@XmlElement(name = "signature-library-release") private SignatureLibraryRelease getSignatureLibraryReleaseShallow() { if (this.signatureLibraryRelease == null) { return null; } return new SignatureLibraryRelease(this.signatureLibraryRelease.getLibrary(), this.signatureLibraryRelease.getVersion()); }
/** * This private method is responsible for retrieving OR persisting (as appropriate) * a SignatureLibraryRelease method for the version of TMHMM being handled by this * DAO. * * @return the retrieved / persisted SignatureLibraryRelease object. */ private SignatureLibraryRelease loadTMHMMRelease() { SignatureLibraryRelease release = null; final Query releaseQuery = entityManager.createQuery("select r from SignatureLibraryRelease r where r.version = :version and r.library = :signatureLibrary"); releaseQuery.setParameter("version", signatureLibraryRelease.getVersion()); releaseQuery.setParameter("signatureLibrary", signatureLibraryRelease.getLibrary()); @SuppressWarnings("unchecked") List<SignatureLibraryRelease> releaseList = releaseQuery.getResultList(); if (releaseList.size() == 1 && releaseList.get(0) != null) { release = releaseList.get(0); } else if (releaseList.size() > 1) { throw new IllegalStateException("There is more than one SignatureLibraryRelease record for version " + signatureLibraryRelease.getVersion() + " of TMHMM in the databases."); } else { entityManager.persist(new SignatureLibraryRelease(signatureLibraryRelease.getLibrary(), signatureLibraryRelease.getVersion())); } return release; }
final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = analysisI5toI4.get(signatureLibrary.getName()); if (analysis == null) {
LOGGER.debug("SignatureLibraryRelease: " + job4Debug.getId() + ": " + job4Debug.getLibraryRelease().getLibrary().getName() + ", " + job4Debug.getLibraryRelease().getVersion() + ", " + "active: " + job4Debug.isActive()); if(job4Debug.getLibraryRelease().getLibrary().getName().equalsIgnoreCase("gene3d")){ LOGGER.debug("Gene3d: " + job4Debug.getLibraryRelease().getVersion() + " - " + job4Debug.getSteps()); if(job4Debug.getLibraryRelease().getLibrary().getName().equalsIgnoreCase("panther")) { LOGGER.debug("panther: " + job4Debug.getLibraryRelease().getVersion() + " - " + job4Debug.getSteps()); if(signatureLibraryRelease != null) { analysisJobMap.put(signatureLibraryRelease.getLibrary().getName().toUpperCase(), signatureLibraryRelease); if (LOGGER.isDebugEnabled()) { LOGGER.debug("Name: " + signatureLibraryRelease.getLibrary().getName() + " version: " + signatureLibraryRelease.getVersion() + " name: " + signatureLibraryRelease.getLibrary().getName()); analysesToRun.append(analysisJobMap.get(key).getLibrary().getName() + "-" + analysisJobMap.get(key)); analysesToDisplay.add(String.join("-", analysisJobMap.get(key).getLibrary().getName(), analysisJobMap.get(key).getVersion()));
final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String description = signature.getDescription();
final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String description = signature.getDescription();
final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = analysisI5toI4.get(signatureLibrary.getName()); if (analysis == null) {
final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String version = signature.getSignatureLibraryRelease().getVersion();
final String signatureAc = signature.getAccession(); final String signatureModels = match.getSignatureModels(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String version = signature.getSignatureLibraryRelease().getVersion();
final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String description = signature.getDescription();
final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String description = signature.getDescription();