Examples with ReactionParticipant cbit.vcell.model.ReactionParticipant used on opensource projects

Example 16 with ReactionParticipant

use of cbit.vcell.model.ReactionParticipant in project vcell by virtualcell.

the class ITextWriter method writeReactions.

// each reaction has its own table, ordered by the structures.
protected void writeReactions(Chapter physioChapter, Model model) throws DocumentException {
    if (model == null) {
        return;
    }
    Paragraph reactionParagraph = new Paragraph();
    reactionParagraph.add(new Chunk("Structures and Reactions Diagram").setLocalDestination(model.getName()));
    Section reactionDiagramSection = physioChapter.addSection(reactionParagraph, physioChapter.numberDepth() + 1);
    try {
        addImage(reactionDiagramSection, encodeJPEG(generateDocReactionsImage(model, null)));
    } catch (Exception e) {
        e.printStackTrace();
        throw new DocumentException(e.getClass().getName() + ": " + e.getMessage());
    }
    for (int i = 0; i < model.getNumStructures(); i++) {
        ReactionStep[] reactionSteps = model.getReactionSteps();
        ReactionStep rs = null;
        Table modifierTable = null;
        Table reactionTable = null;
        boolean firstTime = true;
        Section reactStructSection = null;
        for (int j = 0; j < reactionSteps.length; j++) {
            if (reactionSteps[j].getStructure() == model.getStructure(i)) {
                // can also use structureName1.equals(structureName2)
                if (firstTime) {
                    Paragraph linkParagraph = new Paragraph();
                    linkParagraph.add(new Chunk("Reaction(s) in " + model.getStructure(i).getName()).setLocalDestination(model.getStructure(i).getName()));
                    reactStructSection = physioChapter.addSection(linkParagraph, physioChapter.numberDepth() + 1);
                    firstTime = false;
                }
                rs = reactionSteps[j];
                String type;
                if (rs instanceof SimpleReaction) {
                    type = "Reaction";
                } else {
                    type = "Flux";
                }
                // write Reaction equation as a table
                // Get the image arrow cell depending on type of reactionStep : MassAction => double arrow, otherwise, forward arrow
                boolean bReversible = false;
                if (rs.getKinetics() instanceof MassActionKinetics) {
                    bReversible = true;
                }
                Cell arrowImageCell = getReactionArrowImageCell(bReversible);
                // Get reactants and products strings
                ReactionCanvas rc = new ReactionCanvas();
                rc.setReactionStep(rs);
                ReactionCanvasDisplaySpec rcdSpec = rc.getReactionCanvasDisplaySpec();
                String reactants = rcdSpec.getLeftText();
                String products = rcdSpec.getRightText();
                // Create table and add cells for reactants, arrow(s) images, products
                int[] widths = { 8, 1, 8 };
                reactionTable = getTable(3, 100, 0, 2, 2);
                // Add reactants as cell
                Cell tableCell = createCell(reactants, getBold());
                tableCell.setHorizontalAlignment(Cell.ALIGN_RIGHT);
                tableCell.setBorderColor(Color.white);
                reactionTable.addCell(tableCell);
                // add arrow(s) image as cell
                if (arrowImageCell != null) {
                    arrowImageCell.setHorizontalAlignment(Cell.ALIGN_CENTER);
                    arrowImageCell.setBorderColor(Color.white);
                    reactionTable.addCell(arrowImageCell);
                }
                // add products as cell
                tableCell = createCell(products, getBold());
                tableCell.setBorderColor(Color.white);
                reactionTable.addCell(tableCell);
                // reactionTable.setBorderColor(Color.white);
                reactionTable.setWidths(widths);
                // Identify modifiers,
                ReactionParticipant[] rpArr = rs.getReactionParticipants();
                Vector<ReactionParticipant> modifiersVector = new Vector<ReactionParticipant>();
                for (int k = 0; k < rpArr.length; k += 1) {
                    if (rpArr[k] instanceof Catalyst) {
                        modifiersVector.add(rpArr[k]);
                    }
                }
                // Write the modifiers in a separate table, if present
                if (modifiersVector.size() > 0) {
                    modifierTable = getTable(1, 50, 0, 1, 1);
                    modifierTable.addCell(createCell("Modifiers List", getBold(DEF_HEADER_FONT_SIZE), 1, 1, Element.ALIGN_CENTER, true));
                    StringBuffer modifierNames = new StringBuffer();
                    for (int k = 0; k < modifiersVector.size(); k++) {
                        modifierNames.append(((Catalyst) modifiersVector.elementAt(k)).getName() + "\n");
                    }
                    modifierTable.addCell(createCell(modifierNames.toString().trim(), getFont()));
                    modifiersVector.removeAllElements();
                }
                Section reactionSection = reactStructSection.addSection(type + " " + rs.getName(), reactStructSection.numberDepth() + 1);
                // Annotation
                VCMetaData vcMetaData = rs.getModel().getVcMetaData();
                if (vcMetaData.getFreeTextAnnotation(rs) != null) {
                    Table annotTable = getTable(1, 100, 1, 3, 3);
                    annotTable.addCell(createCell("Reaction Annotation", getBold(DEF_HEADER_FONT_SIZE), 1, 1, Element.ALIGN_CENTER, true));
                    annotTable.addCell(createCell(vcMetaData.getFreeTextAnnotation(rs), getFont()));
                    reactionSection.add(annotTable);
                // reactionSection.add(new Paragraph("\""+rs.getAnnotation()+"\""));
                }
                // reaction table
                if (reactionTable != null) {
                    reactionSection.add(reactionTable);
                    // re-set reactionTable
                    reactionTable = null;
                }
                if (modifierTable != null) {
                    reactionSection.add(modifierTable);
                    modifierTable = null;
                }
                // Write kinetics parameters, etc. in a table
                writeKineticsParams(reactionSection, rs);
            }
        }
    }
}

Example 17 with ReactionParticipant

use of cbit.vcell.model.ReactionParticipant in project vcell by virtualcell.

the class ReactionPropertiesPanel method initKineticChoices.

private void initKineticChoices() {
    KineticsDescription[] kineticTypes = reactionStep == null || reactionStep instanceof SimpleReaction ? Simple_Reaction_Kinetic_Types : Flux_Reaction_KineticTypes;
    javax.swing.DefaultComboBoxModel model = new DefaultComboBoxModel();
    for (int i = 0; i < kineticTypes.length; i++) {
        if (!(kineticTypes[i].equals(KineticsDescription.Macroscopic_irreversible) || kineticTypes[i].equals(KineticsDescription.Microscopic_irreversible))) {
            model.addElement(kineticTypes[i]);
        } else // macroscopic/microscopic irreversible
        {
            // reactions on membrane in a 3D geometry
            if (reactionStep != null && reactionStep.getStructure() != null && reactionStep.getStructure() instanceof Membrane) {
                // check if reactants are all on membrane and calculate sum of reactants' stoichiometry
                ReactionParticipant[] rps = reactionStep.getReactionParticipants();
                int order = 0;
                boolean bAllMembraneReactants = true;
                for (ReactionParticipant rp : rps) {
                    if (rp instanceof Reactant) {
                        if (!(rp.getStructure() instanceof Membrane)) {
                            bAllMembraneReactants = false;
                            break;
                        }
                        order += rp.getStoichiometry();
                    }
                }
                // add only if 2nd order membrane reaction
                if (order == 2 && bAllMembraneReactants && !reactionStep.hasCatalyst()) {
                    model.addElement(kineticTypes[i]);
                }
            }
        }
    }
    getKineticsTypeComboBox().setModel(model);
    return;
}

Example 18 with ReactionParticipant

use of cbit.vcell.model.ReactionParticipant in project vcell by virtualcell.

the class ModelProcessEquation method parseReaction.

public static ReactionParticipant[] parseReaction(ReactionStep reactionStep, Model model, String equationString) throws ExpressionException, PropertyVetoException {
    int gotoIndex = equationString.indexOf(REACTION_GOESTO);
    if (gotoIndex < 1 && equationString.length() == 0) {
        throw new ExpressionException("Syntax error! " + REACTION_GOESTO + " not found. (e.g. a+b->c)");
    }
    if (reactionStep == null) {
        return null;
    }
    String leftHand = equationString.substring(0, gotoIndex);
    String rightHand = equationString.substring(gotoIndex + REACTION_GOESTO.length());
    StringTokenizer st = new StringTokenizer(leftHand, "+");
    ArrayList<ReactionParticipant> rplist = new ArrayList<ReactionParticipant>();
    HashMap<String, SpeciesContext> speciesContextMap = new HashMap<String, SpeciesContext>();
    Structure rxnStructure = reactionStep.getStructure();
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex).trim();
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, rxnStructure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        // if (reactionStep instanceof SimpleReaction) {
        rplist.add(new Reactant(null, (SimpleReaction) reactionStep, sc, stoichi));
    // } else if (reactionStep instanceof FluxReaction) {
    // rplist.add(new Flux(null, (FluxReaction) reactionStep, sc));
    // }
    }
    st = new StringTokenizer(rightHand, "+");
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex);
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, rxnStructure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        // if (reactionStep instanceof SimpleReaction) {
        rplist.add(new Product(null, (SimpleReaction) reactionStep, sc, stoichi));
    // } else if (reactionStep instanceof FluxReaction) {
    // rplist.add(new Flux(null, (FluxReaction) reactionStep, sc));
    // }
    }
    return rplist.toArray(new ReactionParticipant[0]);
}

Example 19 with ReactionParticipant

use of cbit.vcell.model.ReactionParticipant 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 ReactionParticipant

use of cbit.vcell.model.ReactionParticipant in project vcell by virtualcell.

the class ReactionCartoonTool method getLineTypeFromAttachment.

private LineType getLineTypeFromAttachment(SpeciesContext speciesContext, Point worldPoint) throws Exception {
    Shape mouseOverShape = getReactionCartoon().pickWorld(worldPoint);
    if (mouseOverShape instanceof ReactionStepShape) {
        // check if the ReactionStep already has a ReactionParticipant for
        // this SpeciesContext
        ReactionStep reactionStep = (ReactionStep) mouseOverShape.getModelObject();
        ReactionParticipant[] rps = reactionStep.getReactionParticipants();
        if (mouseOverShape instanceof SimpleReactionShape) {
            switch(mouseOverShape.getAttachmentFromAbs(worldPoint)) {
                case Shape.ATTACH_LEFT:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.REACTANT;
                    }
                case Shape.ATTACH_CENTER:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Catalyst && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.CATALYST;
                    }
                case Shape.ATTACH_RIGHT:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Product && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.PRODUCT;
                    }
            }
        } else if (mouseOverShape instanceof FluxReactionShape) {
            switch(mouseOverShape.getAttachmentFromAbs(worldPoint)) {
                case Shape.ATTACH_LEFT:
                    {
                        // return LineType.FLUX;
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.REACTANT;
                    }
                case Shape.ATTACH_CENTER:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Catalyst && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.CATALYST;
                    }
                case Shape.ATTACH_RIGHT:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            // return LineType.FLUX;
                            if (rps[i] instanceof Product && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.PRODUCT;
                    }
            }
        }
    }
    return LineType.NULL;
}