Examples with CyIdentifiable org.cytoscape.model.CyIdentifiable used on opensource projects

Example 1 with CyIdentifiable

use of org.cytoscape.model.CyIdentifiable in project EnrichmentMapApp by BaderLab.

the class SessionModelIO method mapSuids.

private static Set<Long> mapSuids(Set<Long> oldSuids, CySession session, Class<? extends CyIdentifiable> type) {
    Set<Long> newSuids = new HashSet<>();
    for (Long suid : oldSuids) {
        if (session != null) {
            // If we are loading from a session file then we need to re-map the ids
            CyIdentifiable obj = session.getObject(suid, type);
            suid = obj.getSUID();
        }
        newSuids.add(suid);
    }
    return newSuids;
}

Example 2 with CyIdentifiable

use of org.cytoscape.model.CyIdentifiable in project cytoscape-api by cytoscape.

the class SUIDUtil method saveSUIDs.

/**
	 * This method may be used to save a list of SUIDs that have been sent to a remote
	 * service so that they may be restored later
	 *
	 * @param job the job that we're saving the SUIDs for
	 * @param network the network that the SUIDs are part of
	 * @param objs the Cytoscape objects whose SUIDs we want to save
	 */
public static void saveSUIDs(CyJob job, CyNetwork network, List<? extends CyIdentifiable> objs) {
    Map<Identifiable, CyTable> suidMap = new HashMap<>();
    // Add the network table to the map, we depend on having the network
    // available to us for the restore
    String columnName = getColumnName(job);
    // First, make sure we've saved the network SUID
    CyTable hiddenTable = createColumn(network, Identifiable.NETWORK, columnName);
    CyRow netRow = hiddenTable.getRow(network.getSUID());
    if (netRow != null)
        netRow.set(columnName, network.getSUID());
    for (CyIdentifiable cyId : objs) {
        Identifiable type = getType(cyId);
        if (!suidMap.containsKey(type)) {
            hiddenTable = createColumn(network, type, columnName);
            if (hiddenTable != null)
                suidMap.put(type, hiddenTable);
        }
        CyRow row = suidMap.get(type).getRow(cyId.getSUID());
        if (row != null)
            row.set(columnName, cyId.getSUID());
    }
}

Example 3 with CyIdentifiable

use of org.cytoscape.model.CyIdentifiable in project EnrichmentMapApp by BaderLab.

the class RadialHeatMapChart method getLayers.

@Override
public List<RadialHeatMapLayer> getLayers(final CyNetworkView networkView, final View<? extends CyIdentifiable> view) {
    final CyNetwork network = networkView.getModel();
    final CyIdentifiable model = view.getModel();
    final double startAngle = get(START_ANGLE, Double.class, 0.0);
    final Rotation rotation = get(ROTATION, Rotation.class, Rotation.ANTICLOCKWISE);
    final List<String> labels = getItemLabels(network, model);
    final Map<String, List<Double>> data = getData(network, model);
    final List<Color> colors = getColors(data);
    final double size = 32;
    final Rectangle2D bounds = new Rectangle2D.Double(-size / 2, -size / 2, size, size);
    final boolean showLabels = get(SHOW_ITEM_LABELS, Boolean.class, false);
    final float itemFontSize = convertFontSize(get(ITEM_LABEL_FONT_SIZE, Integer.class, 1));
    final float borderWidth = get(BORDER_WIDTH, Float.class, 0.25f);
    final Color borderColor = get(BORDER_COLOR, Color.class, Color.DARK_GRAY);
    final boolean global = get(GLOBAL_RANGE, Boolean.class, true);
    final List<Double> range = global ? getList(RANGE, Double.class) : null;
    final RadialHeatMapLayer layer = new RadialHeatMapLayer(data, labels, showLabels, itemFontSize, colors, borderWidth, borderColor, startAngle, rotation, range, bounds);
    return Collections.singletonList(layer);
}

Example 4 with CyIdentifiable

use of org.cytoscape.model.CyIdentifiable in project cytoscape-api by cytoscape.

the class CySessionTest method testSetObjectMap.

@Test
public void testSetObjectMap() {
    Map<Object, CyNetwork> netMap = new HashMap<Object, CyNetwork>();
    CyNetwork net1 = mock(CyNetwork.class);
    netMap.put("A", net1);
    CyNetwork net2 = mock(CyNetwork.class);
    netMap.put("B", net2);
    Map<Object, CyNetworkView> viewMap = new HashMap<Object, CyNetworkView>();
    CyNetworkView view1 = mock(CyNetworkView.class);
    viewMap.put("A", view1);
    Map<Object, CyNode> nodeMap = new HashMap<Object, CyNode>();
    CyNode n1 = mock(CyNode.class);
    nodeMap.put(new Long(1), n1);
    CyNode n2 = mock(CyNode.class);
    nodeMap.put(new Long(2), n2);
    Map<Object, CyEdge> edgeMap = new HashMap<Object, CyEdge>();
    CyEdge e1 = mock(CyEdge.class);
    edgeMap.put(new Long(3), e1);
    Map<Class<? extends CyIdentifiable>, Map<Object, ? extends CyIdentifiable>> objMap = new HashMap<Class<? extends CyIdentifiable>, Map<Object, ? extends CyIdentifiable>>();
    objMap.put(CyNetwork.class, netMap);
    objMap.put(CyNetworkView.class, viewMap);
    objMap.put(CyNode.class, nodeMap);
    objMap.put(CyEdge.class, edgeMap);
    session = new CySession.Builder().objectMap(objMap).build();
    assertNotNull(session);
    assertSame(net1, session.getObject("A", CyNetwork.class));
    assertSame(net2, session.getObject("B", CyNetwork.class));
    assertSame(view1, session.getObject("A", CyNetworkView.class));
    assertSame(n1, session.getObject(new Long(1), CyNode.class));
    assertSame(n2, session.getObject(new Long(2), CyNode.class));
    assertSame(e1, session.getObject(new Long(3), CyEdge.class));
    assertNull(session.getObject("A", View.class));
    assertNull(session.getObject("B", CyNetworkView.class));
}

Example 5 with CyIdentifiable

use of org.cytoscape.model.CyIdentifiable in project cytoscape-api by cytoscape.

the class SUIDUtil method restoreSUIDs.

/**
	 * Method to restore Cytoscape objects based on a list of SUIDs that were sent to the remote
	 * service as saved in the hidden table. 
	 *
	 * @param job the {@link CyJob} we're restoring
	 * @param network the network the SUIDs are part of.  See {@link SaveSUID.restoreNetwork()} for
	 * a method to get the network
	 * @param oldIds the list of old SUIDs that were sent to the remote server and saved
	 * in the session
	 * @param clear if true, remove the columns for this job
	 * @return a map that relates the original id to the Cytoscape object
	 */
public static Map<Long, CyIdentifiable> restoreSUIDs(CyJob job, CyNetwork network, List<Long> oldIds, boolean clear) {
    Map<Long, CyIdentifiable> objMap = new HashMap<>();
    Set<Long> suidSet = new HashSet<Long>(oldIds);
    String columnName = getColumnName(job);
    // First, determine which types have our column
    CyTable networkTable = network.getTable(CyNetwork.class, CyNetwork.HIDDEN_ATTRS);
    if (networkTable.getColumn(columnName) != null) {
        Long id = network.getRow(network).get(columnName, Long.class);
        if (suidSet.contains(id))
            objMap.put(id, network);
        if (clear)
            networkTable.deleteColumn(columnName);
    }
    CyTable nodeTable = network.getTable(CyNode.class, CyNetwork.HIDDEN_ATTRS);
    if (nodeTable.getColumn(columnName) != null) {
        for (CyNode node : network.getNodeList()) {
            Long id = nodeTable.getRow(node.getSUID()).get(columnName, Long.class);
            if (id == null)
                continue;
            if (suidSet.contains(id)) {
                objMap.put(id, node);
            }
        }
        if (clear)
            nodeTable.deleteColumn(columnName);
    }
    CyTable edgeTable = network.getTable(CyEdge.class, CyNetwork.HIDDEN_ATTRS);
    if (edgeTable.getColumn(columnName) != null) {
        for (CyEdge edge : network.getEdgeList()) {
            Long id = edgeTable.getRow(edge.getSUID()).get(columnName, Long.class);
            if (id == null)
                continue;
            if (suidSet.contains(id))
                objMap.put(id, edge);
        }
        if (clear)
            edgeTable.deleteColumn(columnName);
    }
    return objMap;
}