public AbstractInteractionCluster(String mappingIdDbNames){ this.queryStart = 0; this.queryRange = 200; this.binary2Encore = new Binary2Encore(); setMappingIdDbNames( mappingIdDbNames ); }
/** * Add a new typeToPudmed map to the existent typeToPudmed map * @param typeToPubmed */ public void addTypeToPubmed(Map<String, List<String>> typeToPubmed) { this.typeToPubmed = setMapping(this.typeToPubmed, typeToPubmed); }
public InteractionCluster(String miqlQuery, String querySource, String mappingIdDbNames){ super(mappingIdDbNames); this.addMIQLQuery(miqlQuery); this.addQuerySource(querySource); }
@Override protected void processMethodAndType(EncoreInteraction encoreInteraction, EncoreInteraction mappingEncoreInteraction) { mappingEncoreInteraction.addMethodToPubmed(encoreInteraction.getMethodToPubmed()); mappingEncoreInteraction.addTypeToPubmed(encoreInteraction.getTypeToPubmed()); }
@Override protected EncoreInteraction convertEncoreInteractionFrom(BinaryInteraction binaryInteraction, String[] strings) { this.binary2Encore.setIdDbNameList(strings); return binary2Encore.getEncoreInteractionForScoring(binaryInteraction); }
@Override protected EncoreInteraction convertEncoreInteractionFrom(BinaryInteraction interaction, String[] idDbNameList) { this.binary2Encore.setIdDbNameList(idDbNameList); return this.binary2Encore.getEncoreInteraction(interaction); }
public void setBinaryInteractionIterator(File file, boolean hasHeader) throws ClusterServiceException { final InputStream inputStream; try { inputStream = new FileInputStream(file); } catch (FileNotFoundException e) { throw new ClusterServiceException( "No file found", e ); } setBinaryInteractionIterator(inputStream, hasHeader); }
public void addPublicationId(List<CrossReference> publicationIds) { for(CrossReference publicationId:publicationIds){ this.addPublicationId(publicationId); } }
public void addConfidenceValues(List<Confidence> confidenceValues) { for(Confidence confidenceValue:confidenceValues){ addConfidenceValue(confidenceValue); } }
public void addOrganismsB(List<CrossReference> organismsB) { for(CrossReference organismB:organismsB){ addOrganismB(organismB); } }
@Override protected ClusterContext initialValue() { return new ClusterContext(); } };
public void addAuthors(List<Author> authors) { for(Author author:authors){ addAuthor(author); } }
public void addSourceDatabases(List<CrossReference> sourceDatabases) { for(CrossReference sourceDatabase:sourceDatabases){ this.addSourceDatabase(sourceDatabase); } }
public void addOrganismsA(List<CrossReference> organismsA) { for(CrossReference organismA:organismsA){ addOrganismA(organismA); } }
public InteractionCluster(String miqlQuery, String querySource, int queryStart, int queryRange, String mappingIdDbNames){ super(queryStart, queryRange, mappingIdDbNames); this.addMIQLQuery(miqlQuery); this.addQuerySource(querySource); }
/** * Add a new methodToPudmed map to the existent methodToPudmed map * @param methodToPubmed */ public void addMethodToPubmed(Map<String, List<String>> methodToPubmed) { this.methodToPubmed = setMapping(this.methodToPubmed, methodToPubmed); }
public InteractionCluster(String miqlQuery, String querySource){ super(0, 200); this.addMIQLQuery(miqlQuery); this.addQuerySource(querySource); }
/** * Associate a type to a pubmed id * @param type * @param pubmed */ public void addTypeToPubmed(String type, String pubmed) { typeToPubmed = setMapping(typeToPubmed, type, pubmed); }
public InteractionCluster(String miqlQuery, String querySource, int queryStart, int queryRange){ super(queryStart, queryRange); this.addMIQLQuery(miqlQuery); this.addQuerySource(querySource); }
/** * Associate a method to a pubmed id * @param method * @param pubmed */ public void addMethodToPubmed(String method, String pubmed) { methodToPubmed = setMapping(methodToPubmed, method, pubmed); }