/** * Given a SignalP organism type return the associated SignalP signature library. * * @param type Organism type * @return Signature library */ public static SignatureLibrary getSignatureLibraryFromType(SignalPOrganismType type) { if (type.equals(SignalPOrganismType.EUK)) { return SignatureLibrary.SIGNALP_EUK; } else if (type.equals(SignalPOrganismType.GRAM_POSITIVE)) { return SignatureLibrary.SIGNALP_GRAM_POSITIVE; } else if (type.equals(SignalPOrganismType.GRAM_NEGATIVE)) { return SignatureLibrary.SIGNALP_GRAM_NEGATIVE; } return null; }
public SignalPMatchParser(String typeShortName, SignatureLibraryRelease signatureLibraryRelease) { this.type = SignalPOrganismType.getSignalPOrganismTypeByShortName(typeShortName); this.signatureLibraryRelease = signatureLibraryRelease; }
LOGGER.error("SignalP organsim type not set in job XML, or not a valid value"); throw new IllegalStateException("SignalP organsim type not set in job XML"); } else if (!type.equals(SignalPOrganismType.getSignalPOrganismTypeByShortName(typeString))) { LOGGER.error("SignalP organsim type in file:" + typeString + " does not match that supplied in job XML: " + type.getTypeShortName()); throw new IllegalStateException("SignalP organsim type in file:" + typeString + " does not match that supplied in job XML: " + type.getTypeShortName()); SignatureLibrary signatureLibrary = SignalPOrganismType.getSignatureLibraryFromType(type); if (signatureLibrary == null) { throw new IllegalStateException("Invalid signature library for SignalP raw match");
@Override public int hashCode() { int result = super.hashCode(); result = 31 * result + (orgType != null ? orgType.hashCode() : 0); return result; } }
LOGGER.error("SignalP organsim type not set in job XML, or not a valid value"); throw new IllegalStateException("SignalP organsim type not set in job XML"); } else if (!type.equals(SignalPOrganismType.getSignalPOrganismTypeByShortName(typeString))) { LOGGER.error("SignalP organsim type in file:" + typeString + " does not match that supplied in job XML: " + type.getTypeShortName()); throw new IllegalStateException("SignalP organsim type in file:" + typeString + " does not match that supplied in job XML: " + type.getTypeShortName()); SignatureLibrary signatureLibrary = SignalPOrganismType.getSignatureLibraryFromType(type); if (signatureLibrary == null) { throw new IllegalStateException("Invalid signature library for SignalP raw match");
public SignalPMatchParser(String typeShortName, SignatureLibraryRelease signatureLibraryRelease) { this.type = SignalPOrganismType.getSignalPOrganismTypeByShortName(typeShortName); this.signatureLibraryRelease = signatureLibraryRelease; }