Examples with AllStructureSuite cbit.vcell.graph.structures.AllStructureSuite used on opensource projects

Example 1 with AllStructureSuite

use of cbit.vcell.graph.structures.AllStructureSuite 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();
}

Example 2 with AllStructureSuite

use of cbit.vcell.graph.structures.AllStructureSuite in project vcell by virtualcell.

the class ReactionCartoonTool method layout.

public void layout(String layoutName, boolean bWarn) throws Exception {
    System.out.println(layoutName);
    // -----Turn off user forced reaction diagram structure order
    if (getReactionCartoon().getStructureSuite() instanceof AllStructureSuite) {
        AllStructureSuite allStructureSuite = ((AllStructureSuite) getReactionCartoon().getStructureSuite());
        if (allStructureSuite.getModelStructureOrder()) {
            // make auto-sort
            allStructureSuite.setModelStructureOrder(false);
            // get auto-sorted structures
            List<Structure> autoSortedStructures = allStructureSuite.getStructures();
            ArrayList<Diagram> newDiagramOrderList = new ArrayList<Diagram>();
            for (Structure structure : autoSortedStructures) {
                newDiagramOrderList.add(getModel().getDiagram(structure));
            }
            Diagram[] autosortDiagramOrder = newDiagramOrderList.toArray(new Diagram[0]);
            if (bWarn && autoSortedStructures.size() > 1) {
                // no point in warning if there's just one structure
                final String OK = "OK";
                String response = DialogUtils.showWarningDialog(getGraphPane(), "Re-organizing species/reaction display positions...", new String[] { OK, "Cancel" }, OK);
                if (response != null && response.equals(OK)) {
                    // getModel().setDiagrams(autosortDiagramOrder);
                    allStructureSuite.setModelStructureOrder(true);
                } else {
                    allStructureSuite.setModelStructureOrder(true);
                    return;
                }
            } else {
                getModel().setDiagrams(autosortDiagramOrder);
            }
        }
    }
    // -----
    GraphLayoutTasks.dispatchTasks(getGraphPane(), graphEmbeddingManager, this, layoutName);
}

Example 3 with AllStructureSuite

use of cbit.vcell.graph.structures.AllStructureSuite 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;
}

Example 4 with AllStructureSuite

use of cbit.vcell.graph.structures.AllStructureSuite in project vcell by virtualcell.

the class BioModelEditorModelPanel method bioModelChange.

private void bioModelChange() {
    if (bioModel == null) {
        return;
    }
    reactionCartoonEditorPanel.setModel(bioModel.getModel());
    reactionCartoonEditorPanel.setStructureSuite(new AllStructureSuite(this));
    bioModel.getRelationshipModel().removeRelationShipListener(reactionCartoonEditorPanel.getReactionCartoonFull());
    bioModel.getRelationshipModel().removeRelationShipListener(reactionCartoonEditorPanel.getReactionCartoonMolecule());
    bioModel.getRelationshipModel().removeRelationShipListener(reactionCartoonEditorPanel.getReactionCartoonRule());
    bioModel.getRelationshipModel().addRelationShipListener(reactionCartoonEditorPanel.getReactionCartoonFull());
    bioModel.getRelationshipModel().addRelationShipListener(reactionCartoonEditorPanel.getReactionCartoonMolecule());
    bioModel.getRelationshipModel().addRelationShipListener(reactionCartoonEditorPanel.getReactionCartoonRule());
    reactionCartoonEditorPanel.getReactionCartoonFull().refreshRelationshipInfo(bioModel.getRelationshipModel());
    reactionCartoonEditorPanel.getReactionCartoonMolecule().refreshRelationshipInfo(bioModel.getRelationshipModel());
    reactionCartoonEditorPanel.getReactionCartoonRule().refreshRelationshipInfo(bioModel.getRelationshipModel());
    // cartoonEditorPanel.setBioModel(bioModel);
    reactionTableModel.setBioModel(bioModel);
    structureTableModel.setBioModel(bioModel);
    speciesTableModel.setBioModel(bioModel);
    molecularTypeTableModel.setBioModel(bioModel);
    observableTableModel.setBioModel(bioModel);
// reactionCartoonEditorPanel.specialLayout();
}

Example 5 with AllStructureSuite

use of cbit.vcell.graph.structures.AllStructureSuite in project vcell by virtualcell.

the class ReactionCartoonTool method updateRXContainerDropTargetInfoMap.

private HashMap<RXContainerDropTargetInfo, Boolean> updateRXContainerDropTargetInfoMap(Point pointWorld) {
    HashMap<RXContainerDropTargetInfo, Boolean> rxContainerDropTargetInfoMap = null;
    if (rxContainerDropTargetInfoMap == null) {
        // System.out.println("-----redoing map...");
        AllStructureSuite allStructureSuite = (getReactionCartoon().getStructureSuite() instanceof AllStructureSuite ? (AllStructureSuite) getReactionCartoon().getStructureSuite() : null);
        if (allStructureSuite == null) {
            throw new RuntimeException("Expecting " + AllStructureSuite.class.getName());
        }
        rxContainerDropTargetInfoMap = new HashMap<ReactionCartoonTool.RXContainerDropTargetInfo, Boolean>();
        Structure[] originalOrderedStructArr = allStructureSuite.getStructures().toArray(new Structure[0]);
        for (int i = 0; i < originalOrderedStructArr.length; i++) {
            Shape currentRXContainerShape = getReactionCartoon().getShapeFromModelObject(originalOrderedStructArr[i]);
            if (i == 0) {
                rxContainerDropTargetInfoMap.put(new RXContainerDropTargetInfo((ReactionContainerShape) currentRXContainerShape, null, RXContainerDropTargetInfo.INSERT_BEGINNING), false);
            } else {
                rxContainerDropTargetInfoMap.put(new RXContainerDropTargetInfo((ReactionContainerShape) currentRXContainerShape, (ReactionContainerShape) getReactionCartoon().getShapeFromModelObject(originalOrderedStructArr[i - 1]), null), false);
            }
            if (i == (originalOrderedStructArr.length - 1)) {
                rxContainerDropTargetInfoMap.put(new RXContainerDropTargetInfo((ReactionContainerShape) currentRXContainerShape, null, RXContainerDropTargetInfo.INSERT_END), false);
            }
        }
    }
    // System.out.println("-----Starting to update selection..."+pointWorld);
    for (RXContainerDropTargetInfo rxcContainerDropTargetInfo : rxContainerDropTargetInfoMap.keySet()) {
        if (rxcContainerDropTargetInfo.absoluteRectangle.contains(pointWorld)) {
            // System.out.println(rxcContainerDropTargetInfo.dropShape.getLabel()+" "+rxcContainerDropTargetInfo.closestNeighborShape);
            rxContainerDropTargetInfoMap.put(rxcContainerDropTargetInfo, true);
        } else {
            rxContainerDropTargetInfoMap.put(rxcContainerDropTargetInfo, false);
        }
    }
    return rxContainerDropTargetInfoMap;
}