Examples with Shape cbit.gui.graph.Shape used on opensource projects

Example 16 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class CartoonTool method actionPerformed.

public final void actionPerformed(ActionEvent event) {
    if (getGraphModel() == null) {
        return;
    }
    Shape popupMenuShape = getGraphModel().getSelectedShape();
    menuAction(popupMenuShape, event.getActionCommand());
}

Example 17 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class GraphPane method getToolTipText.

@Override
public String getToolTipText(MouseEvent event) {
    if (graphModel == null) {
        return getToolTipText();
    }
    Point unzoomedMousePos = graphModel.getResizeManager().unzoom(event.getPoint());
    Shape pickedShape = graphModel.pickWorld(unzoomedMousePos);
    if (pickedShape == null) {
        return getToolTipText();
    }
    if (pickedShape instanceof ReactionContainerShape) {
        return ((ReactionContainerShape) pickedShape).getSpecialToolTipText(unzoomedMousePos);
    }
    return pickedShape.getLabel();
}

Example 18 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class PathwayGraphTool method selectEventFromWorld.

private void selectEventFromWorld(Rectangle rect, boolean bShift, boolean bCntrl) {
    if (!bShift && !bCntrl) {
        getGraphModel().clearSelection();
        List<Shape> shapes = getGraphModel().pickWorld(rect);
        for (Shape shape : shapes) {
            if (shape instanceof BioPaxShape) {
                getGraphModel().selectShape(shape);
            }
        }
    } else if (bShift) {
        if (getGraphModel().getSelectedShape() instanceof PathwayContainerShape) {
            getGraphModel().clearSelection();
        }
        List<Shape> shapes = getGraphModel().pickWorld(rect);
        for (Shape shape : shapes) {
            if (shape instanceof BioPaxShape) {
                getGraphModel().selectShape(shape);
            }
        }
    } else if (bCntrl) {
        if (getGraphModel().getSelectedShape() instanceof PathwayContainerShape) {
            getGraphModel().clearSelection();
        }
        List<Shape> shapes = getGraphModel().pickWorld(rect);
        for (Shape shape : shapes) {
            if (shape instanceof BioPaxShape) {
                if (shape.isSelected()) {
                    getGraphModel().deselectShape(shape);
                } else {
                    getGraphModel().selectShape(shape);
                }
            }
        }
    }
}

Example 19 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class ReactionCartoonTool method menuAction.

@Override
protected void menuAction(Shape shape, String menuAction) {
    if (shape == null) {
        return;
    }
    if (menuAction.equals(CartoonToolMiscActions.Properties.MENU_ACTION)) {
        if (shape instanceof FluxReactionShape) {
        // showFluxReactionPropertiesDialog((FluxReactionShape) shape);
        } else if (shape instanceof SimpleReactionShape) {
        // showSimpleReactionPropertiesDialog((SimpleReactionShape) shape);
        } else if (shape instanceof ReactantShape) {
        // Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
        // Point graphPaneLocation = getGraphPane().getLocationOnScreen();
        // locationOnScreen.translate(graphPaneLocation.x,
        // graphPaneLocation.y);
        // showReactantPropertiesDialog((ReactantShape) shape,
        // locationOnScreen);
        } else if (shape instanceof ProductShape) {
        // Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
        // Point graphPaneLocation = getGraphPane().getLocationOnScreen();
        // locationOnScreen.translate(graphPaneLocation.x,
        // graphPaneLocation.y);
        // showProductPropertiesDialog((ProductShape) shape,
        // locationOnScreen);
        } else if (shape instanceof SpeciesContextShape) {
        // showEditSpeciesDialog(getGraphPane(), getReactionCartoon()
        // .getModel(), ((SpeciesContextShape) shape)
        // .getSpeciesContext());
        } else if (shape instanceof ReactionContainerShape) {
        // ReactionContainerShape rcs = (ReactionContainerShape) shape;
        // if (rcs.getStructure() instanceof Feature) {
        // //
        // // showFeaturePropertyDialog is invoked in two modes:
        // //
        // // 1) parent!=null and child==null
        // // upon ok, it adds a new feature to the supplied parent.
        // //
        // // 2) parent==null and child!=null
        // // upon ok, edits the feature name
        // //
        // showFeaturePropertiesDialog(getGraphPane(),
        // (getReactionCartoon().getModel() == null ? null
        // : getReactionCartoon().getModel()), null,
        // (Feature) rcs.getStructure());
        // } else if (rcs.getStructure() instanceof Membrane) {
        // showMembranePropertiesDialog(getGraphPane(), (Membrane) rcs
        // .getStructure());
        // }
        }
    } else if (menuAction.equals(CartoonToolMiscActions.AddSpecies.MENU_ACTION)) {
        if (shape instanceof ReactionContainerShape) {
            getGraphModel().deselectShape(shape);
            // showCreateSpeciesContextDialog(getGraphPane(),
            // getReactionCartoon().getModel(),
            // ((ReactionContainerShape) shape).getStructure(), null);
            SpeciesContext speciesContext = getReactionCartoon().getModel().createSpeciesContext(((ReactionContainerShape) shape).getStructure());
            getGraphModel().select(speciesContext);
        }
    } else if (menuAction.equals(CartoonToolEditActions.Copy.MENU_ACTION)) {
        if (shape instanceof SpeciesContextShape || shape instanceof ReactionStepShape || // rule participants whose rule is not selected won't
        shape instanceof RuleParticipantSignatureDiagramShape || // be copied since standalone they are meaningless
        shape instanceof ReactionRuleDiagramShape) {
            SpeciesContext[] spArray = getSelectedSpeciesContextArray();
            ReactionStep[] rsArray = getSelectedReactionStepArray();
            ReactionRule[] rrArray = getSelectedReactionRuleArray();
            MolecularType[] mtArray = getSelectedMolecularTypeArray(rrArray, rsArray, spArray);
            Structure[] structArray = getSelectedStructuresArray(rrArray, rsArray, spArray, mtArray);
            Structure fromStruct = null;
            ReactionContainerShape rcs = null;
            Shape parentShape = shape.getParent();
            if (parentShape instanceof ReactionContainerShape) {
                rcs = (ReactionContainerShape) parentShape;
                fromStruct = rcs.getStructure();
            }
            ReactionSpeciesCopy reactionSpeciesCopy = new ReactionSpeciesCopy(spArray, rsArray, rrArray, mtArray, fromStruct, structArray);
            VCellTransferable.sendToClipboard(reactionSpeciesCopy);
        }
    } else if (/*menuAction.equals(CartoonToolEditActions.Paste.MENU_ACTION)
				|| */
    menuAction.equals(CartoonToolEditActions.PasteNew.MENU_ACTION)) {
        if (shape instanceof ReactionContainerShape) {
            pasteReactionsAndSpecies(((ReactionContainerShape) shape).getStructure());
        }
    } else if (menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
        try {
            if (getGraphModel().getSelectedShape() instanceof ReactionContainerShape && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
                getModel().removeStructure(((ReactionContainerShape) getGraphModel().getSelectedShape()).getStructure());
                return;
            }
            if (getSelectedReactionStepArray() != null || getSelectedSpeciesContextArray() != null) {
                deleteReactionsAndSpecies(getGraphPane(), getSelectedReactionStepArray(), getSelectedSpeciesContextArray());
            }
            if (getSelectedReactionParticipantArray() != null && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
                ReactionParticipant[] reactionParticipantArr = getSelectedReactionParticipantArray();
                String response = DialogUtils.showWarningDialog(getGraphPane(), "Delete " + reactionParticipantArr.length + " Reaction Stoichiometries", new String[] { RXSPECIES_DELETE, RXSPECIES_CANCEL }, RXSPECIES_CANCEL);
                if (response != null && response.equals(RXSPECIES_DELETE)) {
                    for (int i = 0; i < reactionParticipantArr.length; i++) {
                        ReactionStep reactionStep = reactionParticipantArr[i].getReactionStep();
                        reactionStep.removeReactionParticipant(reactionParticipantArr[i]);
                    }
                }
            }
        } catch (UserCancelException uce) {
            return;
        } catch (PropertyVetoException e) {
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage());
        } catch (Exception e) {
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
        }
    } else if (menuAction.equals(CartoonToolMiscActions.SearchReactions.MENU_ACTION)) {
        try {
            if (shape instanceof ReactionContainerShape) {
                showReactionBrowserDialog(((ReactionContainerShape) shape).getStructure(), null);
            }
        } catch (Exception e) {
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
        }
    } else if (menuAction.equals(CartoonToolSaveAsImageActions.MenuAction.MENU_ACTION)) {
        try {
            String resType = null;
            if (shape instanceof ReactionContainerShape) {
                showSaveReactionImageDialog();
            }
        } catch (Exception e) {
            e.printStackTrace();
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
        }
    } else if (menuAction.equals(CartoonToolMiscActions.Annotate.MENU_ACTION)) {
        if (shape instanceof ReactionStepShape) {
            // MIRIAMHelper.showMIRIAMAnnotationDialog(((SimpleReactionShape)shape).getReactionStep());
            // System.out.println("Menu action annotate activated...");
            ReactionStep rs = ((ReactionStepShape) shape).getReactionStep();
            VCMetaData vcMetaData = rs.getModel().getVcMetaData();
            try {
                String newAnnotation = DialogUtils.showAnnotationDialog(getGraphPane(), vcMetaData.getFreeTextAnnotation(rs));
                vcMetaData.setFreeTextAnnotation(rs, newAnnotation);
            } catch (UtilCancelException e) {
            // Do Nothing
            } catch (Throwable exc) {
                exc.printStackTrace(System.out);
                DialogUtils.showErrorDialog(getGraphPane(), "Failed to edit annotation!\n" + exc.getMessage(), exc);
            }
        }
    } else {
    // default action is to ignore
    }
}

Example 20 with Shape

use of cbit.gui.graph.Shape in project vcell by virtualcell.

the class ReactionCartoonTool method mouseDragged.

@Override
public void mouseDragged(MouseEvent event) {
    if (getGraphPane().getComponentCount() > 0) {
        // we're editing, cancel
        stopEditing();
    }
    if (event.isPopupTrigger()) {
        return;
    }
    boolean bShift = (event.getModifiers() & InputEvent.SHIFT_MASK) == InputEvent.SHIFT_MASK;
    boolean bCntrl = (event.getModifiers() & InputEvent.CTRL_MASK) == InputEvent.CTRL_MASK;
    if (mode == Mode.SELECT && bStartRxContainerLabel) {
        if (dragStructTimer != null) {
            dragStructTimer.stop();
        }
        Point dragPointWorld = getGraphModel().getResizeManager().unzoom(event.getPoint());
        RXContainerDropTargetInfo lastTrueRXContainerDropTargetInfo = getSelectedContainerDropTargetInfo();
        lastRXContainerDropTargetInfoMap = updateRXContainerDropTargetInfoMap(dragPointWorld);
        RXContainerDropTargetInfo currentTrueRXContainerDropTargetInfo = getSelectedContainerDropTargetInfo();
        // System.out.println(lastTrueRXContainerDropTargetInfo+" "+currentTrueRXContainerDropTargetInfo);
        if (dragStructTimer != null || !Compare.isEqualOrNull(lastTrueRXContainerDropTargetInfo, currentTrueRXContainerDropTargetInfo)) {
            activateDropTargetEnable();
            getGraphPane().repaint();
        }
        return;
    }
    try {
        switch(mode) {
            case SELECT:
                {
                    Point worldPoint = screenToWorld(event.getX(), event.getY());
                    if (bMoving) {
                        if (movingShape instanceof ReactionContainerShape) {
                            bMoving = false;
                            return;
                        }
                        List<Shape> selectedShapes = getReactionCartoon().getSelectedShapes();
                        // constrain to stay within the corresponding parent for the
                        // "movingShape" as well as all other selected (hence
                        // moving) shapes.
                        Point movingParentLoc = movingShape.getParent().getSpaceManager().getAbsLoc();
                        Dimension movingParentSize = movingShape.getParent().getSpaceManager().getSize();
                        worldPoint.x = Math.max(movingOffsetWorld.x + movingParentLoc.x, Math.min(movingOffsetWorld.x + movingParentLoc.x + movingParentSize.width - movingShape.getSpaceManager().getSize().width, worldPoint.x));
                        worldPoint.y = Math.max(movingOffsetWorld.y + movingParentLoc.y, Math.min(movingOffsetWorld.x + movingParentLoc.y + movingParentSize.height - movingShape.getSpaceManager().getSize().height, worldPoint.y));
                        for (Shape shape : selectedShapes) {
                            if (shape != movingShape) {
                                Point selectedParentLoc = shape.getParent().getSpaceManager().getAbsLoc();
                                Dimension selectedParentSize = shape.getParent().getSpaceManager().getSize();
                                int selectedMovingOffsetX = movingOffsetWorld.x + (movingShape.getSpaceManager().getAbsLoc().x - shape.getSpaceManager().getAbsLoc().x);
                                int selectedMovingOffsetY = movingOffsetWorld.y + (movingShape.getSpaceManager().getAbsLoc().y - shape.getSpaceManager().getAbsLoc().y);
                                worldPoint.x = Math.max(selectedMovingOffsetX + selectedParentLoc.x, Math.min(selectedMovingOffsetX + selectedParentLoc.x + selectedParentSize.width - shape.getSpaceManager().getSize().width, worldPoint.x));
                                worldPoint.y = Math.max(selectedMovingOffsetY + selectedParentLoc.y, Math.min(selectedMovingOffsetY + selectedParentLoc.y + selectedParentSize.height - shape.getSpaceManager().getSize().height, worldPoint.y));
                            }
                        }
                        getGraphPane().setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
                        Point newMovingPoint = new Point(worldPoint.x - movingOffsetWorld.x, worldPoint.y - movingOffsetWorld.y);
                        int deltaX = newMovingPoint.x - movingPointWorld.x;
                        int deltaY = newMovingPoint.y - movingPointWorld.y;
                        movingPointWorld = newMovingPoint;
                        movingShape.getSpaceManager().setRelPos(movingPointWorld.x - movingParentLoc.x, movingPointWorld.y - movingParentLoc.y);
                        // them also
                        for (Shape shape : selectedShapes) {
                            if (shape != movingShape) {
                                shape.getSpaceManager().move(deltaX, deltaY);
                            }
                        }
                        getGraphPane().invalidate();
                        ((JViewport) getGraphPane().getParent()).revalidate();
                        getGraphPane().repaint();
                    } else if (bRectStretch) {
                        // constain to stay within parent
                        Point parentLoc = rectShape.getParent().getSpaceManager().getAbsLoc();
                        Dimension parentSize = rectShape.getParent().getSpaceManager().getSize();
                        worldPoint.x = Math.max(1, Math.min(parentSize.width - 1, worldPoint.x - parentLoc.x)) + parentLoc.x;
                        worldPoint.y = Math.max(1, Math.min(parentSize.height - 1, worldPoint.y - parentLoc.y)) + parentLoc.y;
                        getGraphPane().setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
                        // getGraphPane().repaint();
                        Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
                        AffineTransform oldTransform = g.getTransform();
                        g.scale(0.01 * getReactionCartoon().getZoomPercent(), 0.01 * getReactionCartoon().getZoomPercent());
                        g.setXORMode(Color.white);
                        rectShape.setEnd(endPointWorld);
                        rectShape.paint(g, 0, 0);
                        endPointWorld = worldPoint;
                        rectShape.setEnd(endPointWorld);
                        rectShape.paint(g, 0, 0);
                        g.setTransform(oldTransform);
                    } else {
                        Shape shape = (getGraphModel().getSelectedShape() != null ? getGraphModel().getSelectedShape() : getReactionCartoon().pickWorld(worldPoint));
                        if (!bCntrl && !bShift && (shape instanceof SpeciesContextShape || shape instanceof ReactionStepShape || shape instanceof RuleParticipantSignatureDiagramShape || shape instanceof ReactionRuleDiagramShape)) {
                            bMoving = true;
                            movingShape = shape;
                            movingPointWorld = shape.getSpaceManager().getAbsLoc();
                            movingOffsetWorld = new Point(worldPoint.x - movingPointWorld.x, worldPoint.y - movingPointWorld.y);
                        } else if (shape instanceof ReactionContainerShape || bShift || bCntrl) {
                            if (rectShape == null) {
                                return;
                            }
                            if (startPointWorld != null && worldPoint != null && startPointWorld.equals(worldPoint)) {
                                // Don't start stretching until mouse moves at least 1 from startpoint
                                return;
                            }
                            bRectStretch = true;
                            endPointWorld = new Point((startPointWorld != null ? startPointWorld.x : worldPoint.x), (startPointWorld != null ? startPointWorld.y : worldPoint.y));
                            rectShape.setEnd(endPointWorld);
                            if (!(shape instanceof ReactionContainerShape)) {
                                shape.getParent().addChildShape(rectShape);
                            } else {
                                shape.addChildShape(rectShape);
                            }
                            Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
                            AffineTransform oldTransform = g.getTransform();
                            g.scale(0.01 * getReactionCartoon().getZoomPercent(), 0.01 * getReactionCartoon().getZoomPercent());
                            g.setXORMode(Color.white);
                            rectShape.paint(g, 0, 0);
                            g.setTransform(oldTransform);
                        }
                    }
                    break;
                }
            case LINE:
            case LINEDIRECTED:
            case LINECATALYST:
                {
                    int x = event.getX();
                    int y = event.getY();
                    Point worldPoint = new Point((int) (x * 100.0 / getReactionCartoon().getZoomPercent()), (int) (y * 100.0 / getReactionCartoon().getZoomPercent()));
                    if (bLineStretch) {
                        // repaint last location with XOR
                        Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
                        g.setXORMode(Color.white);
                        edgeShape.setEnd(endPointWorld);
                        AffineTransform oldTransform = g.getTransform();
                        g.scale(getReactionCartoon().getZoomPercent() * 0.01, getReactionCartoon().getZoomPercent() * 0.01);
                        edgeShape.paint_NoAntiAlias(g, 0, 0);
                        g.setTransform(oldTransform);
                        // set label and color for line depending on attachment area on ReactionStepShape
                        LineType lineType;
                        if (Mode.LINE.equals(mode)) {
                            SpeciesContext speciesContext = (SpeciesContext) edgeShape.getStartShape().getModelObject();
                            lineType = getLineTypeFromAttachment(speciesContext, worldPoint);
                        } else if (Mode.LINECATALYST.equals(mode)) {
                            lineType = LineType.CATALYST;
                        } else if (edgeShape.getStartShape() instanceof SpeciesContextShape) {
                            lineType = LineType.REACTANT;
                        } else {
                            lineType = LineType.PRODUCT;
                        }
                        edgeShape.setLabel(lineType.getLabel());
                        edgeShape.setForgroundColor(lineType.getColor());
                        getGraphPane().setCursor(lineType.getCursor());
                        // move line and paint with XOR
                        endPointWorld = worldPoint;
                        edgeShape.setEnd(worldPoint);
                        oldTransform = g.getTransform();
                        g.scale(getReactionCartoon().getZoomPercent() * 0.01, getReactionCartoon().getZoomPercent() * 0.01);
                        edgeShape.paint_NoAntiAlias(g, 0, 0);
                        g.setTransform(oldTransform);
                    } else {
                        if (edgeShape != null) {
                            return;
                        }
                        if (startShape instanceof SpeciesContextShape || ((Mode.LINEDIRECTED.equals(mode) || Mode.LINECATALYST.equals(mode)) && startShape instanceof ElipseShape)) {
                            ElipseShape startElipseShape = (ElipseShape) startShape;
                            bLineStretch = true;
                            endPointWorld = worldPoint;
                            edgeShape = new RubberBandEdgeShape(startElipseShape, null, getReactionCartoon());
                            edgeShape.setEnd(worldPoint);
                            Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
                            g.setXORMode(Color.white);
                            AffineTransform oldTransform = g.getTransform();
                            g.scale(getReactionCartoon().getZoomPercent() * 0.01, getReactionCartoon().getZoomPercent() * 0.01);
                            edgeShape.paint(g, 0, 0);
                            g.setTransform(oldTransform);
                        } else if ((Mode.LINEDIRECTED.equals(mode) || Mode.LINECATALYST.equals(mode)) && startShape instanceof ContainerShape) {
                            bLineStretch = true;
                            endPointWorld = worldPoint;
                            edgeShape = new RubberBandEdgeShape((ElipseShape) null, null, getReactionCartoon());
                            edgeShape.setStart(startPointWorld);
                            edgeShape.setEnd(worldPoint);
                            Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
                            g.setXORMode(Color.white);
                            AffineTransform oldTransform = g.getTransform();
                            g.scale(getReactionCartoon().getZoomPercent() * 0.01, getReactionCartoon().getZoomPercent() * 0.01);
                            edgeShape.paint(g, 0, 0);
                            g.setTransform(oldTransform);
                        }
                    }
                    break;
                }
            default:
                {
                    break;
                }
        }
    } catch (Exception e) {
        System.out.println("CartoonTool.mouseDragged: uncaught exception");
        e.printStackTrace(System.out);
    }
}