public static String getStructureImageFilePath(Node node) {
Graph2D graph = (Graph2D) node.getGraph();
NodeRealizer nr = graph.getRealizer(node);
String fileName = nr.getLabelText();
fileName = fileName + ".png";
return NUCLEOTIDE_DIRECTORY + System.getProperty("file.separator") + fileName;
}
private Node createNode(String label, Graph2D graph) {
Node node = graph.createNode();
NodeRealizer nodeRealizer = graph.getRealizer(node);
nodeRealizer.getLabel().setText(label);
return node;
}
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 Node createChemNode(String label, Graph2D graph) {
Node chem = createNode(label, graph);
NodeRealizer nodeRealizer = graph.getRealizer(chem);
nodeRealizer.setTransparent(false);
NodeLabel nl = nodeRealizer.getLabel(0);
// nodeRealizer.setSize(_layoutMetrics.getChemNodeSize(),
// _layoutMetrics.getChemNodeSize());
nodeRealizer.setSize(nl.getBox().getWidth() + 10, nl.getBox().getHeight());
nl.setFontSize(_layoutMetrics.getChemNodeFontSize());
nl.setFontStyle(Font.BOLD);
nl.setModel(NodeLabel.INTERNAL);
nl.setPosition(NodeLabel.CENTER);
nl.setAlignment(NodeLabel.ALIGN_CENTER);
nl.setTextColor(Color.BLACK);
return chem;
}
private Node createErrorNode(String label, Graph2D graph) {
Node node = createNode(label, graph);
NodeRealizer nodeRealizer = graph.getRealizer(node);
nodeRealizer.setTransparent(true);
nodeRealizer.setLineColor(Color.white);
NodeLabel nl = nodeRealizer.getLabel(0);
nl.setFontSize(_layoutMetrics.getLabelFontSize() + 15);
nl.setFontStyle(Font.PLAIN);
nl.setModel(NodeLabel.INTERNAL);
nl.setPosition(NodeLabel.CENTER);
nl.setAlignment(NodeLabel.ALIGN_LEFT);
nl.setTextColor(Color.cyan);
nodeRealizer.setSize(nl.getBox().getWidth(), nl.getBox().getHeight());
return node;
}
/**
* 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;
}