The CCD Annotations plugin works by importing or exporting annotated networks. When disabled, users can still have their annotations relayouted byĬlicking Layout -> Relayout CCD Annotations. This can be enabled or disabled by clicking the Automatic CCD Annotation Relayout button This is called Automatic Annotation Relayouting. When a network component is moved, associated annotations are re-layouted to maintain a Newly created annotations are placed relative to the components which they are annotating. They want the search results to return the union (default) of annotations across the set of When searching for annotations over a subset of nodes and/or edges, users can choose whether Simply choose the Selected option and select Graph to a sub-graph of selected components. Clicking on a search result will highlight and select theĪdditionally, the search scope can be narrowed from all of the nodes and edges of a Users can search via annotation name and description, then choose to further filter Searching for annotations is done in the Search tab of the CCD Annotations panel. If Automatic CCD Annotation Relayout is enabled. Annotations can be moved, but will be re-positioned When a new annotation is created, it is positioned relative to its associated graphĬomponents using their average location. Of nodes and/or edges from the network and click the Create button to generate the annotation.Īt least one network component is required. Once an annotation is chosen and a value is provided, select a set Users can select from a list of pre-existing annotations in which they provide the value orĬreate a new annotation. This panel contains most of the functionality of the app, including creation, search,Ĭreating an annotation is done in the Create tab of the CCD Annotations panel. The CCD Annotations app provides a panel in Cytoscape's left Control Panel. The aforementioned views appear in the storageĮngine of the plugin and on import/export functionality of Cytoscape. The Semantic view is responsible for annotation, search, filter actions, inĪgreement with Cytoscape's OSGi specifications. The Visualization view is responsible for rendering an annotation on a networkĪnd is mostly handled by Cytoscape's visualization engine. Notion of an annotations: the Visualization and the Semantic view. Also, the user can search, filter, and sort annotations based onĬCD-annotation-plugin follows a dual level In detail, by using this plugin a user is able to connect annotations with The goal of this plugin is to extend Cytoscape's annotating capabilities. Restart Cytoscape for the changes to take effect.Locate the build directory and select the jar file ccd-annotations-cytoscape-X.X.X.jar.Open the App Manager via Apps -> App Manager. ![]() If Cytoscape is open, you must restart it for the changes to take effect.Copy the jar file to the $CYTOSCAPE_HOME/apps/ directory.Locate your Cytoscape installation directory ( $CYTOSCAPE_HOME).Locate the jar file ccd-annotations-cytoscape-X.X.X.jar in the target/ directory.Mvn clean package (add option -DskipTests to skip unit tests) Install Cytoscape Apps Directory (Recommended) This app aims to bring CCD annotations to Cytoscape.
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