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
/**
* Method to determine whether a node is an ancestor of another node.
*
* @param ancestor GO term node which may or may not be an ancestor of 'child'.
* @param child GO term node with may or may not be a child of 'ancestor'.
* @return true if 'ancestor' is an ancestor of 'child', false otherwise.
*/
private boolean isAncestorNode(Node ancestor, Node child) {
DGraphView view = (DGraphView) Cytoscape.getCurrentNetworkView();
// Loop through the outgoing edges of child node (to parent nodes), and check if 'target' is the
// parent node.
// Then recursively call method on each of the parent nodes.
int[] outgoingEdges =
Cytoscape.getCurrentNetwork()
.getAdjacentEdgeIndicesArray(child.getRootGraphIndex(), false, false, true);
for (int outgoingEdge : outgoingEdges) {
EdgeView ev = view.getEdgeView(outgoingEdge);
Node parentNode = ev.getEdge().getTarget();
if (ancestor.equals(parentNode)) {
return true;
}
if (isAncestorNode(ancestor, parentNode)) {
return true;
}
}
return false;
}