Examples with ReactionCartoon cbit.vcell.graph.ReactionCartoon used on opensource projects

Example 1 with ReactionCartoon

use of cbit.vcell.graph.ReactionCartoon 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 2 with ReactionCartoon

use of cbit.vcell.graph.ReactionCartoon in project vcell by virtualcell.

the class ReactionCartoonTool method deleteReactionsAndSpecies.

public static void deleteReactionsAndSpecies(Component requester, ReactionStep[] reactionStepArr, SpeciesContext[] speciesContextArr) throws Exception, UserCancelException {
    if ((speciesContextArr == null && reactionStepArr == null) || (reactionStepArr == null && speciesContextArr != null && speciesContextArr.length == 0) || (speciesContextArr == null && reactionStepArr != null && reactionStepArr.length == 0) || (speciesContextArr != null && speciesContextArr.length == 0 && reactionStepArr != null && reactionStepArr.length == 0)) {
        return;
    }
    int rxCount = (reactionStepArr != null ? reactionStepArr.length : 0);
    int speciesCount = (speciesContextArr != null ? speciesContextArr.length : 0);
    boolean bHasBoth = speciesCount > 0 && rxCount > 0;
    ReactionCartoon rxCartoon = null;
    if (requester instanceof GraphPane && ((GraphPane) requester).getGraphModel() instanceof ReactionCartoon) {
        rxCartoon = (ReactionCartoon) (((GraphPane) requester).getGraphModel());
    } else if (requester instanceof ReactionCartoonEditorPanel) {
        rxCartoon = ((ReactionCartoonEditorPanel) requester).getReactionCartoon();
    } else {
        throw new IllegalArgumentException("ReactionCartoonTool.deleteSpeciesContext not implemented for type '" + requester.getClass().getName() + "'");
    }
    DeleteSpeciesInfo deleteSpeciesInfo = null;
    final String DETAILS = "Details...";
    while (true) {
        String response = DialogUtils.showWarningDialog(requester, RXSPECIES_DELETE + " " + (bHasBoth ? "Reactions and Species." : (rxCount > 0 ? "Reactions." : (speciesCount > 0 ? "Species." : ""))), RXSPECIES_DELETE + " " + (bHasBoth ? rxCount + " Reactions and " + speciesCount + " Species." : (rxCount > 0 ? rxCount + " Reactions." : (speciesCount > 0 ? speciesCount + " Species." : ""))), new String[] { RXSPECIES_DELETE, DETAILS, RXSPECIES_CANCEL }, RXSPECIES_DELETE);
        if (response == null || response.equals(RXSPECIES_CANCEL)) {
            throw UserCancelException.CANCEL_GENERIC;
        }
        deleteSpeciesInfo = (deleteSpeciesInfo == null ? detailsDeleteSpecies(requester, speciesContextArr, reactionStepArr, rxCartoon) : deleteSpeciesInfo);
        if (response.equals(DETAILS)) {
            TableListResult tableListResult = showDeleteDetails(requester, deleteSpeciesInfo, reactionStepArr, false);
        // if(!tableListResult.selectedOption.equals(RXSPECIES_BACK)){
        // //if(!tableListResult.selectedOption.equals((bCut?RXSPECIES_CUT:RXSPECIES_DELETE))){
        // throw UserCancelException.CANCEL_GENERIC;
        // }
        } else {
            break;
        }
    }
    if (deleteSpeciesInfo != null) {
        for (Boolean errors : deleteSpeciesInfo.getbUnresolvableHashMap().values()) {
            if (errors) {
                while (true) {
                    String response = DialogUtils.showWarningDialog(requester, "Error warning.", "Warning: 1 or more SpeciesContexts have Model references that could cause Model corruption if " + RXSPECIES_DELETE + ".", new String[] { DETAILS, RXSPECIES_CANCEL }, DETAILS);
                    if (response == null || response.equals(RXSPECIES_CANCEL)) {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                    showDeleteDetails(requester, deleteSpeciesInfo, reactionStepArr, true);
                }
            }
        }
    }
    if (reactionStepArr != null) {
        for (int i = 0; i < reactionStepArr.length; i += 1) {
            rxCartoon.getModel().removeReactionStep(reactionStepArr[i]);
        }
    }
    if (deleteSpeciesInfo != null) {
        // remove all ReactionParticipants ("lines" between reaction and species in "Reaction Diagram") that have this speciesContext before deleting SpeciesContext
        for (SpeciesContext objSpeciesContext : deleteSpeciesInfo.getRxPartHashMap().keySet()) {
            if (deleteSpeciesInfo.getbUnresolvableHashMap().get(objSpeciesContext)) {
                continue;
            }
            Iterator<ReactionParticipant> iterRxPart = deleteSpeciesInfo.getRxPartHashMap().get(objSpeciesContext).iterator();
            while (iterRxPart.hasNext()) {
                ReactionParticipant objRxPart = iterRxPart.next();
                if (rxCartoon.getObjects().contains(objRxPart)) {
                    // Reaction delete may have already removed
                    objRxPart.getReactionStep().removeReactionParticipant(objRxPart);
                }
            }
        }
        // remove the SpeciesContext
        for (int i = 0; i < speciesContextArr.length; i++) {
            if (deleteSpeciesInfo.getbUnresolvableHashMap().get(speciesContextArr[i])) {
                continue;
            }
            if (rxCartoon.getObjects().contains(speciesContextArr[i])) {
                // Reaction delete may have already removed
                rxCartoon.getModel().removeSpeciesContext(speciesContextArr[i]);
            }
        }
    }
}