xml -------------------------------------------------------------------------------- /viewmodel-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/viewmodel-impl/pom.xml -------------------------------------------------------------------------------- /vizmap-gui-core-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-gui-core-impl/pom.xml -------------------------------------------------------------------------------- /vizmap-gui-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-gui-impl/pom.xml -------------------------------------------------------------------------------- /vizmap-gui-impl/src/main/resources/default_vizmap.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-gui-impl/src/main/resources/default_vizmap.xml -------------------------------------------------------------------------------- /vizmap-gui-impl/src/main/resources/images/decimalDecrease.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-gui-impl/src/main/resources/images/decimalDecrease.png -------------------------------------------------------------------------------- /vizmap-gui-impl/src/main/resources/images/decimalIncrease.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-gui-impl/src/main/resources/images/decimalIncrease.png -------------------------------------------------------------------------------- /vizmap-gui-impl/src/main/resources/vizmapper.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-gui-impl/src/main/resources/vizmapper.props -------------------------------------------------------------------------------- /vizmap-impl/impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-impl/impl/pom.xml -------------------------------------------------------------------------------- /vizmap-impl/impl/src/main/javadoc/org/cytoscape/vizmap/events/package.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-impl/impl/src/main/javadoc/org/cytoscape/vizmap/events/package.html -------------------------------------------------------------------------------- /vizmap-impl/impl/src/main/javadoc/org/cytoscape/vizmap/package.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-impl/impl/src/main/javadoc/org/cytoscape/vizmap/package.html -------------------------------------------------------------------------------- /vizmap-impl/impl/src/main/resources/cross_browser_color_code.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-impl/impl/src/main/resources/cross_browser_color_code.txt -------------------------------------------------------------------------------- /vizmap-impl/impl/src/test/resources/log4j.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-impl/impl/src/test/resources/log4j.properties -------------------------------------------------------------------------------- /vizmap-impl/it/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-impl/it/pom.xml -------------------------------------------------------------------------------- /vizmap-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/vizmap-impl/pom.xml -------------------------------------------------------------------------------- /webservice-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/webservice-impl/pom.xml -------------------------------------------------------------------------------- /webservice-impl/src/main/resources/images/icons/import-net-db-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/webservice-impl/src/main/resources/images/icons/import-net-db-32.png -------------------------------------------------------------------------------- /work-headless-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-headless-impl/pom.xml -------------------------------------------------------------------------------- /work-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-impl/pom.xml -------------------------------------------------------------------------------- /work-impl/src/main/java/org/cytoscape/work/internal/CyActivator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-impl/src/main/java/org/cytoscape/work/internal/CyActivator.java -------------------------------------------------------------------------------- /work-impl/src/main/java/org/cytoscape/work/internal/sync/DelegateTask.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-impl/src/main/java/org/cytoscape/work/internal/sync/DelegateTask.java -------------------------------------------------------------------------------- /work-impl/src/test/java/org/cytoscape/work/internal/properties/Line.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-impl/src/test/java/org/cytoscape/work/internal/properties/Line.java -------------------------------------------------------------------------------- /work-impl/src/test/java/org/cytoscape/work/internal/properties/Point.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-impl/src/test/java/org/cytoscape/work/internal/properties/Point.java -------------------------------------------------------------------------------- /work-impl/src/test/java/org/cytoscape/work/internal/sync/TunableHolder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-impl/src/test/java/org/cytoscape/work/internal/sync/TunableHolder.java -------------------------------------------------------------------------------- /work-swing-impl/impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-swing-impl/impl/pom.xml -------------------------------------------------------------------------------- /work-swing-impl/impl/src/main/resources/images/open-file-24.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-swing-impl/impl/src/main/resources/images/open-file-24.png -------------------------------------------------------------------------------- /work-swing-impl/it/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-swing-impl/it/pom.xml -------------------------------------------------------------------------------- /work-swing-impl/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/work-swing-impl/pom.xml -------------------------------------------------------------------------------- /y-layouts.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/cytoscape-impl/HEAD/y-layouts.txt --------------------------------------------------------------------------------