private void realizeChemEdge(
Graph2D graph, Edge newEdge, Attachment sourceAttachment, Attachment targetAttachment) {
EdgeMap edgeTypeMap = (EdgeMap) graph.getDataProvider(EdgeMapKeys.EDGE_INFO);
EdgeRealizer er = graph.getRealizer(newEdge);
er.setLineColor(Color.BLACK);
er.setLineType(LineType.LINE_1);
edgeTypeMap.set(newEdge, new SViewEdgeInfo(EdgeType.CHEM, sourceAttachment, targetAttachment));
}
private void test(int seed) {
RandomGraphGenerator rg = new RandomGraphGenerator(seed);
rg.setNodeCount(100);
rg.setEdgeCount(300);
rg.allowCycles(true);
Graph graph1 = rg.generate();
EdgeMap cycleEdge = Maps.createIndexEdgeMap(new boolean[graph1.E()]);
// find a set of edges whose reversal make the given graph
// acyclic. reverse whose edges
t1.start();
Cycles.findCycleEdges(graph1, cycleEdge);
int count1 = 0;
for (EdgeCursor ec = graph1.edges(); ec.ok(); ec.next()) {
if (cycleEdge.getBool(ec.edge())) {
graph1.reverseEdge(ec.edge());
count1++;
}
}
t1.stop();
// check acyclicity of graph
if (GraphChecker.isCyclic(graph1)) {
D.bug("graph1 still contains cycles!!!");
EdgeList cycle = Cycles.findCycle(graph1, true);
error("cycle = " + cycle);
}
rg.setSeed(seed);
Graph graph2 = rg.generate();
// use alternative DFS based method to detect
// with a set of cyclicity edges.
t2.start();
Cycles.findCycleEdgesDFS(graph2, cycleEdge);
int count2 = 0;
for (EdgeCursor ec = graph2.edges(); ec.ok(); ec.next()) {
if (cycleEdge.getBool(ec.edge())) {
graph2.reverseEdge(ec.edge());
count2++;
}
}
t2.stop();
if (GraphChecker.isCyclic(graph2)) {
D.bug("graph2 still contains cycles!!!");
EdgeList cycle = Cycles.findCycle(graph2, true);
error("cycle = " + cycle);
}
akku1 += count1;
akku2 += count2;
}
private void addBranchToBranchEdge(
Edge currentEdge, Attachment sourceAttachment, Attachment targetAttachment) {
EdgeMap edgeTypeMap = (EdgeMap) _graph.getDataProvider(EdgeMapKeys.EDGE_INFO);
Node sourceNode = _viewModel.getViewNode(currentEdge.source());
Node targetNode = _viewModel.getViewNode(currentEdge.target());
Edge newEdge = _graph.createEdge(sourceNode, targetNode);
edgeTypeMap.set(
newEdge, new SViewEdgeInfo(EdgeType.BRANCH_BRANCH, sourceAttachment, targetAttachment));
sourceNode = getViewStartingNode(newEdge.source(), _graph);
targetNode = getViewStartingNode(newEdge.target(), _graph);
_viewModel.addComplentaryViewNodes(sourceNode, targetNode);
}
/**
* get the starting node of the sequence in where the current node is sitting in
*
* @deprecated use getViewStartingNode
* @param node
* @param graph
* @return
*/
@Deprecated
private Node getStartingNode(Node node, Graph2D graph) {
if (_viewModel.getStartingViewNodeList().contains(node)) {
return node;
} else {
NodeCursor pres = node.predecessors();
Edge edge;
Node currentNode = node;
EdgeMap edgeMap = (EdgeMap) graph.getDataProvider(EdgeMapKeys.EDGE_INFO);
Node preNode = currentNode;
while (pres.ok()) {
for (; pres.ok(); pres.next()) {
edge = currentNode.getEdge(pres.node());
EdgeType edgeType = ((SViewEdgeInfo) edgeMap.get(edge)).getType();
if ((edgeType == EdgeType.REGULAR) || (edgeType == EdgeType.MODIFIED_P)) {
currentNode = pres.node();
break;
}
}
if (currentNode != preNode) {
pres = currentNode.predecessors();
preNode = currentNode;
} else {
break;
}
}
if (_viewModel.getStartingViewNodeList().contains(currentNode)) {
return currentNode;
} else {
return null;
}
}
}
/**
* Create a standard graph. Each graph contains 3 nodes, base<-R->P where R and P are standard
* monomers
*
* @param notation : the base monomer id. A, T, C, G, U
* @return a graph that represents a notation
*/
@Deprecated
public static Graph2D createNucleictideNodeGraph(String notation)
throws MonomerException, IOException, JDOMException {
// a graph is used in here because we need to associate data with every nodes
Graph2D graph = new Graph2D();
graph.setDefaultNodeRealizer(new MonomerNodeRealizer());
NodeMap nodePropertiesNodeMap = graph.createNodeMap();
graph.addDataProvider(NodeMapKeys.MONOMER_REF, nodePropertiesNodeMap);
EdgeMap edgeMap = graph.createEdgeMap();
graph.addDataProvider(EdgeMapKeys.EDGE_INFO, edgeMap);
GraphCopier copier = new GraphCopier(graph.getGraphCopyFactory());
copier.setDataProviderContentCopying(true);
copier.setEdgeMapCopying(true);
copier.setNodeMapCopying(true);
String baseMonomerID = notation.substring(notation.indexOf("(") + 1, notation.indexOf(")"));
baseMonomerID = baseMonomerID.replace("[", "");
baseMonomerID = baseMonomerID.replace("]", "");
Node baseNode = copier.copy(createNucleicAcidBaseNode(baseMonomerID), graph).firstNode();
NodeRealizer baseNodeRealizer = graph.getRealizer(baseNode);
baseNodeRealizer.setCenter(centerX, centerY + size + distance);
String r = notation.substring(0, notation.indexOf("("));
r = r.replace("[", "");
r = r.replace("]", "");
Node rNode = copier.copy(createNucleicAcidBackboneNode(r, Monomer.ID_R), graph).firstNode();
NodeRealizer rNodeRealizer = graph.getRealizer(rNode);
rNodeRealizer.setCenter(centerX, centerY);
String p = notation.substring(notation.indexOf(")") + 1);
p = p.replace("[", "");
p = p.replace("]", "");
Node pNode = copier.copy(createNucleicAcidBackboneNode(p, Monomer.ID_P), graph).firstNode();
NodeRealizer pNodeRealizer = graph.getRealizer(pNode);
pNodeRealizer.setCenter(centerX + size + distance, centerY);
MonomerInfo pKeys = (MonomerInfo) nodePropertiesNodeMap.get(pNode);
MonomerInfo rKeys = (MonomerInfo) nodePropertiesNodeMap.get(rNode);
MonomerInfo baseKeys = (MonomerInfo) nodePropertiesNodeMap.get(baseNode);
// r->p
Edge edge = graph.createEdge(rNode, pNode);
Attachment sourceAttachment =
rKeys.getAttachment(Attachment.BACKBONE_MONOMER_RIGHT_ATTACHEMENT);
Attachment targetAttachment = pKeys.getAttachment(Attachment.BACKBONE_MONOMER_LEFT_ATTACHEMENT);
rKeys.setConnection(sourceAttachment, true);
pKeys.setConnection(targetAttachment, true);
edgeMap.set(edge, new EditorEdgeInfoData(sourceAttachment, targetAttachment));
// r->base
edge = graph.createEdge(rNode, baseNode);
sourceAttachment = rKeys.getAttachment(Attachment.BACKBONE_MONOMER_BRANCH_ATTACHEMENT);
targetAttachment = baseKeys.getAttachment(Attachment.BRANCH_MONOMER_ATTACHEMENT);
rKeys.setConnection(sourceAttachment, true);
baseKeys.setConnection(targetAttachment, true);
edgeMap.set(edge, new EditorEdgeInfoData(sourceAttachment, targetAttachment));
return graph;
}