use of cbit.vcell.graph.structures.StructureSuite in project vcell by virtualcell.
the class ITextWriter method generateDocReactionsImage.
public static BufferedImage generateDocReactionsImage(Model model, Integer width) throws Exception {
// if (model == null || !isValidResolutionSetting(resolution)) {
// throw new IllegalArgumentException("Invalid parameters for generating reactions image for model: " + model.getName());
// }
ReactionCartoon rcartoon = new ReactionCartoonFull();
rcartoon.setModel(model);
StructureSuite structureSuite = new AllStructureSuite(new Model.Owner() {
@Override
public Model getModel() {
return model;
}
});
rcartoon.setStructureSuite(structureSuite);
rcartoon.refreshAll();
// dummy settings to get the real dimensions.
BufferedImage dummyBufferedImage = new BufferedImage(DEF_IMAGE_WIDTH, DEF_IMAGE_HEIGHT, BufferedImage.TYPE_3BYTE_BGR);
Graphics2D dummyGraphics = (Graphics2D) dummyBufferedImage.getGraphics();
Dimension prefDim = rcartoon.getPreferedCanvasSize(dummyGraphics);
dummyGraphics.dispose();
// double width = prefDim.getWidth();
// double height = prefDim.getHeight();
double widthHeightRatio = (double) prefDim.getWidth() / (double) prefDim.getHeight();
if (width == null) {
width = ITextWriter.DEF_IMAGE_WIDTH;
}
int height = (int) ((double) width / widthHeightRatio);
// int MAX_IMAGE_HEIGHT = 532;
// if (width < ITextWriter.DEF_IMAGE_WIDTH) {
// width = ITextWriter.DEF_IMAGE_WIDTH;
// }
// height= height * width/prefDim.getWidth();
// if (height < ITextWriter.DEF_IMAGE_HEIGHT) {
// height = ITextWriter.DEF_IMAGE_HEIGHT;
// } else if (height > MAX_IMAGE_HEIGHT) {
// height = MAX_IMAGE_HEIGHT;
// }
// width= width * height/prefDim.getHeight();
Dimension newDim = new Dimension((int) width, (int) height);
rcartoon.getResizeManager().setZoomPercent((int) (100 * width / prefDim.getWidth()));
BufferedImage bufferedImage = new BufferedImage(newDim.width, newDim.height, BufferedImage.TYPE_3BYTE_BGR);
Graphics2D g = (Graphics2D) bufferedImage.getGraphics();
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
GraphContainerLayoutReactions containerLayout = new GraphContainerLayoutReactions();
containerLayout.layout(rcartoon, g, prefDim);
rcartoon.paint(g);
g.dispose();
return bufferedImage;
}
use of cbit.vcell.graph.structures.StructureSuite in project vcell by virtualcell.
the class ReactionCartoonTool method mouseReleased.
@Override
public void mouseReleased(MouseEvent event) {
if (getReactionCartoon() == null) {
return;
}
try {
if (dragStructTimer != null) {
dragStructTimer.stop();
}
endPointWorld = getReactionCartoon().getResizeManager().unzoom(event.getPoint());
Shape endShape = getReactionCartoon().pickWorld(endPointWorld);
if (event.isPopupTrigger() && mode == Mode.SELECT) {
// win, linux popup
popupMenu(getReactionCartoon().getSelectedShape(), event.getX(), event.getY());
return;
}
if (mode == Mode.SELECT && bStartRxContainerLabel) {
resetDropTargets(null, mode == Mode.STRUCTURE);
if (endShape != null && endShape instanceof ReactionContainerShape) {
Rectangle labelOutlineRectangle = ((ReactionContainerShape) endShape).getLabelOutline(endShape.getAbsX(), endShape.getAbsY());
boolean bLabel = labelOutlineRectangle.contains(startPointWorld.x, startPointWorld.y);
getGraphPane().setCursor((bLabel ? Cursor.getPredefinedCursor(Cursor.HAND_CURSOR) : Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)));
}
bStartRxContainerLabel = false;
RXContainerDropTargetInfo trueRXContainerDropTargetInfo = getSelectedContainerDropTargetInfo();
lastRXContainerDropTargetInfoMap = null;
if (trueRXContainerDropTargetInfo == null) {
// turn off rxDropTargetRectangles
getGraphPane().repaint();
return;
}
StructureSuite structureSuite = null;
structureSuite = getReactionCartoon().getStructureSuite();
if (structureSuite != null) {
Structure[] originalOrderedStructArr = structureSuite.getStructures().toArray(new Structure[0]);
// find where user wants to put the structure
try {
if (trueRXContainerDropTargetInfo != null) {
ArrayList<Structure> newStructOrderList = new ArrayList<Structure>(Arrays.asList(originalOrderedStructArr));
newStructOrderList.remove(((ReactionContainerShape) startShape).getStructure());
int indexEnd = newStructOrderList.indexOf(((ReactionContainerShape) trueRXContainerDropTargetInfo.dropShape).getStructure());
int indexClosestNeighbor = (trueRXContainerDropTargetInfo.closestNeighborShape == null ? (trueRXContainerDropTargetInfo.insertFlag == RXContainerDropTargetInfo.INSERT_BEGINNING ? 0 : newStructOrderList.size()) : newStructOrderList.indexOf(((ReactionContainerShape) trueRXContainerDropTargetInfo.closestNeighborShape).getStructure()));
if (indexClosestNeighbor < indexEnd) {
newStructOrderList.add(indexEnd, ((ReactionContainerShape) startShape).getStructure());
} else {
newStructOrderList.add(indexClosestNeighbor, ((ReactionContainerShape) startShape).getStructure());
}
if (structureSuite instanceof AllStructureSuite) {
((AllStructureSuite) structureSuite).setModelStructureOrder(true);
}
ArrayList<Diagram> newDiagramOrderList = new ArrayList<Diagram>();
for (Structure structure : newStructOrderList) {
newDiagramOrderList.add(getModel().getDiagram(structure));
}
getModel().setDiagrams(newDiagramOrderList.toArray(new Diagram[0]));
}
} catch (Exception e) {
e.printStackTrace();
}
}
return;
}
// else do select and move
switch(mode) {
case SELECT:
{
getGraphPane().setCursor(Cursor.getDefaultCursor());
if (bMoving) {
getGraphPane().invalidate();
((JViewport) getGraphPane().getParent()).revalidate();
getGraphPane().repaint();
saveDiagram();
} else if (bRectStretch) {
Point absLoc = rectShape.getSpaceManager().getRelPos();
Dimension size = rectShape.getSpaceManager().getSize();
// remove temporary rectangle
getReactionCartoon().removeShape(rectShape);
rectShape = null;
Rectangle rect = new Rectangle(absLoc.x, absLoc.y, size.width, size.height);
boolean bShift = (event.getModifiers() & InputEvent.SHIFT_MASK) == InputEvent.SHIFT_MASK;
boolean bCntrl = (event.getModifiers() & InputEvent.CTRL_MASK) == InputEvent.CTRL_MASK;
selectEventFromWorld(rect, bShift, bCntrl);
getGraphPane().repaint();
}
bMoving = false;
movingShape = null;
bRectStretch = false;
rectShape = null;
break;
}
case LINEDIRECTED:
{
getGraphPane().setCursor(Cursor.getDefaultCursor());
if (bLineStretch && getDragDistanceSquared() >= MIN_DRAG_DISTANCE_TO_CREATE_NEW_ELEMENTS_SQUARED) {
bLineStretch = false;
// set label and color for line depending on which shape the edge started.
// (rather than attachment area on ReactionStepShape)
LineType lineType = getLineTypeFromDirection(startShape, endPointWorld);
if (endShape instanceof SimpleReactionShape) {
SimpleReaction simpleReaction = (SimpleReaction) endShape.getModelObject();
Object startShapeObject = null;
if (startShape != null) {
startShapeObject = startShape.getModelObject();
}
if (startShapeObject instanceof SpeciesContext) {
SpeciesContext speciesContext = (SpeciesContext) startShapeObject;
lineAction(speciesContext, simpleReaction);
} else if (startShapeObject instanceof Structure) {
Structure structure = (Structure) startShapeObject;
lineActon(structure, simpleReaction);
}
} else if (endShape instanceof SpeciesContextShape) {
SpeciesContext speciesContextEnd = (SpeciesContext) endShape.getModelObject();
Object startShapeObject = null;
if (startShape != null) {
startShapeObject = startShape.getModelObject();
}
if (startShapeObject instanceof SimpleReaction) {
SimpleReaction simpleReaction = (SimpleReaction) startShapeObject;
lineAction(simpleReaction, speciesContextEnd);
} else if (startShapeObject instanceof FluxReaction) {
FluxReaction fluxReaction = (FluxReaction) startShapeObject;
lineAction(fluxReaction, speciesContextEnd);
} else if (startShapeObject instanceof SpeciesContext) {
SpeciesContext speciesContextStart = (SpeciesContext) startShapeObject;
if (!speciesContextStart.equals(speciesContextEnd)) {
lineAction(speciesContextStart, speciesContextEnd);
}
} else if (startShapeObject instanceof Structure) {
Structure startStructure = (Structure) startShapeObject;
lineAction(startStructure, speciesContextEnd);
}
} else if (endShape instanceof FluxReactionShape) {
FluxReaction fluxReaction = (FluxReaction) endShape.getModelObject();
fluxReaction.setModel(getModel());
Object startShapeObject = null;
if (startShape != null) {
startShapeObject = startShape.getModelObject();
}
if (startShapeObject instanceof SpeciesContext) {
SpeciesContext speciesContext = (SpeciesContext) startShapeObject;
lineAction(speciesContext, fluxReaction);
} else if (startShapeObject instanceof Structure) {
Structure structure = (Structure) startShapeObject;
lineActon(structure, fluxReaction);
}
// remove temporary edge
getReactionCartoon().removeShape(edgeShape);
edgeShape = null;
} else if (endShape instanceof ReactionContainerShape) {
Structure endStructure = (Structure) endShape.getModelObject();
Object startObject = null;
if (startShape != null) {
startObject = startShape.getModelObject();
}
if (startObject instanceof SimpleReaction) {
SimpleReaction reaction = (SimpleReaction) startObject;
lineAction(reaction, endStructure);
} else if (startObject instanceof FluxReaction) {
FluxReaction reaction = (FluxReaction) startObject;
lineAction(reaction, endStructure);
} else if (startObject instanceof SpeciesContext) {
SpeciesContext speciesContextStart = (SpeciesContext) startObject;
lineAction(speciesContextStart, endStructure);
} else if (startObject instanceof Structure) {
Structure startStructure = (Structure) startObject;
lineAction(startStructure, endStructure, endShape);
}
}
}
saveDiagram();
break;
}
case LINECATALYST:
{
getGraphPane().setCursor(Cursor.getDefaultCursor());
if (bLineStretch && getDragDistanceSquared() >= MIN_DRAG_DISTANCE_TO_CREATE_NEW_ELEMENTS_SQUARED) {
bLineStretch = false;
// set label and color for line depending on which shape the edge started.
// (rather than attachment area on ReactionStepShape)
Object startObject = startShape.getModelObject();
Object endObject = endShape.getModelObject();
ReactionStep reactionStep = null;
SpeciesContext speciesContext = null;
if (startObject instanceof ReactionStep) {
reactionStep = (ReactionStep) startObject;
if (endObject instanceof SpeciesContext) {
if (StructureUtil.reactionHereCanHaveParticipantThere(reactionStep.getStructure(), ((SpeciesContext) endObject).getStructure())) {
speciesContext = (SpeciesContext) endObject;
}
} else if (endObject instanceof Structure) {
Structure endStructure = (Structure) endObject;
if (StructureUtil.reactionHereCanHaveParticipantThere(reactionStep.getStructure(), endStructure)) {
speciesContext = getReactionCartoon().getModel().createSpeciesContext(endStructure);
getReactionCartoon().notifyChangeEvent();
Point endPos = edgeShape.getEnd();
positionShapeForObject(endStructure, speciesContext, endPos);
}
}
} else if (startObject instanceof SpeciesContext) {
speciesContext = (SpeciesContext) startObject;
if (endObject instanceof ReactionStep) {
if (StructureUtil.reactionHereCanHaveParticipantThere(((ReactionStep) endObject).getStructure(), speciesContext.getStructure())) {
reactionStep = (ReactionStep) endObject;
}
} else if (endObject instanceof Structure) {
Structure endStructure = (Structure) endObject;
if (StructureUtil.reactionHereCanHaveParticipantThere(endStructure, speciesContext.getStructure())) {
reactionStep = getReactionCartoon().getModel().createSimpleReaction(endStructure);
getReactionCartoon().notifyChangeEvent();
Point endPos = edgeShape.getEnd();
positionShapeForObject(endStructure, reactionStep, endPos);
}
}
} else if (startObject instanceof Structure) {
Structure startStructure = (Structure) startObject;
if (endObject instanceof ReactionStep) {
reactionStep = (ReactionStep) endObject;
if (StructureUtil.reactionHereCanHaveParticipantThere(reactionStep.getStructure(), startStructure)) {
speciesContext = getReactionCartoon().getModel().createSpeciesContext(startStructure);
getReactionCartoon().notifyChangeEvent();
positionShapeForObject(startStructure, speciesContext, startPointWorld);
}
} else if (endObject instanceof SpeciesContext) {
speciesContext = (SpeciesContext) endObject;
if (StructureUtil.reactionHereCanHaveParticipantThere(startStructure, speciesContext.getStructure())) {
reactionStep = getReactionCartoon().getModel().createSimpleReaction(startStructure);
getReactionCartoon().notifyChangeEvent();
positionShapeForObject(startStructure, reactionStep, startPointWorld);
}
} else if (endObject instanceof Structure) {
Structure endStructure = (Structure) endObject;
if (StructureUtil.reactionHereCanHaveParticipantThere(startStructure, endStructure)) {
speciesContext = getReactionCartoon().getModel().createSpeciesContext(endStructure);
reactionStep = getReactionCartoon().getModel().createSimpleReaction(startStructure);
getReactionCartoon().notifyChangeEvent();
Point endPos = edgeShape.getEnd();
positionShapeForObject(endStructure, speciesContext, endPos);
positionShapeForObject(startStructure, reactionStep, startPointWorld);
} else if (StructureUtil.reactionHereCanHaveParticipantThere(endStructure, startStructure)) {
speciesContext = getReactionCartoon().getModel().createSpeciesContext(startStructure);
reactionStep = getReactionCartoon().getModel().createSimpleReaction(endStructure);
getReactionCartoon().notifyChangeEvent();
positionShapeForObject(startStructure, speciesContext, startPointWorld);
Point endPos = edgeShape.getEnd();
positionShapeForObject(endStructure, reactionStep, endPos);
}
}
}
if (reactionStep != null && speciesContext != null) {
Catalyst catalyst = null;
for (ReactionParticipant participant : reactionStep.getReactionParticipants()) {
if (participant instanceof Catalyst && participant.getSpeciesContext().equals(speciesContext)) {
catalyst = (Catalyst) participant;
}
}
if (catalyst == null) {
reactionStep.addCatalyst(speciesContext);
getReactionCartoon().notifyChangeEvent();
}
// add reactionParticipant to model
} else {
getGraphPane().repaint();
}
}
saveDiagram();
break;
}
default:
{
break;
}
}
} catch (Exception e) {
System.out.println("CartoonTool.mouseReleased: uncaught exception");
e.printStackTrace(System.out);
}
resetMouseActionHistory();
getGraphPane().repaint();
}
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