/**
* create an (modified) amino acid node
*
* @param monomerID
* @return amino acid node graph
*/
@Deprecated
public static Graph2D createAminoAcidNode(String monomerID)
throws MonomerException, IOException, JDOMException {
MonomerFactory monomerFactory = MonomerFactory.getInstance();
Map<String, Map<String, Monomer>> monomerDB = monomerFactory.getMonomerDB();
Graph2D graph = new Graph2D();
MonomerInfo monomerKeys = new MonomerInfo(Monomer.PEPTIDE_POLYMER_TYPE, monomerID);
Monomer monomer = monomerDB.get(monomerKeys.getPolymerType()).get(monomerKeys.getMonomerID());
if (monomer == null) {
throw new MonomerException("Invalid HELM notation " + monomerID);
}
MonomerNodeRealizer nodeRealizer = new MonomerNodeRealizer(MonomerNodeRealizer.DIAMOND);
nodeRealizer.setSize(size, size);
nodeRealizer.setLabelText(monomerID);
nodeRealizer.setFillColor(ColorMap.getAminoAcidColor(monomer.getNaturalAnalog()));
nodeRealizer.getLabel().setFontSize(calculateFontSize(monomerID));
Node node = graph.createNode(nodeRealizer);
NodeMap nodeMap = graph.createNodeMap();
nodeMap.set(node, monomerKeys);
graph.addDataProvider(NodeMapKeys.MONOMER_REF, nodeMap);
return graph;
}
/**
* create a registared chemical structure node
*
* @param monomerID
* @return chemcial modifier node graph
*/
@Deprecated
public static Graph2D createChemNode(String monomerID)
throws MonomerException, IOException, JDOMException {
MonomerFactory monomerFactory = MonomerFactory.getInstance();
Map<String, Map<String, Monomer>> monomerDB = monomerFactory.getMonomerDB();
MonomerInfo monomerKeys = new MonomerInfo(Monomer.CHEMICAL_POLYMER_TYPE, monomerID);
Monomer monomer = monomerDB.get(monomerKeys.getPolymerType()).get(monomerKeys.getMonomerID());
if (monomer == null) {
throw new MonomerException("Invalid chemical ID " + monomerID);
}
Graph2D graph = new Graph2D();
MonomerNodeRealizer nodeRealizer = new MonomerNodeRealizer(MonomerNodeRealizer.HEXAGON);
nodeRealizer.setSize(size, size);
nodeRealizer.setLabelText(monomerID);
nodeRealizer.getLabel().setFontSize(calculateFontSize(monomerID));
nodeRealizer.setFillColor(new Color(200, 0, 255)); // was Color.magenta;
Node node = graph.createNode(nodeRealizer);
NodeMap nodeMap = graph.createNodeMap();
nodeMap.set(node, monomerKeys);
graph.addDataProvider(NodeMapKeys.MONOMER_REF, nodeMap);
return graph;
}
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 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);
}
private Edge addSimpleEdge(Edge currentEdge) {
Node sourceFrom = currentEdge.source();
Node from = _viewModel.getViewNode(sourceFrom);
if (from == null) {
from = realizeNeigbour(_graph, sourceFrom);
}
Node sourceTo = currentEdge.target();
Node to = _viewModel.getViewNode(sourceTo);
if (to == null) {
to = realizeNeigbour(_graph, sourceTo);
}
Edge newEdge = _graph.createEdge(from, to);
return newEdge;
}
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;
}
/**
* 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;
}
}
}
/**
* Build a (modified) nucleic acid base node, this node should already registared in the database
*
* @param monomerID : the name of the base node
* @return a graph contains a single (base) node
*/
@Deprecated
public static Graph2D createNucleicAcidBaseNode(String monomerID)
throws MonomerException, IOException, JDOMException {
MonomerFactory monomerFactory = MonomerFactory.getInstance();
Map<String, Map<String, Monomer>> monomerDB = monomerFactory.getMonomerDB();
Graph2D graph = new Graph2D();
MonomerNodeRealizer baseNodeRealizer = new MonomerNodeRealizer(MonomerNodeRealizer.DIAMOND);
graph.setDefaultNodeRealizer(baseNodeRealizer);
baseNodeRealizer.setSize(size, size);
MonomerInfo monomerKeys = new MonomerInfo(Monomer.NUCLIEC_ACID_POLYMER_TYPE, monomerID);
Monomer baseMonomer =
monomerDB.get(monomerKeys.getPolymerType()).get(monomerKeys.getMonomerID());
if (baseMonomer == null) {
throw new MonomerException("Invalid base monomer " + monomerID);
}
Node baseNode = graph.createNode();
Color fillColor = ColorMap.getNucleotidesColor(baseMonomer.getNaturalAnalog());
baseNodeRealizer.setFillColor(fillColor);
Color textColor = Color.BLACK;
// was: Color textColor = new Color(23 - fillColor.getRGB());
// but we want identical view at left panel and at sequence panel, so
// textColor is always set to black.
baseNodeRealizer.setLabelText(monomerID);
baseNodeRealizer.getLabel().setTextColor(textColor);
baseNodeRealizer.getLabel().setFontSize(calculateFontSize(monomerID));
graph.setRealizer(baseNode, baseNodeRealizer);
NodeMap nodePropertiesNodeMap = graph.createNodeMap();
graph.addDataProvider(NodeMapKeys.MONOMER_REF, nodePropertiesNodeMap);
nodePropertiesNodeMap.set(baseNode, monomerKeys);
return graph;
}
/**
* create a (modified) nucleic acid backbone node. this monomer should already registared in the
* monomer database
*
* @param monomerID
* @return A graph contains a nucleic acid backbone node
*/
@Deprecated
public static Graph2D createNucleicAcidBackboneNode(String monomerID, String naturalAnalog)
throws MonomerException, IOException, JDOMException {
final String url = MacromoleculeEditor.class.getResource("resource/").getFile();
MonomerFactory monomerFactory = MonomerFactory.getInstance();
Map<String, Map<String, Monomer>> monomerDB = monomerFactory.getMonomerDB();
Graph2D graph = new Graph2D();
MonomerNodeRealizer backboneNodeRealizer = null;
if (naturalAnalog.equalsIgnoreCase(Monomer.ID_R)) {
backboneNodeRealizer = new MonomerNodeRealizer(MonomerNodeRealizer.ROUND_RECT);
} else if (naturalAnalog.equalsIgnoreCase(Monomer.ID_P)) {
backboneNodeRealizer = new MonomerNodeRealizer(MonomerNodeRealizer.ELLIPSE);
} else {
backboneNodeRealizer = new MonomerNodeRealizer(MonomerNodeRealizer.OCTAGON);
}
backboneNodeRealizer.setFillColor(ColorMap.getNucleotidesColor(naturalAnalog));
backboneNodeRealizer.setSize(size, size);
graph.setDefaultNodeRealizer(backboneNodeRealizer);
MonomerInfo monomerKeys = new MonomerInfo(Monomer.NUCLIEC_ACID_POLYMER_TYPE, monomerID);
Monomer monomer = monomerDB.get(monomerKeys.getPolymerType()).get(monomerKeys.getMonomerID());
if (monomer == null) {
throw new MonomerException("Invalid backbone monomer ID " + monomerID);
}
Node baseNode = graph.createNode();
backboneNodeRealizer.setLabelText(monomerID);
backboneNodeRealizer.setFillColor(ColorMap.getNucleotidesColor(monomer.getNaturalAnalog()));
graph.setRealizer(baseNode, backboneNodeRealizer);
NodeMap nodePropertiesNodeMap = graph.createNodeMap();
graph.addDataProvider(NodeMapKeys.MONOMER_REF, nodePropertiesNodeMap);
nodePropertiesNodeMap.set(baseNode, monomerKeys);
return graph;
}
/**
* a dummy base node with no monomer attached to it
*
* @param monomerID
* @return dummy nucleic acid base node graph
*/
public static Graph2D createDummyNucleicAcidBaseNode(String monomerID) {
Graph2D graph = new Graph2D();
MonomerNodeRealizer baseNodeRealizer = new MonomerNodeRealizer(MonomerNodeRealizer.DIAMOND);
graph.setDefaultNodeRealizer(baseNodeRealizer);
final int size = 30;
baseNodeRealizer.setSize(size, size);
MonomerInfo monomerKeys = new MonomerInfo(Monomer.NUCLIEC_ACID_POLYMER_TYPE, monomerID);
Node baseNode = graph.createNode();
Color fillColor = ColorMap.getNucleotidesColor("X");
baseNodeRealizer.setFillColor(fillColor);
Color textColor = new Color(23 - fillColor.getRGB());
baseNodeRealizer.setLabelText(monomerID);
baseNodeRealizer.getLabel().setTextColor(textColor);
baseNodeRealizer.getLabel().setFontSize(14);
graph.setRealizer(baseNode, baseNodeRealizer);
NodeMap nodePropertiesNodeMap = graph.createNodeMap();
graph.addDataProvider(NodeMapKeys.MONOMER_REF, nodePropertiesNodeMap);
nodePropertiesNodeMap.set(baseNode, monomerKeys);
NodeLabel anotationLabel = new NodeLabel("");
anotationLabel.setModel(NodeLabel.FREE);
anotationLabel.setFreeOffset(
-baseNodeRealizer.getHeight() / 2, -baseNodeRealizer.getWidth() / 4);
anotationLabel.setTextColor(ANOTATION_COLOR);
anotationLabel.setFontSize(baseNodeRealizer.getLabel().getFontSize() + 2);
baseNodeRealizer.addLabel(anotationLabel);
return graph;
}
/**
* 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;
}
public static String getNotation(Node node) {
Graph2D graph = (Graph2D) node.getGraph();
NodeMap nodeMap = (NodeMap) graph.getDataProvider(NodeMapKeys.FOLDER_NODE_NOTATION);
return (String) nodeMap.get(node);
}
private Node getViewStartingNode(Node node, Graph2D view) {
NodeMap startingNodeMap = (NodeMap) _graph.getDataProvider(NodeMapKeys.NODE2STARTING_NODE);
return (Node) startingNodeMap.get(node);
}