/** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void actionPerformed(ActionEvent e) { selectFromFile(); Cytoscape.getCurrentNetworkView().updateView(); }
private void setHiddenNodes(final CyNetworkView view, final HiddenNodes hidden) { if (hidden == null) { return; } final Iterator it = hidden.getNode().iterator(); while (it.hasNext()) { final Node hiddenNodeObject = (Node) it.next(); final CyNode hiddenNode = Cytoscape.getCyNode(hiddenNodeObject .getId(), false); view.hideGraphObject(view.getNodeView(hiddenNode)); } }
/** * DOCUMENT ME! * * @return DOCUMENT ME! */ public CyNetwork getNetwork() { return networkView.getNetwork(); }
public void actionPerformed(ActionEvent e) { final CyNetworkView currentNetworkView = Cytoscape.getCurrentNetworkView(); currentNetworkView.hideGraphObject(nodeView); currentNetworkView.updateView(); } }
/** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void actionPerformed(ActionEvent e) { CyNetworkView view = Cytoscape.getCurrentNetworkView(); final int[] selectedEdges = view.getSelectedEdgeIndices(); if (selectedEdges != null) { for (int i = 0; i < selectedEdges.length; i++) { EdgeView ev = view.getEdgeView(selectedEdges[i]); ev.setLineType(EdgeView.CURVED_LINES); } view.updateView(); } }
public void run() { CyLayoutAlgorithm layoutAlgorithm = CyLayouts.getLayout("force-directed"); networkView.applyLayout(layoutAlgorithm); Cytoscape.getCurrentNetworkView().fitContent(); } });
result.addMessage("networkview: current network view is "+current.getIdentifier()); result.addResult("currentview", current); return result; CyNetworkView view = Cytoscape.createNetworkView(net); result.addResult("newview",view); result.addMessage("networkview: created view for :"+view.getIdentifier()); } else if (command.equals(FIT)) { CyNetworkView view = viewMap.get(net.getIdentifier()); view.fitContent(); result.addMessage("networkview: fit view to content for "+net.getTitle()); view.updateView(); result.addMessage("networkview: view '"+net.getTitle()+"' updated"); if (nodes == null || nodes.length() == 0) { ((DingNetworkView) view).fitSelected(); view.updateView(); result.addMessage("networkview: focused '"+net.getTitle()+"' on selected nodes/edges"); } else { view.updateView(); result.addMessage("networkview: focused '"+net.getIdentifier()+"' on node(s)"); double factor = Double.parseDouble(getArg(command, FACTOR, args)); String scale = getArg(command, SCALE, args); double zoom = view.getZoom();
double maxY = Double.MIN_VALUE; final CyNetworkView graphView = Cytoscape.getCurrentNetworkView(); Iterator iter = graphView.getNodeViewsIterator(); iter = graphView.getEdgeViewsIterator(); || (graphView.getSelectedNodeIndices().length == 0); || graphView.getNodeView(currentEdgeView.getEdge().getSource()).isSelected() || graphView.getNodeView(currentEdgeView.getEdge().getTarget()).isSelected())) { currentEdgeView.getBend().removeAllHandles(); } else { final double yOff = minY - border; final FixedGraph fixedGraph = (FixedGraph) (graphView.getNetwork());
CyNetwork cyNet = myView.getNetwork(); List<EdgeView> edgeViews = myView.getSelectedEdges(); List<NodeView> nodeViews = myView.getSelectedNodes(); CyNode cyNode; CyEdge cyEdge; if ( graphObj instanceof giny.model.Node) { cyNode = (CyNode) graphObj; nv = Cytoscape.getCurrentNetworkView().getNodeView(cyNode); if ( !nodeViews.contains(nv) ) nodeViews.add(nv); } else if ( graphObj instanceof giny.model.Edge) { cyEdge = (CyEdge) graphObj; ev = Cytoscape.getCurrentNetworkView().getEdgeView(cyEdge); if ( !edgeViews.contains(ev) ) edgeViews.add(ev);
InnerCanvas innerCanvas = graphView.getCanvas(); NodeView nodeView = Cytoscape.getCurrentNetworkView().getNodeView(node); double scaleFactor = Math.min(innerCanvas.getWidth() / width, (innerCanvas.getHeight() / height)); Cytoscape.getCurrentNetworkView().setZoom(scaleFactor); Cytoscape.getCurrentNetworkView().updateView();
return; this.network = networkView.getNetwork(); networkView.fitContent(); else networkView.updateView();
Iterator ni = origView.getGraphPerspective().nodesIterator(); while (ni.hasNext()) { Node n = (Node) ni.next(); NodeView onv = origView.getNodeView(n); NodeView nnv = newView.getNodeView(n); newView.setZoom(origView.getZoom()); Point2D origCenter = ((DGraphView)origView).getCenter(); ((DGraphView)newView).setCenter(origCenter.getX(), origCenter.getY()); Iterator ei = origView.getGraphPerspective().edgesIterator(); while (ei.hasNext()) { Edge ee = (Edge) ei.next(); EdgeView oev = origView.getEdgeView(ee); EdgeView nev = newView.getEdgeView(ee);
final NodeView nv = view.getNodeView(selectedNode); if (nv != null) nv.setSelectedPaint(selectedNodeColor); final Edge selectedEdge = this.getEdge(objectName); if (selectedEdge != null) { final EdgeView ev = view.getEdgeView(selectedEdge); if (ev != null) ev.setSelectedPaint(selectedEdgeColor);
/** * Constructor. * * @param cyNetwork CyNetwork * @param cyNodes Set<CyNode> * @param cyEdges Set<CyEdge> */ public MergeNetworkEdit(CyNetwork cyNetwork, Set<CyNode> cyNodes, Set<CyEdge> cyEdges) { super("Merge Network"); // check args if (cyNetwork == null || cyNodes == null || cyEdges == null) throw new IllegalArgumentException("network, nodes, or edges is null"); // init args this.cyNetwork = cyNetwork; this.cyEdges = cyEdges; this.cyNodes = new HashMap<CyNode, Point2D.Double>(); CyNetworkView view = Cytoscape.getNetworkView(cyNetwork.getIdentifier()); if (view != null || view != Cytoscape.getNullNetworkView()) { for (CyNode cyNode : cyNodes) { NodeView nv = view.getNodeView(cyNode); Point2D.Double point = new Point2D.Double(nv.getXPosition(), nv.getYPosition()); this.cyNodes.put(cyNode, point); } } }
new_network_view.getNodeView(node) .setOffset(current_network_view.getNodeView(node).getXPosition(), current_network_view.getNodeView(node).getYPosition()); new_network_view.fitContent(); VisualStyle newVS = current_network_view.getVisualStyle();
String text; for (Object node : net.getNetwork().nodesList()) { text = net.getNodeView((Node) node).getLabel().getText(); strLen = text.length(); String text; for (Object node : net.getNetwork().nodesList()) { text = net.getNodeView((Node) node).getLabel().getText(); strLen = text.length(); Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
int modificationCount) { CyNetwork cyNetwork = networkView.getNetwork(); NodeView nodeView = networkView.getNodeView(node); DNodeView dingNodeView = (DNodeView) nodeView;
@SuppressWarnings("unchecked") public static void setNodeToolTips(CyNetworkView networkView) { // grab node attributes CyAttributes nodeAttributes = Cytoscape.getNodeAttributes(); // iterate through the nodes Iterator<NodeView> nodesIt = networkView.getNodeViewsIterator(); while (nodesIt.hasNext()) { NodeView nodeView = nodesIt.next(); String id = nodeView.getNode().getIdentifier(); String tip = nodeAttributes.getStringAttribute(id, MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE) + "\n" + nodeAttributes.getListAttribute(id, MapBioPaxToCytoscape.BIOPAX_CELLULAR_LOCATIONS); nodeView.setToolTip(tip); if(log.isDebugging()) log.debug("tooltip set "+ tip + " for node " + id); } networkView.updateView(); } }
/** * Deletes labelPosition attribute of selected nodes (if selectedOnly) or all nodes * This has the effect of moving labels back to their parent nodes position */ protected void resetLabelPositions() { // logger.info("Reseting labels position"); CyAttributes nodeAtts = Cytoscape.getNodeAttributes(); Collection<CyNode> selectedNodes = (Collection<CyNode>)network.getSelectedNodes(); // Go through all nodes deleting the label position attribute for (CyNode node: (List<CyNode>)network.nodesList()) { if (!supportsSelectedOnly() || !selectedOnly || selectedNodes.contains(node) ) if (nodeAtts.hasAttribute(node.getIdentifier(), "node.labelPosition")) { nodeAtts.deleteAttribute(node.getIdentifier(), "node.labelPosition"); // logger.info("Deleted label position attribute of node: " + node.toString() ); } } // redraw the network so that the new label positions are visible networkView.updateView(); networkView.redrawGraph(true, true); }
public void undo() { super.undo(); for (final NodeView nodeView : hiddenNodeViews) { networkView.showGraphObject(nodeView); nodeView.setSelected(true); GinyUtils.showEdges(networkView, nodeView); } networkView.updateView(); hideSelectedNodesAction.setEnabled(true); } }