Examples with VizmapReader org.cytoscape.io.read.VizmapReader used on opensource projects

Example 1 with VizmapReader

use of org.cytoscape.io.read.VizmapReader in project cytoscape-impl by cytoscape.

the class ImportDefaultVizmapTask method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    final VizmapReader reader;
    final VizmapReaderManager vizmapReaderMgr = servicesUtil.get(VizmapReaderManager.class);
    if (vizmapFile.exists() == false) {
        // get the file from resource
        final URL url = this.getClass().getClassLoader().getResource(VizMapperProxy.PRESET_VIZMAP_FILE);
        reader = vizmapReaderMgr.getReader(url.toURI(), url.getPath());
    } else {
        reader = vizmapReaderMgr.getReader(vizmapFile.toURI(), vizmapFile.getName());
    }
    logger.debug("Default vizmap file = " + vizmapFile.getName());
    if (reader == null)
        throw new NullPointerException("Failed to find Default Vizmap loader.");
    insertTasksAfterCurrentTask(reader, new AddVisualStylesTask(reader));
}

Example 2 with VizmapReader

use of org.cytoscape.io.read.VizmapReader in project cytoscape-impl by cytoscape.

the class LoadVizmapFileTask method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setProgress(0.0);
    taskMonitor.setTitle("Load Styles from File");
    taskMonitor.setStatusMessage("Looking for a reader...");
    if (file == null)
        throw new NullPointerException("No file specified.");
    VizmapReaderManager readerManager = serviceRegistrar.getService(VizmapReaderManager.class);
    VizmapReader reader = readerManager.getReader(file.toURI(), file.getName());
    taskMonitor.setProgress(0.9);
    if (reader == null)
        throw new NullPointerException("Failed to find appropriate reader for file: " + file);
    addStyleTask = new AddVisualStylesTask(reader);
    insertTasksAfterCurrentTask(reader, addStyleTask);
    taskMonitor.setProgress(1.0);
}

Example 3 with VizmapReader

use of org.cytoscape.io.read.VizmapReader in project cytoscape-impl by cytoscape.

the class LoadVizmapFileTaskFactoryTest method testObserver.

@Test
public void testObserver() throws Exception {
    VizmapReaderManager vizmapReaderMgr = mock(VizmapReaderManager.class);
    VizmapReader reader = mock(VizmapReader.class);
    when(vizmapReaderMgr.getReader(any(URI.class), any(String.class))).thenReturn(reader);
    VisualMappingManager vmMgr = mock(VisualMappingManager.class);
    SynchronousTaskManager<?> syncTaskManager = mock(SynchronousTaskManager.class);
    SyncTunableMutatorFactory mutatorFactory = new SyncTunableMutatorFactory(new SyncTunableHandlerFactory());
    TunableRecorderManager recorderManager = new TunableRecorderManager();
    TunableSetter tunableSetter = new TunableSetterImpl(mutatorFactory, recorderManager);
    CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(VizmapReaderManager.class)).thenReturn(vizmapReaderMgr);
    when(serviceRegistrar.getService(VisualMappingManager.class)).thenReturn(vmMgr);
    when(serviceRegistrar.getService(SynchronousTaskManager.class)).thenReturn(syncTaskManager);
    when(serviceRegistrar.getService(TunableSetter.class)).thenReturn(tunableSetter);
    LoadVizmapFileTaskFactory factory = new LoadVizmapFileTaskFactoryImpl(serviceRegistrar);
    File file = new File("");
    TaskObserver observer = mock(TaskObserver.class);
    TaskIterator iterator = factory.createTaskIterator(file, observer);
    TaskMonitor taskMonitor = mock(TaskMonitor.class);
    while (iterator.hasNext()) {
        Task t = iterator.next();
        t.run(taskMonitor);
        if (t instanceof ObservableTask)
            observer.taskFinished((ObservableTask) t);
    }
    verify(observer, times(1)).taskFinished(any(ObservableTask.class));
}

Example 4 with VizmapReader

use of org.cytoscape.io.read.VizmapReader in project cytoscape-impl by cytoscape.

the class Cy2SessionReaderImpl method extractVizmap.

private void extractVizmap(InputStream is, String entryName) throws Exception {
    VizmapReader reader = vizmapReaderMgr.getReader(is, entryName);
    reader.run(taskMonitor);
    visualStyles.addAll(reader.getVisualStyles());
}

Example 5 with VizmapReader

use of org.cytoscape.io.read.VizmapReader in project cytoscape-impl by cytoscape.

the class Cy3SessionReaderImpl method extractVizmap.

private void extractVizmap(InputStream is, String entryName) throws Exception {
    VizmapReader reader = vizmapReaderMgr.getReader(is, entryName);
    reader.run(taskMonitor);
    visualStyles.addAll(reader.getVisualStyles());
}