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; } }
/** * 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); }
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; }
/** * 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); }
if ( !getSequence().equals( other.getSequence() ) ) { return false; if ( other.getSequence() != null ) { return false;
if ( !getSequence().equals( other.getSequence() ) ) { return false; if ( other.getSequence() != null ) { return false;
if ( !getSequence().equals( other.getSequence() ) ) { return false; if ( other.getSequence() != null ) { return false;
Polymer polymer = (Polymer) interactor; final String sequence = polymer.getSequence(); if (sequence != null) { sb.append(polymer.getSequence()); usedSequence = true;
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); } }
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 );
p.setSequence(((Polymer) interactor).getSequence()); p.setCrc64(((Polymer) interactor).getCrc64());
p.setSequence(((Polymer) interactor).getSequence()); p.setCrc64(((Polymer) interactor).getCrc64());
if (polymer.getSequence() != null){ RigDataModel rig = buildRigDataModel(polymer); if (rig != null){
String sequence = polymer.getSequence(); r.prepareSequence(polymer.getSequence());
Polymer polymer = (Polymer) intactObject; if (polymer.getSequence() != null){ String sequence; if (isCheckInitializedCollections()){ sequence = polymer.getSequence();
final String seq = ( ( Polymer ) interactor ).getSequence(); final int length = ( seq == null ? 0 : seq.length() );