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();
}