/**
* 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;
}
/**
* 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 (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;
}
/**
* 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;
}
/**
* 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;
}