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

Example 81 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-impl by cytoscape.

the class LayoutEdgeTest method testLayoutEdgeConstructor2.

@Test
public void testLayoutEdgeConstructor2() {
    CyNetworkFactory nFactory = support.getNetworkFactory();
    CyNetwork newNetwork = nFactory.createNetwork();
    CyNode s = newNetwork.addNode();
    CyNode t = newNetwork.addNode();
    CyEdge e = newNetwork.addEdge(s, t, true);
    final CyNetworkViewFactory viewFactory = support.getNetworkViewFactory();
    CyNetworkView newView = viewFactory.createNetworkView(newNetwork);
    final View<CyNode> sourceView = newView.getNodeView(s);
    final View<CyNode> targetView = newView.getNodeView(t);
    assertNotNull(sourceView);
    assertNotNull(targetView);
    CyRow sRow = newNetwork.getRow(s);
    CyRow tRow = newNetwork.getRow(t);
    final LayoutNode layoutNodeS = new LayoutNode(sourceView, 0, sRow);
    final LayoutNode layoutNodeT = new LayoutNode(targetView, 1, tRow);
    final LayoutEdge layoutEdge2 = new LayoutEdge(e, layoutNodeS, layoutNodeT, newNetwork.getRow(e));
    assertNotNull(layoutEdge2);
}

Example 82 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-impl by cytoscape.

the class PartitionUtilTest method testPartition.

@Test
public void testPartition() {
    NetworkViewTestSupport networkSupport = new NetworkViewTestSupport();
    CyNetwork network = networkSupport.getNetworkFactory().createNetwork();
    {
        // Partition 1
        CyNode n1 = network.addNode();
        CyNode n2 = network.addNode();
        CyNode n3 = network.addNode();
        CyNode n4 = network.addNode();
        network.addEdge(n1, n2, false);
        network.addEdge(n2, n3, false);
        network.addEdge(n3, n4, false);
    }
    {
        // Partition 2
        CyNode n1 = network.addNode();
        CyNode n2 = network.addNode();
        CyNode n3 = network.addNode();
        CyNode n4 = network.addNode();
        network.addEdge(n1, n2, false);
        network.addEdge(n2, n3, false);
        network.addEdge(n3, n4, false);
        // cycle
        network.addEdge(n4, n1, false);
    }
    {
        // Partition 3
        CyNode n1 = network.addNode();
        CyNode n2 = network.addNode();
        CyNode n3 = network.addNode();
        CyNode n4 = network.addNode();
        network.addEdge(n1, n2, true);
        network.addEdge(n1, n3, true);
        network.addEdge(n1, n4, true);
        network.addEdge(n2, n3, true);
        network.addEdge(n3, n4, true);
        network.addEdge(n4, n1, true);
    }
    CyNetworkView networkView = networkSupport.getNetworkViewFactory().createNetworkView(network);
    EdgeWeighter edgeWeighter = new EdgeWeighter();
    List<LayoutPartition> result = PartitionUtil.partition(networkView, false, edgeWeighter);
    assertNotNull(result);
    assertEquals(3, result.size());
}

Example 83 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-impl by cytoscape.

the class ImportTablePanel method attributeRadioButtonActionPerformed.

private void attributeRadioButtonActionPerformed(ActionEvent evt) {
    final CyNetwork network = serviceRegistrar.getService(CyApplicationManager.class).getCurrentNetwork();
    if (nodeRadioButton.isSelected()) {
        if (network != null)
            selectedAttributes = network.getDefaultNodeTable();
        objType = NODE;
    } else if (edgeRadioButton.isSelected()) {
        if (network != null)
            selectedAttributes = network.getDefaultEdgeTable();
        objType = EDGE;
    } else {
        logger.info("\nNote: ImportTextTableFDialog.attributeRadioButtonActionPerformed():Import network table not implemented yet!\n");
        objType = NETWORK;
    }
    updateMappingAttributeComboBox();
    setKeyList();
}

Example 84 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-impl by cytoscape.

the class PopupMenuHelper method selectElementsFromSelectedRows.

private void selectElementsFromSelectedRows(final JTable table, final Class<? extends CyIdentifiable> tableType) {
    final Thread t = new Thread() {

        @Override
        public void run() {
            final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
            final CyNetwork net = applicationManager.getCurrentNetwork();
            if (net != null) {
                final BrowserTableModel tableModel = (BrowserTableModel) table.getModel();
                final int[] selectedRows = table.getSelectedRows();
                final Set<CyRow> targetRows = new HashSet<CyRow>();
                for (final int rowIndex : selectedRows) {
                    // Getting the row from data table solves the problem with hidden or moved SUID column.
                    // However, since the rows might be sorted we need to convert the index to model.
                    final ValidatedObjectAndEditString selected = (ValidatedObjectAndEditString) tableModel.getValueAt(table.convertRowIndexToModel(rowIndex), CyNetwork.SUID);
                    targetRows.add(tableModel.getRow(selected.getValidatedObject()));
                }
                final CyTable cyTable = tableType == CyNode.class ? net.getDefaultNodeTable() : net.getDefaultEdgeTable();
                for (final CyRow cyRow : cyTable.getAllRows()) cyRow.set(CyNetwork.SELECTED, targetRows.contains(cyRow));
                final CyNetworkView view = applicationManager.getCurrentNetworkView();
                if (view != null) {
                    final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
                    eventHelper.flushPayloadEvents();
                    view.updateView();
                }
            }
        }
    };
    t.start();
}

Example 85 with CyNetwork

use of org.cytoscape.model.CyNetwork 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);
    }
}