use of org.cytoscape.service.util.CyServiceRegistrar in project cytoscape-impl by cytoscape.
the class GMLFileFilterTest method setUp.
@Before
public void setUp() {
Set<String> extensions = new HashSet<String>();
Set<String> contentTypes = new HashSet<String>();
String description = "GML";
Properties properties = new Properties();
CyProperty<Properties> cyProperties = new SimpleCyProperty<Properties>("test", properties, Properties.class, SavePolicy.DO_NOT_SAVE);
CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
when(serviceRegistrar.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)")).thenReturn(cyProperties);
filter = new GMLFileFilter(extensions, contentTypes, description, DataCategory.NETWORK, new StreamUtilImpl(serviceRegistrar));
}
use of org.cytoscape.service.util.CyServiceRegistrar in project cytoscape-impl by cytoscape.
the class SessionFileFilterTest method setUp.
@Before
public void setUp() {
extensions = new HashSet<String>();
contentTypes = new HashSet<String>();
Properties properties = new Properties();
CyProperty<Properties> cyProperties = new SimpleCyProperty<Properties>("test", properties, Properties.class, SavePolicy.DO_NOT_SAVE);
CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
when(serviceRegistrar.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)")).thenReturn(cyProperties);
streamUtil = new StreamUtilImpl(serviceRegistrar);
}
use of org.cytoscape.service.util.CyServiceRegistrar in project PhenomeScape by soulj.
the class NetworkNameChangedListener method handleEvent.
public void handleEvent(RowsSetEvent e) {
// First check whether the Name field of any of the rows got changed.
if (e.containsColumn(CyNetwork.NAME)) {
CyServiceRegistrar cyServiceRegistrar = controlPanel.cyServiceRegistrar;
DefaultComboBoxModel networkModel = (DefaultComboBoxModel) networkComboBox.getModel();
networkModel.removeAllElements();
for (CyNetwork cyNetwork : cyServiceRegistrar.getService(CyNetworkManager.class).getNetworkSet()) {
String cyNetworkName = cyNetwork.getRow(cyNetwork).get(CyNetwork.NAME, String.class);
networkModel.addElement(cyNetworkName);
}
}
}
use of org.cytoscape.service.util.CyServiceRegistrar in project clusterMaker2 by RBVI.
the class CyActivator method start.
public void start(BundleContext bc) {
// See if we have a graphics console or not
boolean haveGUI = true;
CySwingApplication swingAppRef = getService(bc, CySwingApplication.class);
if (swingAppRef == null) {
// if haveGUI is false, we don't want to provide any hooks to the treeview
haveGUI = false;
}
CyApplicationManager appRef = getService(bc, CyApplicationManager.class);
CyServiceRegistrar serviceRegistrar = getService(bc, CyServiceRegistrar.class);
CyGroupManager groupManager = getService(bc, CyGroupManager.class);
CyGroupFactory groupFactory = getService(bc, CyGroupFactory.class);
CyTableFactory tableFactory = getService(bc, CyTableFactory.class);
CyTableManager tableManager = getService(bc, CyTableManager.class);
// Create our context object. This will probably keep track of all of the
// registered clustering algorithms, settings, etc.
ClusterManagerImpl clusterManager = new ClusterManagerImpl(appRef, serviceRegistrar, groupFactory, groupManager, tableFactory, tableManager);
registerServiceListener(bc, clusterManager, "addClusterAlgorithm", "removeClusterAlgorithm", ClusterTaskFactory.class);
registerServiceListener(bc, clusterManager, "addClusterVisualizer", "removeClusterVisualizer", ClusterVizFactory.class);
registerServiceListener(bc, clusterManager, "addRankingAlgorithm", "removeRankingAlgorithm", RankFactory.class);
// Register each of our algorithms
// Attribute clusterers
registerService(bc, new AttributeClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new AutoSOMETaskFactory(clusterManager, true), ClusterTaskFactory.class, new Properties());
registerService(bc, new FeatureVectorTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new HierarchicalTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new KMeansTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new KMedoidTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new HopachPAMTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new PAMTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// FIXME: FFT is seriously broken!
registerService(bc, new FFTTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new DBSCANTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
/*
* Hold off on these until we get improve the performance sufficiently
* to allow them to be useful
*/
// registerService(bc, new BicFinderTaskFactory(clusterManager),
// ClusterTaskFactory.class, new Properties());
// registerService(bc, new BiMineTaskFactory(clusterManager),
// ClusterTaskFactory.class, new Properties());
registerService(bc, new ChengChurchTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// Network clusterers
registerService(bc, new NetworkClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new APClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new AutoSOMETaskFactory(clusterManager, false), ClusterTaskFactory.class, new Properties());
registerService(bc, new FuzzifierTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new GLayClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new ConnectedComponentsTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new FCMClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new MCLClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new MCODEClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new SCPSClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new TransClustClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// Cluster ranking
registerService(bc, new MAATaskFactory(clusterManager), RankFactory.class, new Properties());
registerService(bc, new MAMTaskFactory(clusterManager), RankFactory.class, new Properties());
registerService(bc, new PRWPTaskFactory(clusterManager), RankFactory.class, new Properties());
registerService(bc, new PRTaskFactory(clusterManager), RankFactory.class, new Properties());
registerService(bc, new HITSTaskFactory(clusterManager), RankFactory.class, new Properties());
// Filters
registerService(bc, new FilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new BestNeighborFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new CuttingEdgeFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new DensityFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new HairCutFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// registerService(bc, new UITaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// Visualizations
registerService(bc, new NewNetworkViewFactory(clusterManager, false), ClusterVizFactory.class, new Properties());
registerService(bc, new NewNetworkViewFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
registerService(bc, new HeatMapViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
registerService(bc, new KnnViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
registerService(bc, new BiclusterViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
registerService(bc, new TreeViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
registerService(bc, new CreateResultsPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
registerService(bc, new CreateRankingPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
registerService(bc, new DestroyResultsPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
registerService(bc, new DestroyRankingPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
// Dimensionality Reduction
// registerService(bc, new PCAMenuTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new PCATaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new PCoATaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new tSNETaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
{
// Link Network Selections
LinkSelectionTaskFactory linkTaskFactory = new LinkSelectionTaskFactory(clusterManager);
Properties linkSelectionProps = new Properties();
linkSelectionProps.setProperty(INSERT_SEPARATOR_BEFORE, "true");
linkSelectionProps.setProperty(PREFERRED_MENU, "Apps.clusterMaker Visualizations");
linkSelectionProps.setProperty(TITLE, "Link selection across networks");
linkSelectionProps.setProperty(COMMAND, "linkSelection");
linkSelectionProps.setProperty(COMMAND_NAMESPACE, "clusterviz");
linkSelectionProps.setProperty(ENABLE_FOR, "networkAndView");
linkSelectionProps.setProperty(IN_MENU_BAR, "true");
linkSelectionProps.setProperty(MENU_GRAVITY, "100.0");
registerService(bc, linkTaskFactory, NetworkTaskFactory.class, linkSelectionProps);
}
{
// UnLink Network Selections
UnlinkSelectionTaskFactory unlinkTaskFactory = new UnlinkSelectionTaskFactory(clusterManager);
Properties unlinkSelectionProps = new Properties();
unlinkSelectionProps.setProperty(PREFERRED_MENU, "Apps.clusterMaker Visualizations");
unlinkSelectionProps.setProperty(TITLE, "Unlink selection across networks");
unlinkSelectionProps.setProperty(COMMAND, "unlinkSelection");
unlinkSelectionProps.setProperty(COMMAND_NAMESPACE, "clusterviz");
unlinkSelectionProps.setProperty(ENABLE_FOR, "networkAndView");
unlinkSelectionProps.setProperty(IN_MENU_BAR, "true");
unlinkSelectionProps.setProperty(MENU_GRAVITY, "100.0");
registerService(bc, unlinkTaskFactory, NetworkTaskFactory.class, unlinkSelectionProps);
}
// Commands
// These task factories provide useful commands that only make sense in the context of REST or
// the command interface
{
TaskFactory commandTaskFactory = new CommandTaskFactory(clusterManager, "hascluster");
Properties props = new Properties();
props.setProperty(COMMAND_NAMESPACE, "cluster");
props.setProperty(COMMAND, CommandTaskFactory.HASCLUSTER);
props.setProperty(COMMAND_DESCRIPTION, "Test to see if this network has a cluster of the requested type");
registerService(bc, commandTaskFactory, TaskFactory.class, props);
}
{
TaskFactory commandTaskFactory = new CommandTaskFactory(clusterManager, "getnetworkcluster");
Properties props = new Properties();
props.setProperty(COMMAND_NAMESPACE, "cluster");
props.setProperty(COMMAND, CommandTaskFactory.GETNETWORKCLUSTER);
props.setProperty(COMMAND_DESCRIPTION, "Get a cluster network cluster result");
registerService(bc, commandTaskFactory, TaskFactory.class, props);
}
{
TaskFactory commandTaskFactory = new CommandTaskFactory(clusterManager, "getcluster");
Properties props = new Properties();
props.setProperty(COMMAND_NAMESPACE, "cluster");
props.setProperty(COMMAND, CommandTaskFactory.GETCLUSTER);
props.setProperty(COMMAND_DESCRIPTION, "Get an attribute cluster result");
registerService(bc, commandTaskFactory, TaskFactory.class, props);
}
}
use of org.cytoscape.service.util.CyServiceRegistrar in project clusterMaker2 by RBVI.
the class RunPCA method runOnNodeToAttributeMatrix.
// this method assumes that eigen values
// are sorted in increasing order
public void runOnNodeToAttributeMatrix() {
// System.out.println("runOnNodeToAttributeMatrix");
CyMatrix matrix = CyMatrixFactory.makeLargeMatrix(network, weightAttributes, context.selectedOnly, context.ignoreMissing, false, false);
// System.out.println("Computing principle components");
components = computePCs(matrix);
final Matrix loadingMatrix = calculateLoadingMatrix(matrix);
if (context.pcaResultPanel) {
CyServiceRegistrar registrar = manager.getService(CyServiceRegistrar.class);
CySwingApplication swingApplication = manager.getService(CySwingApplication.class);
ResultPanelPCA panel = new ResultPanelPCA(components, variance, network, networkView);
CytoPanel cytoPanel = swingApplication.getCytoPanel(CytoPanelName.EAST);
registrar.registerService(panel, CytoPanelComponent.class, new Properties());
if (cytoPanel.getState() == CytoPanelState.HIDE)
cytoPanel.setState(CytoPanelState.DOCK);
}
if (context.pcaPlot) {
if (components.length < 2) {
monitor.showMessage(TaskMonitor.Level.ERROR, "Only found " + components.length + " components. Need 2 for scatterplot. " + "Perhaps minimum variance is set too high?");
return;
}
SwingUtilities.invokeLater(new Runnable() {
public void run() {
// System.out.println("Scatter plot dialog call");
ScatterPlotDialog dialog = new ScatterPlotDialog(manager, "PCA", monitor, components, loadingMatrix, variance);
}
});
}
}
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