Examples with Xref org.vcell.pathway.Xref used on opensource projects

Example 16 with Xref

use of org.vcell.pathway.Xref in project vcell by virtualcell.

the class AnnotationMapping method getNameRef.

public static ArrayList<String> getNameRef(ArrayList<Xref> xRef, String entryName) {
    CachedDataBaseReferenceReader dbReader = CachedDataBaseReferenceReader.getCachedReader();
    ArrayList<String> names = new ArrayList<String>();
    for (Xref xref : xRef) {
        try {
            // System.out.println(xref.getDb() + "***" + xref.getId());
            if (xref.getDb().toLowerCase().equals("uniprot")) {
            // String name = dbReader.getMoleculeDataBaseReference(xref.getId());
            // if(name != null)names.add(name);
            // if(xref.getId() != null && xref.getDb().toLowerCase() != null) {
            // names.add(xref.getDb().toLowerCase()+ ":" + xref.getId());
            // }
            // System.out.println(xref.getId() + ">>>>>>>"+ name);
            } else if (xref.getDb().toLowerCase().equals("interpro")) {
            // String name = dbReader.getMoleculeDataBaseReference("interpro", xref.getId());
            // if(name != null)names.add(name);
            // if(xref.getId() != null && xref.getDb().toLowerCase() != null) {
            // names.add(xref.getDb().toLowerCase()+ ":" + xref.getId());
            // }
            // System.out.println(xref.getId() + ">>>>>>>"+ name);
            } else if (xref.getDb().toLowerCase().equals("obo.chebi")) {
                String id = xref.getId().substring(6);
                String name = dbReader.getChEBIName(id);
                if (name != null)
                    names.add(name);
            // System.out.println(xref.getId() + ">>>>>>>"+ name);
            } else if (xref.getDb().toLowerCase().equals("gene_ontology")) {
            // String name = dbReader.getGOTerm(xref.getId());
            // if(name != null) {
            // names.add(name);
            // } else
            // if(xref.getId() != null && xref.getDb().toLowerCase() != null) {
            // names.add(xref.getDb().toLowerCase()+ ":" + xref.getId());
            // }
            // System.out.println(xref.getId() + ">>>>>>>"+ name);
            } else // else if(xref.getDb().toLowerCase().equals("ec-code")){
            // WSDBFetchServerServiceLocator providerLocator = new WSDBFetchServerServiceLocator();
            // WSDBFetchServer server = providerLocator.getWSDbfetch();
            // String[] supported = server.getSupportedDBs();
            // for (int i = 0; i < supported.length; i++) {
            // System.out.println(supported[i]);
            // }
            // String fetchResultStr = server.fetchBatch("embl", xref.getId(),null,null);
            // System.out.println(xref.getId() + ">>>>>>> lookup"+fetchResultStr);
            // }
            {
            // System.out.println(xref.getDb());
            }
        } catch (DbfConnException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (DbfNoEntryFoundException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (DbfParamsException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (DbfException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (InputException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (RemoteException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (ServiceException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (DataAccessException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    if (names.size() == 0 && entryName != null)
        names.add(entryName);
    return names;
}

Example 17 with Xref

use of org.vcell.pathway.Xref in project vcell by virtualcell.

the class AnnotationMapping method getXrefs.

private ArrayList<Xref> getXrefs(BioModel bioModel, HashMap<String, String> refInfo) {
    ArrayList<Xref> xRef = new ArrayList<Xref>();
    for (String id : refInfo.keySet()) {
        String[] temp = (refInfo.get(id)).split(":");
        String db = temp[0];
        String type = temp[1];
        if (db.toUpperCase().contains("OBO.GO")) {
            db = "GENE_ONTOLOGY";
            if (id.contains(":")) {
                id = id.split(":")[1];
            }
        }
        String refId = db + "_" + id;
        Xref xref = (Xref) bioModel.getPathwayModel().findBioPaxObject(refId);
        if (xref == null) {
            if (type.toLowerCase().contains("described")) {
                xref = new PublicationXref();
            } else if (type.toLowerCase().contains("homolog") || db.toUpperCase().contains("TAXONOMY")) {
                xref = new RelationshipXref();
            } else {
                xref = new UnificationXref();
            }
            xref.setId(id);
            xref.setDb(db.toUpperCase());
            xref.setID(refId);
        }
        xRef.add(xref);
    }
    return xRef;
}

Example 18 with Xref

use of org.vcell.pathway.Xref in project vcell by virtualcell.

the class AnnotationMapping method createPhysicalEntity.

private PhysicalEntity createPhysicalEntity(ArrayList<Xref> xRef, ArrayList<String> refName, String name) {
    PhysicalEntity physicalEntity = null;
    if (isSmallMolecule(xRef)) {
        physicalEntity = new SmallMolecule();
    } else {
        physicalEntity = new PhysicalEntity();
    }
    physicalEntity.setName(refName);
    physicalEntity.setID("BIOMODEL_" + name);
    // physicalEntity.setxRef(xRef);
    for (Xref ref : xRef) {
        physicalEntity.getxRef().add(ref);
    }
    return physicalEntity;
}

Example 19 with Xref

use of org.vcell.pathway.Xref in project vcell by virtualcell.

the class AnnotationMapping method createInteraction.

private Interaction createInteraction(ReactionStep reactionStep, ArrayList<Xref> xRef, ArrayList<String> name) {
    Interaction interaction = null;
    if (reactionStep instanceof SimpleReaction) {
        interaction = new BiochemicalReactionImpl();
    } else if (reactionStep instanceof FluxReaction) {
        interaction = new TransportImpl();
    }
    interaction.setName(name);
    interaction.setID("BIOMODEL_" + reactionStep.getName());
    for (Xref ref : xRef) {
        interaction.getxRef().add(ref);
    }
    return interaction;
}

Example 20 with Xref

use of org.vcell.pathway.Xref 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("");
    }
    VCMetaData vcMetaData = bioModel.getVCMetaData();
    MiriamManager miriamManager = vcMetaData.getMiriamManager();
    MIRIAMQualifier qualifier = MIRIAMQualifier.MODEL_isDescribedBy;
    ArrayList<Xref> xrefList = bioPaxObject.getxRef();
    for (Xref xref : xrefList) {
        String url = xref.getURL();
        if (url == null || url.isEmpty()) {
            continue;
        }
        System.out.println(xref.getDb() + ": " + xref.getId());
        try {
            HashSet<MiriamResource> miriamResources = new HashSet<MiriamResource>();
            // http://www.ncbi.nlm.nih.gov/protein/NP_005429	unrecognized (not a valid DataType)
            // http://www.uniprot.org/uniprot/P17275			good
            // TODO: find a mechanism to store the unrecognized ones - they often do work
            MiriamResource mr = miriamManager.createMiriamResource(url);
            miriamResources.add(mr);
            miriamManager.addMiriamRefGroup(mt, qualifier, miriamResources);
        } catch (URNParseFailureException e) {
            e.printStackTrace();
        }
        System.out.println(xref.getDisplayName());
    }
    return mt;
}