/** * Collects all Xref having a CvXrefQualifier( target-species ) linked to the given experiement. * * @param experiment * * @return a Collection of Xref. never null. */ public List<ExperimentXref> getTargetSpeciesXrefs( Experiment experiment ) { List<ExperimentXref> targets = new ArrayList<ExperimentXref>(); for ( ExperimentXref xref : experiment.getXrefs() ) { if ( targetSpeciesQualifier.equals( xref.getCvXrefQualifier() ) ) { targets.add( xref ); } } return targets; }
/** * Gets the first primary reference of an existing experiment without connecting with the database * * @param experiment the experiment * @return the primary reference xref */ public static ExperimentXref getPrimaryReferenceXref(Experiment experiment) { for (ExperimentXref xref : experiment.getXrefs()) { String qualMi = null; if (xref.getCvXrefQualifier() != null) { qualMi = xref.getCvXrefQualifier().getIdentifier(); } if (CvXrefQualifier.PRIMARY_REFERENCE_MI_REF.equals(qualMi)) { return xref; } } return null; }
/** * Gets the first primary reference of an existing experiment without connecting with the database * * @param experiment the experiment * @return the primary reference xref */ public static ExperimentXref getPrimaryReferenceXref(Experiment experiment) { for (ExperimentXref xref : experiment.getXrefs()) { String qualMi = null; if (xref.getCvXrefQualifier() != null) { qualMi = xref.getCvXrefQualifier().getIdentifier(); } if (CvXrefQualifier.PRIMARY_REFERENCE_MI_REF.equals(qualMi)) { return xref; } } return null; }
/** * Retreive a pubmed ID from an IntAct experience. <br> That information should be found in Xref( CvDatabase( pubmed * ), CvXrefQualifier( primary-reference ) ). * * @param experiment the experiment from which we try to retreive the pubmedId. * * @return the pubmedId as a String or null if none were found. */ private static String getPubmedId( Experiment experiment ) { if ( experiment == null ) { return null; } // TODO use the helper to get the real CV term instead of comparing shortlabel. String pubmedId = null; for ( Iterator iterator = experiment.getXrefs().iterator(); iterator.hasNext() && pubmedId == null; ) { Xref xref = (Xref) iterator.next(); if ( CvDatabase.PUBMED.equals( xref.getCvDatabase().getShortLabel() ) ) { if ( CvXrefQualifier.PRIMARY_REFERENCE.equals( xref.getCvXrefQualifier().getShortLabel() ) ) { pubmedId = xref.getPrimaryId(); } } } return pubmedId; }
public Set getPumedIds(Set experiments) { Set pubmeds = new HashSet(); for (Iterator iterator = experiments.iterator(); iterator.hasNext();) { Experiment experiment = (Experiment) iterator.next(); boolean found = false; for (Iterator iterator1 = experiment.getXrefs().iterator(); iterator1.hasNext() && !found;) { Xref xref = (Xref) iterator1.next(); if (getCvContext().getByMiRef(CvDatabase.class, CvDatabase.PUBMED_MI_REF).equals(xref.getCvDatabase()) && getCvContext().getByMiRef(CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF).equals(xref.getCvXrefQualifier())) { found = true; pubmeds.add(xref.getPrimaryId()); } } // xref if (found == false) { getOut().println("ERROR: " + experiment.getShortLabel() + " " + CvDatabase.PUBMED + " has no (" + CvXrefQualifier.PRIMARY_REFERENCE + ") assigned."); } } // experiments return pubmeds; }
private Collection<ExperimentXref> getAllPrimaryRefToPubmedAndDoi( Experiment experiment ) { Collection<ExperimentXref> xrefs = null; for ( ExperimentXref xref : experiment.getXrefs() ) { CvObjectXref cvDatabaseIdentity = CvObjectUtils.getPsiMiIdentityXref( xref.getCvDatabase() ); if ( cvDatabaseIdentity != null && ( CvDatabase.PUBMED_MI_REF.equals( cvDatabaseIdentity.getPrimaryId() ) || CvDatabase.DOI_MI_REF.equals( cvDatabaseIdentity.getPrimaryId() ) ) ) { CvObjectXref cvXrerQualifierIdentity = CvObjectUtils.getPsiMiIdentityXref( xref.getCvXrefQualifier() ); if ( cvXrerQualifierIdentity != null && CvXrefQualifier.PRIMARY_REFERENCE_MI_REF.equals( cvXrerQualifierIdentity.getPrimaryId() ) ) { if ( xrefs == null ) { xrefs = new ArrayList<ExperimentXref>(); } xrefs.add( xref ); } } } if ( xrefs == null ) return Collections.EMPTY_LIST; return xrefs; } }
public Set<String> getPumedIds(Set<Experiment> experiments, final boolean stopOnceOneFound ) { Set<String> pubmeds = new HashSet<String>(); for ( Experiment experiment : experiments ) { boolean found = false; for (Iterator iterator1 = experiment.getXrefs().iterator(); iterator1.hasNext() && !found;) { Xref xref = (Xref) iterator1.next(); if (getPubmed().equals(xref.getCvDatabase()) && getPrimaryReference().equals(xref.getCvXrefQualifier())) { if( stopOnceOneFound ) { found = true; } pubmeds.add(xref.getPrimaryId()); } } // xref if (found == false) { getOut().println("ERROR: " + experiment.getShortLabel() + " " + CvDatabase.PUBMED + " has no (" + CvXrefQualifier.PRIMARY_REFERENCE + ") assigned."); } } // experiments return pubmeds; }
Collection xrefs = experiment.getXrefs(); if ( pubmedXrefs.size() == xrefs.size() ) {
Collection xrefs = experiment.getXrefs(); if ( pubmedXrefs.size() == xrefs.size() ) {
Collection xrefs = experiment.getXrefs(); if ( pubmedXrefs.size() == xrefs.size() ) {
/** * Gets the pubmed ID for an Experiment - whitout hitting the database * @param experiment the experiment to get the pubmed id from * @return the pubmed id */ public static String getPubmedId(Experiment experiment) { String pubmedId = null; Publication publication = experiment.getPublication(); if (publication != null) { pubmedId = publication.getShortLabel(); } if (pubmedId == null) { for (ExperimentXref xref : experiment.getXrefs()) { CvObjectXref idQualXref = CvObjectUtils.getPsiMiIdentityXref(xref.getCvXrefQualifier()); CvObjectXref idCvDatabase = CvObjectUtils.getPsiMiIdentityXref(xref.getCvDatabase()); if (idQualXref.getPrimaryId().equals(CvXrefQualifier.PRIMARY_REFERENCE_MI_REF) && idCvDatabase.getPrimaryId().equals(CvDatabase.PUBMED_MI_REF)) { pubmedId = xref.getPrimaryId(); } } } return pubmedId; }
for (ExperimentXref xref : experiment.getXrefs()) { boolean qualMi = false; boolean dbMi = false;
for (ExperimentXref xref : experiment.getXrefs()) { boolean qualMi = false; boolean dbMi = false;
private boolean extractPrimaryRefFromExperiment(Experiment intactObject, Bibref bibref) { if (!intactObject.getXrefs().isEmpty()){ Collection<uk.ac.ebi.intact.model.Xref> primaryRefs = searchXrefs(intactObject, CvDatabase.PUBMED_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, isCheckInitializedCollections()); if (primaryRefs.isEmpty()){ primaryRefs = searchXrefs(intactObject, CvDatabase.DOI_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, isCheckInitializedCollections()); } if (!primaryRefs.isEmpty()){ Iterator<uk.ac.ebi.intact.model.Xref> iterator = primaryRefs.iterator(); uk.ac.ebi.intact.model.Xref primaryRef = iterator.next(); Xref xref = new Xref(); xref.setPrimaryRef(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier())); bibref.setXref(xref); while (iterator.hasNext()){ primaryRef = iterator.next(); xref.getSecondaryRef().add(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier())); } return true; } } return false; }
Collection<ExperimentXref> xrefs = experiment.getXrefs(); for (Iterator<ExperimentXref> iterator = xrefs.iterator(); iterator.hasNext();) { ExperimentXref experimentXref = iterator.next();
/** * Builds a SHALLOW copy of the Experiment parameter. This means that a new Experiment instance is returned, but you * should be aware that the object references it contains <b>point to the objects referenced in the original object * </b>. * * @param experiment The Experiment you want a shallow copy of * * @return Experiment a new Experiment instance containing new references to the parameter object's attributes. * * @throws NullPointerException thrown if required items are not present in the parameter Experiment instance. */ public static Experiment getShallowCopy( Experiment experiment ) { Experiment ex = new Experiment( experiment.getOwner(), experiment.getShortLabel(), experiment.getBioSource() ); ex.ac = ( experiment.getAc() ); ex.setAnnotations( experiment.getAnnotations() ); ex.setCvInteraction( experiment.getCvInteraction() ); ex.setCvIdentification( experiment.getCvIdentification() ); ex.setFullName( experiment.getFullName() ); ex.setRelatedExperiment( experiment.getRelatedExperiment() ); ex.setXrefs( experiment.getXrefs() ); ex.setPublication( experiment.getPublication() ); return ex; }
/** * Builds a SHALLOW copy of the Experiment parameter. This means that a new Experiment instance is returned, but you * should be aware that the object references it contains <b>point to the objects referenced in the original object * </b>. * * @param experiment The Experiment you want a shallow copy of * * @return Experiment a new Experiment instance containing new references to the parameter object's attributes. * * @throws NullPointerException thrown if required items are not present in the parameter Experiment instance. */ public static Experiment getShallowCopy( Experiment experiment ) { Experiment ex = new Experiment( experiment.getOwner(), experiment.getShortLabel(), experiment.getBioSource() ); ex.ac = ( experiment.getAc() ); ex.setAnnotations( experiment.getAnnotations() ); ex.setCvInteraction( experiment.getCvInteraction() ); ex.setCvIdentification( experiment.getCvIdentification() ); ex.setFullName( experiment.getFullName() ); ex.setRelatedExperiment( experiment.getRelatedExperiment() ); ex.setXrefs( experiment.getXrefs() ); ex.setPublication( experiment.getPublication() ); return ex; }
/** * Builds a SHALLOW copy of the Experiment parameter. This means that a new Experiment instance is returned, but you * should be aware that the object references it contains <b>point to the objects referenced in the original object * </b>. * * @param experiment The Experiment you want a shallow copy of * * @return Experiment a new Experiment instance containing new references to the parameter object's attributes. * * @throws NullPointerException thrown if required items are not present in the parameter Experiment instance. */ public static Experiment getShallowCopy( Experiment experiment ) { Experiment ex = new Experiment( experiment.getOwner(), experiment.getShortLabel(), experiment.getBioSource() ); ex.ac = ( experiment.getAc() ); ex.setAnnotations( experiment.getAnnotations() ); ex.setCvInteraction( experiment.getCvInteraction() ); ex.setCvIdentification( experiment.getCvIdentification() ); ex.setFullName( experiment.getFullName() ); ex.setRelatedExperiment( experiment.getRelatedExperiment() ); ex.setXrefs( experiment.getXrefs() ); ex.setPublication( experiment.getPublication() ); return ex; }