public SignalPRawMatch(String sequenceIdentifier, String model, SignatureLibrary signatureLibrary, String signatureLibraryRelease, int locationStart, int locationEnd, SignalPOrganismType organismType, double dScore, double dCutoff) { super(sequenceIdentifier, model, signatureLibrary, signatureLibraryRelease, locationStart, locationEnd); this.organismType = organismType; this.dScore = dScore; this.dCutoff = dCutoff; if (!(signatureLibrary.equals(SignatureLibrary.SIGNALP_EUK) || signatureLibrary.equals(SignatureLibrary.SIGNALP_GRAM_POSITIVE) || signatureLibrary.equals(SignatureLibrary.SIGNALP_GRAM_NEGATIVE))) { throw new IllegalStateException("Trying to construct a SignalP raw match with invalid signature library: " + signatureLibrary.getName()); } }
@Override public int hashCode() { int result = signatureLibrary.hashCode(); result = 31 * result + methodAccessionToEntry.hashCode(); return result; } }
SignatureLibrary(String name, String description) { setName(name); setDescription(description); }
String signatureLibraryReleaseVersion = simpleMatch.getSigLibRelease(); final SignatureLibrary sigLib = SignatureLibraryLookup.lookupSignatureLibrary(simpleMatch.getSignatureLibraryName()); lookupAnalysesMap.put(sigLib.getName().toUpperCase(), signatureLibraryReleaseVersion);
signatureLibrary = m.getSignatureLibrary(); signatureLibraryRelease = m.getSignatureLibraryRelease(); } else if (!signatureLibrary.equals(m.getSignatureLibrary()) || !signatureLibraryRelease.equals(m.getSignatureLibraryRelease())) { throw new IllegalArgumentException("Filtered matches are from different signature library versions " +
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()));
signatureLibrary = m.getSignatureLibrary(); signatureLibraryRelease = m.getSignatureLibraryRelease(); } else if (!signatureLibrary.equals(m.getSignatureLibrary()) || !signatureLibraryRelease.equals(m.getSignatureLibraryRelease())) { throw new IllegalArgumentException("Filtered matches are from different signature library versions " +
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = analysisI5toI4.get(signatureLibrary.getName()); if (analysis == null) { LOGGER.info("Skipping " + signatureAc + " match, RAW output does not support matches from analysis " + signatureLibrary.getName());
signatureLibrary = m.getSignatureLibrary(); signatureLibraryRelease = m.getSignatureLibraryRelease(); } else if (!signatureLibrary.equals(m.getSignatureLibrary()) || !signatureLibraryRelease.equals(m.getSignatureLibraryRelease())) { throw new IllegalArgumentException("Filtered matches are from different signature library versions " +
@Override public int hashCode() { int result = signatureLibrary.hashCode(); result = 31 * result + methodAccessionToEntry.hashCode(); return result; } }
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = analysisI5toI4.get(signatureLibrary.getName()); if (analysis == null) { LOGGER.info("Skipping " + signatureAc + " match, RAW output does not support matches from analysis " + signatureLibrary.getName());
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String description = signature.getDescription();
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String description = signature.getDescription();
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String version = signature.getSignatureLibraryRelease().getVersion();
if(timeTaken > (waitTimeFactor * waitTimeFactor * 100 * 1000)){ LOGGER.warn("H2 database problem: failed to verify " + count + " matches in database for " + represantiveRawMatch.getSignatureLibrary().getName() + " after " + timeTaken + " ms " + " - matches found : " + matchesFound);
if (represantiveRawMatch.getSignatureLibrary().getName().contains("PANTHER") || represantiveRawMatch.getSignatureLibrary().getName().contains("ProSitePatterns")) { int rmCount = 0; for (RawMatch rawMatch : rawProtein.getMatches()) { rmCount++; Utilities.verboseLog(represantiveRawMatch.getSignatureLibrary().getName() + " " + rmCount + " " + rawMatch.toString()); matchesFound += rawProtein.getMatches().size(); if (LOGGER.isDebugEnabled()) { Utilities.verboseLog("Considering ... " + represantiveRawMatch.getSignatureLibrary().getName()); if (represantiveRawMatch.getSignatureLibrary().getName().contains("PANTHER") || represantiveRawMatch.getSignatureLibrary().getName().contains("ProSitePatterns")) { int rmCount = 0; for (RawMatch rawMatch : rawProtein.getMatches()) { rmCount++; Utilities.verboseLog(represantiveRawMatch.getSignatureLibrary().getName() + "_R2 " + rmCount + " " + rawMatch.toString()); Utilities.verboseLog(represantiveRawMatch.getSignatureLibrary().getName() + " matchesFound: " + matchesFound + " matchCount: " + matchCount + " queryTime: " + queryTime); int retryCount = 0; Utilities.verboseLog(represantiveRawMatch.getSignatureLibrary().getName() + " matchesFound-2: " +matchesFound + " matchCount: " + matchCount); + represantiveRawMatch.getSignatureLibrary().getName() + " after " + timeTaken + " ms " + " - matches found : " + matchesFound;
if(timeTaken > (waitTimeFactor * waitTimeFactor * 100 * 1000)){ LOGGER.warn("H2 database problem: failed to verify " + count + " matches in database for " + represantiveRawMatch.getSignatureLibrary().getName() + " after " + timeTaken + " ms " + " - matches found : " + matchesFound);
final String signatureModels = match.getSignatureModels(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String version = signature.getSignatureLibraryRelease().getVersion();
if(timeTaken > (waitTimeFactor * waitTimeFactor * 100 * 1000)){ LOGGER.warn("H2 database problem: failed to verify " + count + " matches in database for " + represantiveRawMatch.getSignatureLibrary().getName() + " after " + timeTaken + " ms " + " - matches found : " + matchesFound);
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String description = signature.getDescription(); final String matchId = MATCH_STRING + getMatchCounter();