├── .coveralls.yml ├── .gitignore ├── .travis.yml ├── LICENSE.txt ├── README.md ├── docs └── images │ ├── logo.ai │ ├── logo.png │ └── logo300.png ├── examples ├── R │ └── README.md ├── javascript │ └── README.md └── python │ ├── README.md │ └── basic │ ├── .ipynb_checkpoints │ ├── CytoscapeREST_Basic1-checkpoint.ipynb │ └── CytoscapeREST_Basic2-checkpoint.ipynb │ ├── CytoscapeREST_Basic1.ipynb │ ├── CytoscapeREST_Basic2.ipynb │ ├── cytoscape │ ├── __init__.py │ ├── __init__.pyc │ ├── arbor.js │ ├── cyjs.pyc │ ├── loader.js │ ├── main.pyc │ ├── template.html │ ├── viewer.py │ └── viewer.pyc │ └── sample_data │ └── yeast_network.json ├── pom.xml └── src ├── main └── java │ └── org │ └── cytoscape │ └── rest │ └── internal │ ├── CyActivator.java │ ├── EdgeBundler.java │ ├── EncodingUtil.java │ ├── GraphicsWriterManager.java │ ├── MappingFactoryManager.java │ ├── TaskFactoryManager.java │ ├── TaskFactoryManagerImpl.java │ ├── commands │ ├── handlers │ │ ├── MessageHandler.java │ │ ├── TextHTMLHandler.java │ │ └── TextPlainHandler.java │ └── resources │ │ └── CommandResource.java │ ├── datamapper │ ├── GroupMapper.java │ ├── MapperUtil.java │ ├── TableMapper.java │ ├── VisualStyleMapper.java │ └── package-info.java │ ├── model │ ├── CyJsNetwork.java │ ├── CytoscapeVersion.java │ ├── Edge.java │ ├── EdgeData.java │ ├── Elements.java │ ├── MemoryStatus.java │ ├── NetworkData.java │ ├── Node.java │ ├── NodeData.java │ └── ServerStatus.java │ ├── reader │ ├── EdgeListReader.java │ ├── EdgeListReaderFactory.java │ ├── EdgeTableReader.java │ └── package-info.java │ ├── resource │ ├── AbstractResource.java │ ├── AlgorithmicResource.java │ ├── CyExceptionMapper.java │ ├── GlobalTableResource.java │ ├── GroupResource.java │ ├── JsonTags.java │ ├── MiscResource.java │ ├── NetworkFullResource.java │ ├── NetworkNameResource.java │ ├── NetworkResource.java │ ├── NetworkViewResource.java │ ├── RootResource.java │ ├── SessionResource.java │ ├── StyleResource.java │ ├── TableResource.java │ ├── UIResource.java │ └── package-info.java │ ├── serializer │ ├── ContinuousMappingSerializer.java │ ├── CyTableSerializer.java │ ├── DiscreteMappingSerializer.java │ ├── GraphObjectSerializer.java │ ├── GroupModule.java │ ├── GroupSerializer.java │ ├── PassthroughMappingSerializer.java │ ├── RowSerializer.java │ ├── TableModule.java │ ├── TableSerializer.java │ ├── VisualMappingsSerializer.java │ ├── VisualStyleModule.java │ ├── VisualStyleSerializer.java │ └── package-info.java │ └── task │ ├── CyBinder.java │ ├── GrizzlyServerManager.java │ └── HeadlessTaskMonitor.java └── test ├── java └── org │ └── cytoscape │ └── rest │ ├── JSONTranslatorTest.java │ ├── NetworkMapperTest.java │ ├── TableMapperTest.java │ ├── TableModuleTest.java │ ├── inetrnal │ └── reader │ │ └── EdgeListReaderTest.java │ └── service │ ├── AlgorithmicResourceTest.java │ ├── BasicResourceTest.java │ ├── GlobalResourceTest.java │ ├── GroupTest.java │ ├── NetworkDataServiceTest.java │ ├── NetworkNameResourceTest.java │ ├── NetworkResourceDeletionTest.java │ ├── NetworkResourceTest.java │ ├── NetworkViewResourceTest.java │ ├── RootTest.java │ ├── SessionResourceTest.java │ ├── StyleResourceTest.java │ ├── TableResourceTest.java │ └── UiResourceTest.java └── resources ├── galFiltered.cyjs ├── json └── galFiltered.json ├── net10k.txt ├── node_test.js ├── small.el └── table_test.js /.coveralls.yml: -------------------------------------------------------------------------------- 1 | service_name: travis-ci 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | target 2 | .project 3 | .DS_Store 4 | .classpath 5 | .settings -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 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