Examples with GeneAssociationReader org.cytoscape.tableimport.internal.reader.ontology.GeneAssociationReader used on opensource projects

Example 1 with GeneAssociationReader

use of org.cytoscape.tableimport.internal.reader.ontology.GeneAssociationReader in project cytoscape-impl by cytoscape.

the class ImportOntologyAndAnnotationTask method run.

@Override
public void run(TaskMonitor tm) throws Exception {
    tm.setTitle("Importing ontology and annotations");
    tm.setStatusMessage("Loading Ontology...");
    tm.setProgress(-1d);
    final CyNetworkReader loadOBOTask = (CyNetworkReader) factory.createTaskIterator(is, ontologyDagName).next();
    final RegisterOntologyTask registerOntologyTask = new RegisterOntologyTask((CyNetworkReader) loadOBOTask, serviceRegistrar, ontologyDagName);
    final GeneAssociationReader gaReader = new GeneAssociationReader(ontologyDagName, gaStream, gaTableName, serviceRegistrar);
    final MapGeneAssociationTask mapAnnotationTask = new MapGeneAssociationTask(gaReader, serviceRegistrar);
    final TaskIterator taskChain = new TaskIterator(loadOBOTask, registerOntologyTask, gaReader, mapAnnotationTask);
    insertTasksAfterCurrentTask(taskChain);
}