private void applySelectionToNetwork() {
CyNetwork network = Cytoscape.getCurrentNetwork();
network.unselectAllNodes();
network.unselectAllEdges();
Set<String> selection = new HashSet<String>();
for (int i : currentTable.getSelectedRows()) {
selection.add(currentTable.getValueAt(i, 0).toString());
}
NetworkData networkData =
MetScapePlugin.getPluginData().getNetworkData(Networks.getUUID(network));
if (networkData == null) return;
NetworkType networkType = networkData.getNetworkType();
if (networkType == NetworkType.CREG) applySelectionToCREGNetwork(network, selection);
else if (networkType == NetworkType.COMPOUND_REACTION)
applySelectionToCRNetwork(network, selection);
else if (networkType == NetworkType.COMPOUND_GENE)
applySelectionToCGNetwork(network, selection);
else if (networkType == NetworkType.COMPOUND)
applySelectionToCompoundNetwork(network, selection);
CyNetworkView view = Cytoscape.getNetworkView(network.getIdentifier());
if (view != null && initialized) view.redrawGraph(true, true);
else if (!initialized) initialized = true;
}
private void refreshPathwayListForCurrentNetwork() {
Set<String> selectedPathwaySet = new HashSet<String>();
for (int i : currentTable.getSelectedRows())
selectedPathwaySet.add(currentTable.getValueAt(i, 0).toString());
currentModel.setRowCount(0);
SortedSet<String> pathwaySet;
CyNetwork network = Cytoscape.getCurrentNetwork();
NetworkData networkData =
MetScapePlugin.getPluginData().getNetworkData(Networks.getUUID(network));
NetworkType networkType = null;
if (networkData != null) networkType = networkData.getNetworkType();
if (networkType == NetworkType.COMPOUND_REACTION
|| networkType == NetworkType.CREG) { // for C-R and C-R-E-G
pathwaySet = getPathwaySetFromReactionNodes(network);
} else if (networkType == NetworkType.COMPOUND) {
pathwaySet = getPathwaySetFromReactionEdges(network);
} else if (networkType == NetworkType.COMPOUND_GENE) {
pathwaySet = getPathwaySetFromEnzymeReactionEdges(network);
} else {
pathwaySet = new TreeSet<String>();
}
for (String pathway : pathwaySet) {
currentModel.addRow(new Object[] {pathway});
if (selectedPathwaySet.contains(pathway))
currentTable.addRowSelectionInterval(
currentTable.getRowCount() - 1, currentTable.getRowCount() - 1);
}
applySelectionToNetwork();
}
private void switchActiveTable() {
if (tables.get(Cytoscape.getCurrentNetwork()) != currentTable) {
currentTable.getSelectionModel().removeListSelectionListener(PathwayFilterPanel.this);
scrollPane.getViewport().setView(null);
currentTable = tables.get(Cytoscape.getCurrentNetwork());
if (currentTable == null) {
currentTable = new ExtendedJTable();
tables.put(Cytoscape.getCurrentNetwork(), currentTable);
((ExtendedTableModel) currentTable.getModel()).addColumn("Pathways");
currentTable.getRowSorter().toggleSortOrder(0);
currentModel = (ExtendedTableModel) currentTable.getModel();
refreshPathwayListForCurrentNetwork();
}
currentModel = (ExtendedTableModel) currentTable.getModel();
scrollPane.getViewport().setView(currentTable);
currentTable.getSelectionModel().addListSelectionListener(PathwayFilterPanel.this);
}
applySelectionToNetwork();
}
private void createControls() {
buttonPanel = new JPanel();
selectAll = new JButton("Select All Pathways");
selectAll.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
selectAll();
}
});
buttonPanel.add(selectAll);
deselectAll = new JButton("Deselect All Pathways");
deselectAll.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
deselectAll();
}
});
buttonPanel.add(deselectAll);
createSubnetwork = new JButton("Create Subnetwork");
createSubnetwork.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
buildSubnetwork();
}
});
buttonPanel.add(createSubnetwork);
reapplySelection = new JButton("Reapply Selection");
reapplySelection.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
applySelectionToNetwork();
}
});
buttonPanel.add(reapplySelection);
close = new JButton("Close");
close.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
close();
}
});
buttonPanel.add(close);
add(buttonPanel, BorderLayout.NORTH);
tables = new HashMap<CyNetwork, ExtendedJTable>();
currentTable = new ExtendedJTable();
tables.put(Cytoscape.getCurrentNetwork(), currentTable);
currentTable.getSelectionModel().addListSelectionListener(this);
currentModel = (ExtendedTableModel) currentTable.getModel();
currentModel.addColumn("Pathways");
currentTable.getRowSorter().toggleSortOrder(0);
scrollPane = new JScrollPane(currentTable);
refreshPathwayListForCurrentNetwork();
add(scrollPane, BorderLayout.CENTER);
addComponentListener(this);
}
private void deselectAll() {
currentTable.clearSelection();
}
private void selectAll() {
currentTable.selectAll();
}