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

Example 41 with MolecularComponent

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

the class SpeciesContext method checkMolecularTypeConsistency.

// I think this should never fire issues, that's why I keep issue severity to error to force further investigation
// TODO: oct 30, 2015: hasn't fired in 9 months, we replace the issues with exception just to protect ourselves against regressions
private void checkMolecularTypeConsistency(IssueContext issueContext, List<Issue> issueList, MolecularType mtThat, MolecularTypePattern mtpThis) {
    issueContext = issueContext.newChildContext(ContextType.SpeciesContext, this);
    Map<String, MolecularComponent> hashThat = new HashMap<String, MolecularComponent>();
    Map<String, MolecularComponent> hashThis = new HashMap<String, MolecularComponent>();
    for (MolecularComponent mcThat : mtThat.getComponentList()) {
        hashThat.put(mcThat.getName(), mcThat);
    }
    for (MolecularComponentPattern mcpThis : mtpThis.getComponentPatternList()) {
        hashThis.put(mcpThis.getMolecularComponent().getName(), mcpThis.getMolecularComponent());
    }
    Iterator<Entry<String, MolecularComponent>> it = hashThat.entrySet().iterator();
    while (it.hasNext()) {
        String key = ((Map.Entry<String, MolecularComponent>) it.next()).getKey();
        if (hashThis.containsKey(key)) {
            it.remove();
            hashThis.remove(key);
        }
    }
    // any component still present in hashThis it means that it has been deleted in the molecular types definition and is now invalid
    for (String key : hashThat.keySet()) {
        String msg = "All components in the " + mtThat.getDisplayType() + " definition must be present. Missing: " + key + ".";
        throw new RuntimeException(msg);
    // issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_ERROR));
    }
    for (String key : hashThis.keySet()) {
        String msg = "Component " + key + " is no longer defined for the " + mtThat.getDisplayType() + " and must be removed.";
        throw new RuntimeException(msg);
    // issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_ERROR));
    }
}

Example 42 with MolecularComponent

use of org.vcell.model.rbm.MolecularComponent 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;
}