Examples with MolecularType org.vcell.model.rbm.MolecularType used on opensource projects

Example 1 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class ViewGeneratedReactionsPanel method updateShape.

public void updateShape(int selectedRow) {
    GeneratedReactionTableRow reactionTableRow = tableModel.getValueAt(selectedRow);
    String inputString = reactionTableRow.getExpression();
    System.out.println(selectedRow + ": " + inputString);
    // ReactionRule newReactionRule = (ReactionRule)RbmUtils.parseReactionRule(inputString, bioModel);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        // This should not be possible
        throw new RuntimeException("Owner or SimulationContext are null.");
    }
    int arrowIndex = inputString.indexOf("<->");
    boolean bReversible = true;
    if (arrowIndex < 0) {
        arrowIndex = inputString.indexOf("->");
        bReversible = false;
    }
    String left = inputString.substring(0, arrowIndex).trim();
    String right = inputString.substring(arrowIndex + (bReversible ? 3 : 2)).trim();
    if (left.length() == 0 && right.length() == 0) {
        return;
    }
    // we recover the original rule that generated the flattened reaction we now try to transform back into a fake rule
    BNGReaction reactionObject = reactionTableRow.getReactionObject();
    String name = reactionObject.getRuleName();
    if (name.contains(GeneratedReactionTableModel.reverse)) {
        name = name.substring(GeneratedReactionTableModel.reverse.length());
    }
    if (name.endsWith(ReactionRule.DirectHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
    }
    if (name.endsWith(ReactionRule.InverseHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
    }
    // get the name of the original structure from the original rule and make here another structure with the same name
    String strStructure = null;
    Structure ruleStructure;
    SimulationContext sc = owner.getSimulationContext();
    ReactionRule rr = sc.getModel().getRbmModelContainer().getReactionRule(name);
    if (rr != null && rr.getStructure() != null) {
        strStructure = rr.getStructure().getName();
    }
    if (strStructure != null) {
        if (tempModel.getStructure(strStructure) == null) {
            try {
                if (rr.getStructure().getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            } catch (ModelException | PropertyVetoException e) {
                e.printStackTrace();
            }
        }
        ruleStructure = tempModel.getStructure(strStructure);
    } else {
        throw new RuntimeException("Failed to recover a Structure name from the Reaction Rule: " + name);
    }
    // making the fake rules just for display purpose, actually they are the flattened reactions resulted from bngl
    // the name is probably not unique, it's likely that many flattened reactions are derived from the same rule
    ReactionRule reactionRule = tempModel.getRbmModelContainer().createReactionRule(name, ruleStructure, bReversible);
    String regex = "[^!]\\+";
    String[] patterns = left.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            // if compartments are present, we're cheating big time making some fake compartments just for compartment name display purposes
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                // if nothing explicit for a participant, we use by default the structure of the rule
                structure = ruleStructure;
            }
            reactionRule.addReactant(new ReactantPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    patterns = right.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                structure = ruleStructure;
            }
            // BNGLParser parser = new BNGLParser(new StringReader(sp));
            // ASTSpeciesPattern astSpeciesPattern = parser.SpeciesPattern();
            // BnglObjectConstructionVisitor constructionVisitor = new BnglObjectConstructionVisitor(tempModel, null, false);
            // SpeciesPattern speciesPattern = (SpeciesPattern) astSpeciesPattern.jjtAccept(constructionVisitor, null);
            // for(MolecularTypePattern mtp : speciesPattern.getMolecularTypePatterns()) {
            // mtp.setParticipantMatchLabel("*");
            // }
            // System.out.println(speciesPattern.toString());
            reactionRule.addProduct(new ProductPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    // ----------------------------------------------------------------------------------------------------
    List<ReactantPattern> rpList = reactionRule.getReactantPatterns();
    reactantPatternShapeList.clear();
    int xOffset = 20;
    int xOffsetRound = 20;
    if (rpList != null && rpList.size() > 0) {
        for (int i = 0; i < rpList.size(); i++) {
            SpeciesPattern sp = rpList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffsetRound, 20, -1, sp, shapePanel, reactionRule);
            if (i < rpList.size() - 1) {
                sps.addEndText("+");
            } else {
                if (reactionRule.isReversible()) {
                    sps.addEndText("<->");
                } else {
                    sps.addEndText("->");
                }
            }
            xOffset = sps.getRightEnd() + 45;
            xOffsetRound = sps.getRightEnd() + 45;
            reactantPatternShapeList.add(sps);
        }
    }
    // space for the <-> sign
    xOffset += 15;
    List<ProductPattern> ppList = reactionRule.getProductPatterns();
    productPatternShapeList.clear();
    if (ppList != null && ppList.size() > 0) {
        for (int i = 0; i < ppList.size(); i++) {
            SpeciesPattern sp = ppList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffset, 20, -1, sp, shapePanel, reactionRule);
            if (i < ppList.size() - 1) {
                sps.addEndText("+");
            }
            xOffset = sps.getRightEnd() + 45;
            productPatternShapeList.add(sps);
        }
    }
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanel.setPreferredSize(preferredSize);
    shapePanel.repaint();
}

Example 2 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class XmlReader method getRbmMolecularTypePattern.

private MolecularTypePattern getRbmMolecularTypePattern(Element e, Model newModel) {
    RbmModelContainer mc = newModel.getRbmModelContainer();
    Element e1 = e.getChild(XMLTags.RbmMolecularTypeTag, vcNamespace);
    String molecularTypeName = e1.getAttributeValue(XMLTags.NameAttrTag);
    MolecularType mt = mc.getMolecularType(molecularTypeName);
    if (mt == null) {
        System.out.println("XMLReader: getRbmMolecularTypePattern: encountered reference to non-existing MolecularType.");
        return null;
    }
    // we insert the component patterns below
    MolecularTypePattern tp = new MolecularTypePattern(mt, false);
    String index = e.getAttributeValue(XMLTags.RbmIndexAttrTag);
    if (index != null && !index.isEmpty()) {
        tp.setIndex(Integer.parseInt(index));
    }
    String match = e.getAttributeValue(XMLTags.RbmParticipantPatternMatchTag);
    if (match != null && !match.isEmpty()) {
        tp.setParticipantMatchLabel(match);
    }
    List<MolecularComponentPattern> cpl = new ArrayList<MolecularComponentPattern>();
    List<Element> children = e.getChildren(XMLTags.RbmMolecularComponentPatternTag, vcNamespace);
    for (Element e2 : children) {
        MolecularComponentPattern cp = getRbmMolecularComponentPattern(e2, tp, mt, newModel);
        if (cp != null) {
            cpl.add(cp);
        }
    }
    tp.setComponentPatterns(cpl);
    return tp;
}

Example 3 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class Xmlproducer method getXML.

private Element getXML(MolecularTypePattern param) {
    Element e = new Element(XMLTags.RbmMolecularTypePatternTag);
    if (param.hasExplicitParticipantMatch()) {
        e.setAttribute(XMLTags.RbmParticipantPatternMatchTag, mangle(param.getParticipantMatchLabel()));
    }
    e.setAttribute(XMLTags.RbmIndexAttrTag, Integer.toString(param.getIndex()));
    Element e1 = new Element(XMLTags.RbmMolecularTypeTag);
    MolecularType mt = param.getMolecularType();
    e1.setAttribute(XMLTags.NameAttrTag, mangle(mt.getName()));
    e.addContent(e1);
    for (MolecularComponentPattern cp : param.getComponentPatternList()) {
        e.addContent(getXML(cp));
    }
    return e;
}

Example 4 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class XmlReader method getRbmMolecularTypeList.

private void getRbmMolecularTypeList(Element param, Model newModel) {
    RbmModelContainer mc = newModel.getRbmModelContainer();
    List<MolecularType> mtl = mc.getMolecularTypeList();
    List<Element> children = param.getChildren(XMLTags.RbmMolecularTypeTag, vcNamespace);
    for (Element element : children) {
        MolecularType t = getRbmMolecularType(element, newModel);
        if (t != null) {
            mtl.add(t);
        }
    }
}

Example 5 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class Xmlproducer method getXML.

// ============================================================================================================
public Element getXML(RbmModelContainer rbmModelContainer) {
    Element rbmModelContainerElement = new Element(XMLTags.RbmModelContainerTag);
    List<MolecularType> molecularTypeList = rbmModelContainer.getMolecularTypeList();
    if (!molecularTypeList.isEmpty()) {
        Element molecularTypeListElement = new Element(XMLTags.RbmMolecularTypeListTag);
        for (MolecularType mt : molecularTypeList) {
            molecularTypeListElement.addContent(getXML(mt));
        }
        rbmModelContainerElement.addContent(molecularTypeListElement);
    }
    List<RbmObservable> observablesList = rbmModelContainer.getObservableList();
    if (!observablesList.isEmpty()) {
        Element observablesListElement = new Element(XMLTags.RbmObservableListTag);
        for (RbmObservable oo : observablesList) {
            observablesListElement.addContent(getXML(oo));
        }
        rbmModelContainerElement.addContent(observablesListElement);
    }
    List<ReactionRule> reactionList = rbmModelContainer.getReactionRuleList();
    if (!reactionList.isEmpty()) {
        Element reactionListElement = new Element(XMLTags.RbmReactionRuleListTag);
        for (ReactionRule rr : reactionList) {
            reactionListElement.addContent(getXML(rr));
        }
        rbmModelContainerElement.addContent(reactionListElement);
    }
    return rbmModelContainerElement;
}