private boolean isHit(Edge pEdge, BitSet pPassFilter_nodeBits) { // Get the list of relevant nodes for this edge List<Node> adjacentNodes = new ArrayList<Node>(); if (nodeType == NODE_SOURCE) { adjacentNodes.add(pEdge.getSource()); } else if (nodeType == NODE_TARGET) { adjacentNodes.add(pEdge.getTarget()); } else if (nodeType == NODE_SOURCE_TARGET) { adjacentNodes.add(pEdge.getSource()); adjacentNodes.add(pEdge.getTarget()); } else { //nodeType == NODE_UNDEFINED --Neither source or target is selected return false; } int nodeIndex = -1; for (int i=0; i < adjacentNodes.size(); i++) { nodeIndex = network.nodesList().indexOf(adjacentNodes.get(i)); if (pPassFilter_nodeBits.get(nodeIndex) == true) { return true; } } return false; } }
for (final Edge edgeCandidate : edges) { if (knownNodes.contains(edgeCandidate.getSource()) && knownNodes.contains(edgeCandidate.getTarget())) acceptableEdges.add(edgeCandidate.getRootGraphIndex());
/** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void actionPerformed(ActionEvent e) { final CyNetwork currentNetwork = Cytoscape.getCurrentNetwork(); Set<CyEdge> edgeSet = currentNetwork.getSelectedEdges(); final List<Edge> selectedEdges = new ArrayList<Edge>(edgeSet); final Set<Node>nodesToSelect = new HashSet<Node>(); for (Edge edge: selectedEdges) { nodesToSelect.add(edge.getSource()); nodesToSelect.add(edge.getTarget()); } currentNetwork.setSelectedNodeState(nodesToSelect, true); Cytoscape.getCurrentNetworkView().updateView(); } // actionPerformed
giny.model.Node target = edge.getTarget();
final Node target = mapNN.get(edge_ori.getTarget()); if (source==null||target==null) { // some of the node may be exluded when intersection or difference continue;
if (!e2.isDirected()) return false; return matchNode(net1, e1.getSource(), net2, e2.getSource()) && matchNode(net1, e1.getTarget(), net2, e2.getTarget()); } else { //non directed if (e2.isDirected()) return false; if (matchNode(net1, e1.getSource(), net2, e2.getSource()) && matchNode(net1, e1.getTarget(), net2, e2.getTarget())) return true; if (matchNode(net1, e1.getSource(), net2, e2.getTarget()) && matchNode(net1, e1.getTarget(), net2, e2.getSource())) return true; return false;
targetPair.value = new Integer(edge.getTarget().getRootGraphIndex());
CyAttributes edgeAtts = Cytoscape.getEdgeAttributes(); String sourceId = ed.getSource().getIdentifier(); String targetId = ed.getTarget().getIdentifier(); String edgeId = ed.getIdentifier();
/** * An object passes this Filter if it is the source/target * node for an edge that has a matching property for * the given Edge atttribute. */ public boolean passesFilter(Object object) { Filter filter = FilterManager.defaultManager().getFilter(this.filter); if (filter == null) { return false; } if (!(object instanceof Edge)) { return false; } Edge edge = (Edge) object; //get the list of all relevant edges Node adjacentNode; if (target == SOURCE) { return filter.passesFilter(edge.getSource()); } else if (target == TARGET) { return filter.passesFilter(edge.getTarget()); } else { return filter.passesFilter(edge.getSource()) || filter.passesFilter(edge.getTarget()); } }
&& (noNodesSelected || graphView.getNodeView(currentEdgeView.getEdge().getSource()).isSelected() || graphView.getNodeView(currentEdgeView.getEdge().getTarget()).isSelected())) { currentEdgeView.getBend().removeAllHandles(); } else {
new GMLNode("" + (-currentEdge.getSource().getRootGraphIndex()))); currentGML.addMapping("target", new GMLNode("" + (-currentEdge.getTarget().getRootGraphIndex())));
/** * DOCUMENT ME! * * @param args DOCUMENT ME! */ public static void main(String[] args) { final RootGraph root = new FingExtensibleRootGraph(new MyNodeDepot(), new MyEdgeDepot()); final Node n1 = root.getNode(root.createNode()); final Node n2 = root.getNode(root.createNode()); final Node n3 = root.getNode(root.createNode()); final Node n4 = root.getNode(root.createNode()); root.createEdge(n1, n2, false); int edge_idx = root.createEdge(n1, n3, false); final Edge del1 = root.getEdge(edge_idx); edge_idx = root.createEdge(n2, n3, false); final Edge del2 = root.getEdge(edge_idx); root.removeEdge(del1); root.removeEdge(del2); edge_idx = root.createEdge(n1, n4, false); final Edge subedge = root.getEdge(edge_idx); final Node src = subedge.getSource(); final Node target = subedge.getTarget(); if ((src == null) || (target == null)) throw new IllegalStateException("the bug is here"); } }