@Deprecated
public static NodeLabel configAnnotationLabel(NodeLabel annotationLabel, boolean isPeptide) {
annotationLabel.setModel(NodeLabel.EIGHT_POS);
if (isPeptide) {
annotationLabel.setPosition(NodeLabel.N);
} else {
annotationLabel.setPosition(NodeLabel.NW);
}
annotationLabel.setTextColor(ANOTATION_COLOR);
return annotationLabel;
}
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;
}
/**
* 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;
}