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

Example 76 with MolecularType

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

the class Model method removeStructure.

public void removeStructure(Structure removedStructure) throws PropertyVetoException {
    if (removedStructure == null) {
        throw new RuntimeException("structure is null");
    }
    if (!contains(removedStructure)) {
        throw new RuntimeException("structure " + removedStructure.getName() + " not found");
    }
    // Check that the feature is empty
    String prefix = "Remove model compartment Error\n\nStructure to be removed : '" + removedStructure.getName() + "' : ";
    String errorMessage = null;
    for (int i = 0; i < fieldReactionSteps.length; i++) {
        if (fieldReactionSteps[i].getStructure() == removedStructure) {
            errorMessage = "cannot contain Reactions";
            throw new RuntimeException(prefix + errorMessage + ".");
        }
    }
    for (int i = 0; i < fieldSpeciesContexts.length; i++) {
        if (fieldSpeciesContexts[i].getStructure() == removedStructure) {
            errorMessage = "cannot contain Species";
            throw new RuntimeException(prefix + errorMessage + ".");
        }
    }
    for (ReactionRule rr : getRbmModelContainer().getReactionRuleList()) {
        if (rr.getStructure() == removedStructure) {
            errorMessage = "cannot contain Reaction Rules";
            throw new RuntimeException(prefix + errorMessage + ".");
        }
        boolean found = false;
        for (ReactantPattern rp : rr.getReactantPatterns()) {
            if (rp.getStructure() == removedStructure) {
                errorMessage = "cannot contain Reactant Patterns";
                throw new RuntimeException(prefix + errorMessage + ".");
            }
        }
        for (ProductPattern pp : rr.getProductPatterns()) {
            if (pp.getStructure() == removedStructure) {
                errorMessage = "cannot contain Product Patterns";
                throw new RuntimeException(prefix + errorMessage + ".");
            }
        }
    }
    for (RbmObservable o : getRbmModelContainer().getObservableList()) {
        if (o.getStructure() == removedStructure) {
            errorMessage = "cannot contain Observables";
            throw new RuntimeException(prefix + errorMessage + ".");
        }
    }
    for (MolecularType mt : getRbmModelContainer().getMolecularTypeList()) {
        if (mt.getAnchors().contains(removedStructure)) {
            errorMessage = "cannot be Molecule anchor";
            throw new RuntimeException(prefix + errorMessage + ".");
        }
    }
    // 
    // remove this structure
    // 
    Structure[] newStructures = (Structure[]) fieldStructures.clone();
    newStructures = (Structure[]) BeanUtils.removeElement(newStructures, removedStructure);
    setStructures(newStructures);
}

Example 77 with MolecularType

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

the class PathwayMapping method generateSpeciesPattern.

private SpeciesPattern generateSpeciesPattern(BioModel bioModel, PhysicalEntity bioPaxObject, boolean addSubunits) {
    SpeciesPattern sp = new SpeciesPattern();
    if (bioPaxObject instanceof Complex) {
        Complex c = (Complex) bioPaxObject;
        for (PhysicalEntity pc : c.getComponents()) {
            MolecularType mt = createMolecularTypeFromBioPaxObject(bioModel, pc, addSubunits);
            MolecularTypePattern mtp = new MolecularTypePattern(mt);
            sp.addMolecularTypePattern(mtp);
        }
        return sp;
    } else {
        // else if(!(bioPaxObject instanceof Complex))
        MolecularType mt = createMolecularTypeFromBioPaxObject(bioModel, bioPaxObject, addSubunits);
        MolecularTypePattern mtp = new MolecularTypePattern(mt);
        sp.addMolecularTypePattern(mtp);
        return sp;
    }
// return null;
}

Example 78 with MolecularType

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

the class PathwayMapping method createMolecularTypeFromBioPaxObject.

// TODO: not in use
// public void createBioModelEntitiesFromBioPaxObjects(BioModel bioModel, Object[] selectedObjects) throws Exception
// {
// for(int i = 0; i < selectedObjects.length; i++) {
// if(selectedObjects[i] instanceof BioPaxObject) {
// BioPaxObject bioPaxObject = (BioPaxObject)selectedObjects[i];
// if(bioPaxObject instanceof PhysicalEntity && !(bioPaxObject instanceof Complex)) {
// createMolecularTypeFromBioPaxObject(bioModel, (PhysicalEntity)bioPaxObject);
// }
// } else if(selectedObjects[i] instanceof ConversionTableRow) {
// ConversionTableRow ctr = (ConversionTableRow)selectedObjects[i];
// if(ctr.getBioPaxObject() instanceof PhysicalEntity && !(ctr.getBioPaxObject() instanceof Complex)) {
// createMolecularTypeFromBioPaxObject(bioModel, (PhysicalEntity)ctr.getBioPaxObject());
// }
// }
// }
// 
// for(int i = 0; i < selectedObjects.length; i++) {
// if(selectedObjects[i] instanceof BioPaxObject) {
// BioPaxObject bioPaxObject = (BioPaxObject)selectedObjects[i];
// if(bioPaxObject instanceof PhysicalEntity) {
// createSpeciesContextFromBioPaxObject(bioModel, (PhysicalEntity)bioPaxObject);
// } else if(bioPaxObject instanceof Conversion) {
// createReactionStepsFromBioPaxObject(bioModel, (Conversion)bioPaxObject);
// }
// } else if(selectedObjects[i] instanceof ConversionTableRow) {
// ConversionTableRow ctr = (ConversionTableRow)selectedObjects[i];
// if(ctr.getBioPaxObject() instanceof PhysicalEntity) {
// createSpeciesContextFromTableRow(bioModel, (PhysicalEntity)ctr.getBioPaxObject(), ctr.stoich(), ctr.id(), ctr.location());
// } else if(ctr.getBioPaxObject() instanceof Conversion) {
// createReactionStepsFromTableRow(bioModel, (Conversion)ctr.getBioPaxObject(), ctr.stoich(), ctr.id(), ctr.location());
// }
// }
// }
// }
private MolecularType createMolecularTypeFromBioPaxObject(BioModel bioModel, PhysicalEntity bioPaxObject, boolean addSubunits) {
    String name;
    if (bioPaxObject.getName().size() == 0) {
        name = getSafetyName(bioPaxObject.getID());
    } else {
        name = getSafetyName(bioPaxObject.getName().get(0));
    }
    RbmModelContainer rbmmc = bioModel.getModel().getRbmModelContainer();
    if (rbmmc.getMolecularType(name) != null) {
        // already exists
        MolecularType mt = rbmmc.getMolecularType(name);
        // check whether it links to pathway object, create relationship object if not
        if (!bioModel.getRelationshipModel().isRelationship(mt, bioPaxObject)) {
            RelationshipObject ro = new RelationshipObject(mt, bioPaxObject);
            bioModel.getRelationshipModel().addRelationshipObject(ro);
        }
        return mt;
    }
    int numSubunits = 0;
    if (addSubunits) {
        for (String comment : bioPaxObject.getComments()) {
            numSubunits = StringUtils.countMatches(comment, "SUBUNIT:");
        }
    }
    MolecularType mt = new MolecularType(name, bioModel.getModel());
    try {
        for (int i = 0; i < numSubunits; i++) {
            MolecularComponent mc = new MolecularComponent("Subunit" + i);
            mt.addMolecularComponent(mc);
        }
        rbmmc.addMolecularType(mt, true);
        // we know for sure that a relationship can't exist, so we make one
        RelationshipObject ro = new RelationshipObject(mt, bioPaxObject);
        bioModel.getRelationshipModel().addRelationshipObject(ro);
    } catch (ModelException | PropertyVetoException e) {
        e.printStackTrace();
    }
    ArrayList<String> commentList = bioPaxObject.getComments();
    final String htmlStart = "<html><font face = \"Arial\"><font size =\"-2\">";
    final String htmlEnd = "</font></font></html>";
    if (commentList != null && !commentList.isEmpty()) {
        String comment = commentList.get(0);
        if (!comment.isEmpty()) {
            String text = FormatDetails(comment);
            mt.setComment(htmlStart + text + htmlEnd);
        }
    } else {
        mt.setComment("");
    }
    return mt;
}