@XmlElement(name = "signature-library-release") private SignatureLibraryRelease getSignatureLibraryReleaseShallow() { if (this.signatureLibraryRelease == null) { return null; } return new SignatureLibraryRelease(this.signatureLibraryRelease.getLibrary(), this.signatureLibraryRelease.getVersion()); }
@Transactional public SignatureLibraryRelease parse() throws IOException { LOGGER.debug("Starting to parse cddid.tbl file."); SignatureLibraryRelease release = new SignatureLibraryRelease(library, releaseVersion); if (LOGGER.isDebugEnabled() && lineNumber++ % 10000 == 0) { LOGGER.debug("Parsed " + lineNumber + " lines of the cddid.tbl file."); LOGGER.debug("Parsed " + release.getSignatures().size() + " signatures."); release.addSignature(createSignature(accession, name, description, release));
public Signature addSignature(Signature signature) throws IllegalArgumentException { if (signature == null) { throw new IllegalArgumentException("'Signature' must not be null"); } if (signature.getSignatureLibraryRelease() != null) { signature.getSignatureLibraryRelease().removeSignature(signature); } signature.setSignatureLibraryRelease(this); signatures.add(signature); return signature; }
/** * Method to parse a model file and return a SignatureLibraryRelease. * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { LOGGER.debug("Starting to parse hmm file."); SignatureLibraryRelease release = new SignatureLibraryRelease(library, releaseVersion); for (Resource modelFile : modelFiles) { if (modelFile.exists() && modelFile.getFile() != null) { Map<String, String> familyIdFamilyNameMap = readInPantherFamilyNames(modelFile); if (LOGGER.isDebugEnabled()) { LOGGER.debug("number of panther families: " + familyIdFamilyNameMap.keySet().size()); } Map<String, List<String>> pantherParentChildMap = getPantherParentChildMap(familyIdFamilyNameMap.keySet()); for (String parent : pantherParentChildMap.keySet()) { String signatureAcc = parent; String signatureName = familyIdFamilyNameMap.get(signatureAcc); release.addSignature(createSignature(signatureAcc, signatureName, release)); List<String> children = pantherParentChildMap.get(parent); for (String childSignatureAcc : children) { String childSignatureName = familyIdFamilyNameMap.get(childSignatureAcc); release.addSignature(createSignature(childSignatureAcc, childSignatureName, release)); } } } } return release; }
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 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) {
public MobiDBFilteredMatchDAO(SignatureLibraryRelease release) { super(MobiDBMatch.class); this.release = release; this.mobidbReleaseVersion = release.getVersion(); }
/** * This private method is responsible for retrieving OR persisting (as appropriate) * a SignatureLibraryRelease method for the version of MobiDB being handled by this * DAO. * * @return the retrieved / persisted SignatureLibraryRelease object. */ private SignatureLibraryRelease loadMobiDBRelease() { final SignatureLibraryRelease release; final Query releaseQuery = entityManager.createQuery("select r from SignatureLibraryRelease r where r.version = :coilsVersion and r.library = :coilsSignatureLibrary"); releaseQuery.setParameter("coilsVersion", mobidbReleaseVersion); releaseQuery.setParameter("coilsSignatureLibrary", SignatureLibrary.MOBIDB_LITE); @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 " + mobidbReleaseVersion + " of MobiDB in the databases."); } else { release = new SignatureLibraryRelease(SignatureLibrary.MOBIDB_LITE, mobidbReleaseVersion); entityManager.persist(release); } return release; }
private void setSignatures(Set<Signature> signatures) { for (Signature s : signatures) { addSignature(s); } }
public SignatureLibraryRelease parse() throws IOException { LOGGER.debug("Starting to parse hmm file."); SignatureLibraryRelease release = new SignatureLibraryRelease(library, releaseVersion); String signatureName = familyIdFamilyNameMap.get(signatureAcc); release.addSignature(createSignature(signatureAcc, signatureName, release));
final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String version = signature.getSignatureLibraryRelease().getVersion();
final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String description = signature.getDescription();
@Override public String toString() { final StringBuilder sb = new StringBuilder(); sb.append("Job"); if(libraryRelease != null ) { sb.append(" (version:").append(libraryRelease.getVersion()).append(")"); } sb.append("{id='").append(id).append('\''); sb.append(", description='").append(description).append('\''); sb.append(", steps=").append(steps); sb.append('}'); return sb.toString(); }
/** * This private method is responsible for retrieving OR persisting (as appropriate) * a SignatureLibraryRelease method for the version of Phobius being handled by this * DAO. * * @return the retrieved / persisted SignatureLibraryRelease object. */ private SignatureLibraryRelease loadPhobiusRelease() { final SignatureLibraryRelease release; final Query releaseQuery = entityManager.createQuery("select r from SignatureLibraryRelease r where r.version = :phobiusVersion and r.library = :phobiusSignatureLibrary"); releaseQuery.setParameter("phobiusVersion", phobiusVersion); releaseQuery.setParameter("phobiusSignatureLibrary", SignatureLibrary.PHOBIUS); @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 " + phobiusVersion + " of Phobius in the databases."); } else { release = new SignatureLibraryRelease(SignatureLibrary.PHOBIUS, phobiusVersion); entityManager.persist(release); } return release; }
private void createSignature(final SignatureLibraryRelease release, Map<String, String> kdatFileData, final String sigAcc, final String sigName, final String sigDescription) { if (sigName != null) { // If sigName is null, this is the very first one in the file, so nothing to do. String sigAbstract = (storeAbstract) ? kdatFileData.get(sigAcc) : null; final Set<Model> model = Collections.singleton( new Model(sigAcc, sigName, sigDescription) ); release.addSignature( new Signature(sigAcc, sigName, null, sigDescription, sigAbstract, release, model) ); } }
@Transactional public SignatureLibraryRelease parse() throws IOException { LOGGER.debug("Starting to parse cddid.tbl file."); SignatureLibraryRelease release = new SignatureLibraryRelease(library, releaseVersion); if (LOGGER.isDebugEnabled() && lineNumber++ % 10000 == 0) { LOGGER.debug("Parsed " + lineNumber + " lines of the cddid.tbl file."); LOGGER.debug("Parsed " + release.getSignatures().size() + " signatures."); release.addSignature(createSignature(accession, name, description, release));
/** * 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; }
/** * This is rather badly named as there is nothing to parse... * <p/> * however, the point is that it returns a SignatureLibraryRelease for Coils, * containing one big fat Signature called "Coil". * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { final SignatureLibraryRelease release = new SignatureLibraryRelease( this.getSignatureLibrary(), this.getReleaseVersionNumber()); final Signature.Builder builder = new Signature.Builder(COILS_SIGNATURE_NAME); final Signature signature = builder.name(COILS_SIGNATURE_NAME).signatureLibraryRelease(release).build(); release.addSignature(signature); return release; } }
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();