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;
}
public void actionPerformed(ActionEvent e) {
// sum of coordinates
double sx = 0;
double sy = 0;
// coordinates of center of graph
double cx = 0;
double cy = 0;
// coordinates with graph centered at (0,0)
double nx;
double ny;
CyNetworkView parent = Cytoscape.getCurrentNetworkView();
// loop through each node to add up all x and all y coordinates
for (Iterator i = parent.getNodeViewsIterator(); i.hasNext(); ) {
NodeView nodeView = (NodeView) i.next();
// get coordinates of node
double ax = nodeView.getXPosition();
double ay = nodeView.getYPosition();
// sum up coordinates of all the nodes
sx += ax;
sy += ay;
}
// set new coordinates of each node at center (0,0), shrink, then return to
// original center at (cx, cy)
for (Iterator i = parent.getNodeViewsIterator(); i.hasNext(); ) {
NodeView nodeView = (NodeView) i.next();
nodeView.setXPosition(m * ((nodeView.getXPosition()) - cx) + cx);
nodeView.setYPosition(m * ((nodeView.getYPosition()) - cy) + cy);
}
// remove bends
for (Iterator i = parent.getEdgeViewsIterator(); i.hasNext(); ) {
EdgeView edgeView = (EdgeView) i.next();
edgeView.getBend().removeAllHandles();
}
} // Action Performed