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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();
}
Also used : SpeciesPatternLargeShape(cbit.vcell.graph.SpeciesPatternLargeShape) SpeciesPattern(org.vcell.model.rbm.SpeciesPattern) Structure(cbit.vcell.model.Structure) ReactantPattern(cbit.vcell.model.ReactantPattern) ModelException(cbit.vcell.model.ModelException) ReactionRule(cbit.vcell.model.ReactionRule) ProductPattern(cbit.vcell.model.ProductPattern) Dimension(java.awt.Dimension) SimulationContext(cbit.vcell.mapping.SimulationContext) Point(java.awt.Point) PropertyVetoException(java.beans.PropertyVetoException) MolecularType(org.vcell.model.rbm.MolecularType) BNGReaction(cbit.vcell.bionetgen.BNGReaction) Model(cbit.vcell.model.Model) VCellSortTableModel(cbit.vcell.client.desktop.biomodel.VCellSortTableModel) BioModel(cbit.vcell.biomodel.BioModel) MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)

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;
}
Also used : ParticleMolecularType(cbit.vcell.math.ParticleMolecularType) MolecularType(org.vcell.model.rbm.MolecularType) RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer) ParticleMolecularComponentPattern(cbit.vcell.math.ParticleMolecularComponentPattern) MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern) Element(org.jdom.Element) ArrayList(java.util.ArrayList) ParticleMolecularTypePattern(cbit.vcell.math.ParticleMolecularTypePattern) MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)

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;
}
Also used : ParticleMolecularType(cbit.vcell.math.ParticleMolecularType) MolecularType(org.vcell.model.rbm.MolecularType) ParticleMolecularComponentPattern(cbit.vcell.math.ParticleMolecularComponentPattern) MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern) Element(org.jdom.Element)

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);
        }
    }
}
Also used : ParticleMolecularType(cbit.vcell.math.ParticleMolecularType) MolecularType(org.vcell.model.rbm.MolecularType) RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer) Element(org.jdom.Element)

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;
}
Also used : ParticleMolecularType(cbit.vcell.math.ParticleMolecularType) MolecularType(org.vcell.model.rbm.MolecularType) ReactionRule(cbit.vcell.model.ReactionRule) Element(org.jdom.Element) RbmObservable(cbit.vcell.model.RbmObservable)

Aggregations

MolecularType (org.vcell.model.rbm.MolecularType)78 SpeciesPattern (org.vcell.model.rbm.SpeciesPattern)25 MolecularComponent (org.vcell.model.rbm.MolecularComponent)23 Structure (cbit.vcell.model.Structure)20 ArrayList (java.util.ArrayList)20 ReactionRule (cbit.vcell.model.ReactionRule)19 SpeciesContext (cbit.vcell.model.SpeciesContext)19 MolecularTypePattern (org.vcell.model.rbm.MolecularTypePattern)16 PropertyVetoException (java.beans.PropertyVetoException)15 ComponentStateDefinition (org.vcell.model.rbm.ComponentStateDefinition)15 RbmObservable (cbit.vcell.model.RbmObservable)14 List (java.util.List)13 RbmModelContainer (cbit.vcell.model.Model.RbmModelContainer)12 Point (java.awt.Point)12 MolecularComponentPattern (org.vcell.model.rbm.MolecularComponentPattern)12 BioPaxObject (org.vcell.pathway.BioPaxObject)11 RelationshipObject (org.vcell.relationship.RelationshipObject)11 BioModelNode (cbit.vcell.desktop.BioModelNode)10 ModelException (cbit.vcell.model.ModelException)10 ParticleMolecularType (cbit.vcell.math.ParticleMolecularType)9