public Collection<GeneralMessage> check( Polymer polymer ) throws SanityRuleException { Collection<GeneralMessage> messages = new ArrayList<GeneralMessage>(); final String sequence = polymer.getSequence(); if ( sequence == null || sequence.trim().length() == 0 ) { messages.add( new InteractorMessage( MessageDefinition.POLYMER_WITHOUT_SEQUENCE, ( Interactor ) polymer ) ); } return messages; } }
p.setSequence(((Polymer) interactor).getSequence()); p.setCrc64(((Polymer) interactor).getCrc64());
/** * Ensures that the sequence is accessible, reloading it from the database when lazy. * @param polymer the polymer * @return The returned sequence is ensured to be initialized * @since 2.4.0 */ public static String ensureInitializedSequence(Polymer polymer) { Collection<SequenceChunk> sequenceChunks; if (IntactCore.isInitialized(polymer.getSequenceChunks())) { sequenceChunks = polymer.getSequenceChunks(); } else { sequenceChunks = IntactContext.getCurrentInstance().getDaoFactory() .getEntityManager().createQuery("select sc from SequenceChunk sc where sc.parentAc = :parentAc") .setParameter("parentAc", polymer.getAc()).getResultList(); } return polymer.getSequence(sequenceChunks); }
public RigDataModel buildRigDataModel(Polymer interactor) { String taxid; if (interactor.getBioSource() != null) { taxid = interactor.getBioSource().getTaxId(); } else { taxid = UNKNOWN_TAXID; } String seq = interactor.getSequence(); if (seq == null) { return null; } return new RigDataModel(seq, taxid); } }
if ( !crc64.equals( other.getCrc64() ) ) { return false; if ( other.getCrc64() != null ) { return false; if ( !getSequence().equals( other.getSequence() ) ) { return false; if ( other.getSequence() != null ) { return false;
Collection<InteractorXref> interactorXrefs = polymer.getXrefs(); Collection<InteractorAlias> aliases = polymer.getAliases(); if (polymer.getSequence() != null){ RigDataModel rig = buildRigDataModel(polymer); if (rig != null){ "interactor " + polymer.getAc(), e);
polymer.setSequence( sequence ); polymer.setCrc64( Crc64.getCrc64( sequence ) );
/** * Enrich the mitab interactor following data best practices for nucleic acids * @param interactor * @param mitabInteractor * @return the standard InchiKey for the small molecule. Can be null if no standard inchi key available */ public void enrichInteractorFromIntact(uk.ac.ebi.intact.model.Interactor interactor, Interactor mitabInteractor){ if (interactor != null && mitabInteractor != null){ Collection<InteractorXref> interactorXrefs = interactor.getXrefs(); Collection<InteractorAlias> aliases = interactor.getAliases(); // xrefs boolean hasFoundIdentity = processXrefs(mitabInteractor, interactorXrefs); // ac and display long processAccessionAndDisplay(interactor, mitabInteractor, hasFoundIdentity); // convert aliases if (!aliases.isEmpty()){ processAliases(mitabInteractor, aliases); } // uses crc64 for checksum if (interactor instanceof Polymer){ Polymer polymer = (Polymer) interactor; if (polymer.getCrc64() != null){ Checksum checksum = new ChecksumImpl(InteractorConverter.CRC64, polymer.getCrc64()); mitabInteractor.getChecksums().add(checksum); } } } }
if ( !crc64.equals( other.getCrc64() ) ) { return false; if ( other.getCrc64() != null ) { return false; if ( !getSequence().equals( other.getSequence() ) ) { return false; if ( other.getSequence() != null ) { return false;
/** * Enrich the mitab interactor following data best practices for nucleic acids * @param gene * @param mitabInteractor * @return the standard InchiKey for the small molecule. Can be null if no standard inchi key available */ public void enrichGeneFromIntact(uk.ac.ebi.intact.model.Interactor gene, Interactor mitabInteractor){ hasFoundDisplayShort = false; if (gene != null && mitabInteractor != null){ Collection<InteractorXref> interactorXrefs = gene.getXrefs(); Collection<InteractorAlias> aliases = gene.getAliases(); // xrefs boolean hasFoundENSEMBLIdentity = processXrefs(mitabInteractor, interactorXrefs); // convert aliases if (!aliases.isEmpty()){ processAliases(mitabInteractor, aliases); } // ac and display long processAccessionAndDisplay(gene, mitabInteractor, hasFoundENSEMBLIdentity); // uses crc64 for checksum if (gene instanceof Polymer){ Polymer polymer = (Polymer) gene; if (polymer.getCrc64() != null){ Checksum checksum = new ChecksumImpl(InteractorConverter.CRC64, polymer.getCrc64()); mitabInteractor.getChecksums().add(checksum); } } } }
private Collection<Field> fieldsForAnnotation( Interactor interactor ) { Collection<Field> fields = new ArrayList<Field>(); addField( "Interactor AC", ( range.isUndetermined() ? "Yes" : "No" ), fields ); final CvInteractorType type = interactor.getCvInteractorType(); if ( type != null ) { addField( "Type", type.getShortLabel(), fields ); } if ( interactor instanceof Polymer ) { Polymer polymer = ( Polymer ) interactor; final int length = ( polymer.getSequence() == null ? 0 : polymer.getSequence().length() ); addField( "Seq. length", String.valueOf( length ), fields ); } return fields; }
p.setSequence(((Polymer) interactor).getSequence()); p.setCrc64(((Polymer) interactor).getCrc64());
if ( !crc64.equals( other.getCrc64() ) ) { return false; if ( other.getCrc64() != null ) { return false; if ( !getSequence().equals( other.getSequence() ) ) { return false; if ( other.getSequence() != null ) { return false;
/** * Ensures that the sequence is accessible, reloading it from the database when lazy. * @param polymer the polymer * @return The returned sequence is ensured to be initialized * @since 2.4.0 */ public static String ensureInitializedSequence(Polymer polymer) { Collection<SequenceChunk> sequenceChunks; if (IntactCore.isInitialized(polymer.getSequenceChunks())) { sequenceChunks = polymer.getSequenceChunks(); } else { sequenceChunks = IntactContext.getCurrentInstance().getDaoFactory() .getEntityManager().createQuery("select sc from SequenceChunk sc where sc.parentAc = :parentAc") .setParameter("parentAc", polymer.getAc()).getResultList(); } return polymer.getSequence(sequenceChunks); }
Polymer polymer = (Polymer) interactor; final String sequence = polymer.getSequence(); if (sequence != null) { sb.append(polymer.getSequence()); usedSequence = true;
Polymer polymer = (Polymer) interactor; final String sequence = polymer.getSequence(); if (sequence != null) { sb.append(polymer.getSequence()); usedSequence = true;
if( polymer.getSequence() != null && polymer.getSequence().length() > 0 ) { Element sequence = session.createElement( "sequence" ); Text sequenceText = session.createTextNode( polymer.getSequence() ); sequence.appendChild( sequenceText ); element.appendChild( sequence );
if( polymer.getSequence() != null && polymer.getSequence().length() > 0 ) { Element sequence = session.createElement( "sequence" ); Text sequenceText = session.createTextNode( polymer.getSequence() ); sequence.appendChild( sequenceText ); element.appendChild( sequence );
if( polymer.getSequence() != null && polymer.getSequence().length() > 0 ) { Element sequence = session.createElement( "sequence" ); Text sequenceText = session.createTextNode( polymer.getSequence() ); sequence.appendChild( sequenceText ); element.appendChild( sequence );
final String sequence = ((Polymer) interactor).getSequence(); final String sequenceCandidate = ((Polymer) interactorCandidate).getSequence(); if( StringUtils.equals( sequence, sequenceCandidate) ) { ac = interactorCandidate.getAc();