Examples with CySubNetwork org.cytoscape.model.subnetwork.CySubNetwork used on opensource projects

Example 11 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class CyNetworkAutoDeleteTest method testUndoDeletedNodeAndEdge.

@Test
public void testUndoDeletedNodeAndEdge() {
    final String TEST_COLUMN = "testColumn";
    CyNetwork network1 = TestCyNetworkFactory.getInstance();
    CyRootNetwork rootNetwork = ((CySubNetwork) network1).getRootNetwork();
    CyNode n1 = network1.addNode();
    CyNode n2 = network1.addNode();
    CyNode n3 = network1.addNode();
    CyEdge e1 = network1.addEdge(n1, n2, false);
    CyEdge e2 = network1.addEdge(n2, n3, false);
    CyTable defaultNodeTable = network1.getDefaultNodeTable();
    defaultNodeTable.createColumn(TEST_COLUMN, String.class, false);
    CyTable defaultEdgeTable = network1.getDefaultEdgeTable();
    defaultEdgeTable.createColumn(TEST_COLUMN, String.class, false);
    network1.getRow(n1).set(TEST_COLUMN, "my node 1");
    network1.getRow(e1).set(TEST_COLUMN, "my edge 1");
    CyNetwork network2 = rootNetwork.addSubNetwork(Arrays.asList(n1, n2, n3), Arrays.asList(e1, e2));
    network1.removeNodes(Collections.singleton(n1));
    network2.removeNodes(Collections.singleton(n1));
    assertFalse(rootNetwork.containsNode(n1));
    assertFalse(network1.containsNode(n1));
    assertFalse(network2.containsNode(n1));
    assertFalse(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsEdge(e1));
    assertFalse(network2.containsEdge(e1));
    // restore the node to network1
    ((CySubNetwork) network1).addNode(n1);
    assertTrue(rootNetwork.containsNode(n1));
    assertTrue(network1.containsNode(n1));
    assertFalse(network2.containsNode(n1));
    assertFalse(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsEdge(e1));
    assertFalse(network2.containsEdge(e1));
    ((CySubNetwork) network1).addEdge(e1);
    assertTrue(rootNetwork.containsNode(n1));
    assertTrue(network1.containsNode(n1));
    assertFalse(network2.containsNode(n1));
    assertTrue(rootNetwork.containsEdge(e1));
    assertTrue(network1.containsEdge(e1));
    assertFalse(network2.containsEdge(e1));
    // test that the attributes are restored
    assertEquals("my node 1", rootNetwork.getRow(n1).get(TEST_COLUMN, String.class));
    assertEquals("my edge 1", rootNetwork.getRow(e1).get(TEST_COLUMN, String.class));
}

Example 12 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class CyNetworkAutoDeleteTest method testRestoreBug3838_1.

@Test
public void testRestoreBug3838_1() {
    CyNetwork network1 = TestCyNetworkFactory.getInstance();
    CyRootNetwork rootNetwork = ((CySubNetwork) network1).getRootNetwork();
    CyNode n1 = network1.addNode();
    CyNode n2 = network1.addNode();
    CyEdge e1 = network1.addEdge(n1, n2, false);
    network1.removeEdges(Arrays.asList(e1));
    assertTrue(rootNetwork.containsNode(n1));
    assertTrue(rootNetwork.containsNode(n2));
    assertFalse(rootNetwork.containsEdge(e1));
    assertTrue(network1.containsNode(n1));
    assertTrue(network1.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
    rootNetwork.restoreEdge(e1);
    assertTrue(rootNetwork.containsNode(n1));
    assertTrue(rootNetwork.containsNode(n2));
    assertTrue(rootNetwork.containsEdge(e1));
    assertTrue(network1.containsNode(n1));
    assertTrue(network1.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
    network1.removeNodes(Arrays.asList(n1));
    assertFalse(rootNetwork.containsNode(n1));
    assertTrue(rootNetwork.containsNode(n2));
    assertFalse(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsNode(n1));
    assertTrue(network1.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
    rootNetwork.restoreEdge(e1);
    assertTrue(rootNetwork.containsEdge(e1));
    assertTrue(rootNetwork.containsNode(n1));
    assertTrue(rootNetwork.containsNode(n2));
    assertFalse(network1.containsNode(n1));
    assertTrue(network1.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
    CyRow row = rootNetwork.getDefaultEdgeTable().getRow(e1.getSUID());
    assertNotNull(row);
}

Example 13 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class TableBrowserToolBar method createNewAttribute.

private void createNewAttribute(final String type, boolean isShared) {
    try {
        final String[] existingAttrs = getAttributeArray();
        String newAttribName = null;
        do {
            newAttribName = JOptionPane.showInputDialog(this, "Column Name: ", "Create New " + type + " Column", JOptionPane.QUESTION_MESSAGE);
            if (newAttribName == null)
                return;
            newAttribName = newAttribName.trim();
            if (newAttribName.isEmpty()) {
                JOptionPane.showMessageDialog(null, "Column name must not be blank.", "Error", JOptionPane.ERROR_MESSAGE);
                newAttribName = null;
            } else if (Arrays.binarySearch(existingAttrs, newAttribName) >= 0) {
                JOptionPane.showMessageDialog(null, "Column " + newAttribName + " already exists.", "Error", JOptionPane.ERROR_MESSAGE);
                newAttribName = null;
            }
        } while (newAttribName == null);
        final CyTable attrs;
        if (isShared) {
            final CyNetwork network = serviceRegistrar.getService(CyApplicationManager.class).getCurrentNetwork();
            if (network instanceof CySubNetwork) {
                final CyRootNetwork rootNetwork = ((CySubNetwork) network).getRootNetwork();
                CyTable sharedTable = null;
                if (this.objType == CyNode.class)
                    sharedTable = rootNetwork.getSharedNodeTable();
                else if (this.objType == CyEdge.class)
                    sharedTable = rootNetwork.getSharedEdgeTable();
                else if (this.objType == CyNetwork.class)
                    sharedTable = rootNetwork.getSharedNetworkTable();
                else
                    throw new IllegalStateException("Object type is not valid.  This should not happen.");
                attrs = sharedTable;
            } else {
                throw new IllegalArgumentException("This is not a CySubNetwork and there is no shared table.");
            }
        } else {
            attrs = browserTableModel.getDataTable();
        }
        if (type.equals("String"))
            attrs.createColumn(newAttribName, String.class, false);
        else if (type.equals("Floating Point"))
            attrs.createColumn(newAttribName, Double.class, false);
        else if (type.equals("Integer"))
            attrs.createColumn(newAttribName, Integer.class, false);
        else if (type.equals("Long Integer"))
            attrs.createColumn(newAttribName, Long.class, false);
        else if (type.equals("Boolean"))
            attrs.createColumn(newAttribName, Boolean.class, false);
        else if (type.equals("String List"))
            attrs.createListColumn(newAttribName, String.class, false);
        else if (type.equals("Floating Point List"))
            attrs.createListColumn(newAttribName, Double.class, false);
        else if (type.equals("Integer List"))
            attrs.createListColumn(newAttribName, Integer.class, false);
        else if (type.equals("Long Integer List"))
            attrs.createListColumn(newAttribName, Long.class, false);
        else if (type.equals("Boolean List"))
            attrs.createListColumn(newAttribName, Boolean.class, false);
        else
            throw new IllegalArgumentException("unknown column type \"" + type + "\".");
    } catch (IllegalArgumentException e) {
        JOptionPane.showMessageDialog(null, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
    }
}

Example 14 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class CyRootNetworkImpl method removeNodes.

@Override
public boolean removeNodes(final Collection<CyNode> nodes) {
    synchronized (lock) {
        boolean removed = false;
        for (CySubNetwork sub : subNetworks) {
            removed |= sub.removeNodes(nodes);
            if (nodes != null && sub instanceof CySubNetworkImpl)
                ((CySubNetworkImpl) sub).removeRows(nodes, CyNode.class);
        }
        // Explicitly removing from the root network removes from the cache
        if (nodes != null) {
            for (CyNode node : nodes) {
                removedAttributesCache.evict(node);
            }
        }
        // Do we want to do this????? (MK: yes I think so)
        this.removeRows(nodes, CyNode.class);
        removed |= removeNodesInternal(nodes);
        return removed;
    }
}

Example 15 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class CyTableManagerImpl method getLocalTables.

@Override
public Set<CyTable> getLocalTables(final Class<? extends CyIdentifiable> type) {
    final Set<CyTable> localTables = new HashSet<CyTable>();
    final Set<CyNetwork> networks = networkManager.getNetworkSet();
    for (final CyNetwork network : networks) {
        final Map<String, CyTable> objTables = networkTableManager.getTables(network, type);
        if (network instanceof CySubNetwork) {
            final CyTable shared = networkTableManager.getTable(((CySubNetwork) network).getRootNetwork(), type, CyRootNetwork.SHARED_ATTRS);
            localTables.add(shared);
        }
        localTables.addAll(objTables.values());
    }
    return localTables;
}