private String getDomainRegion(LocationFragment locationFragment){ String domainRegion = locationFragment.getStart() + "-" + locationFragment.getEnd() + "-" + locationFragment.getDcStatus().getSymbol(); return domainRegion; }
rawDiscontinuousMatch.setLocFragmentDCStatus(fragmentDCStatus.getSymbol()); newMatchesFromFragment.add(rawDiscontinuousMatch); continue; PfamHmmer3RawMatch pfMatchRegionOne = getTempPfamHmmer3RawMatch(pfamHmmer3RawMatch, newLocationStart, newLocationEnd, fragmentDCStatus); pfMatchRegionOne.setSplitGroup(splitGroup); pfMatchRegionOne.setLocFragmentDCStatus(fragmentDCStatus.getSymbol()); newMatchesFromFragment.add(pfMatchRegionOne); newLocationStart = fragment.getEnd() + 1; PfamHmmer3RawMatch pfMatchRegionTwo = getTempPfamHmmer3RawMatch(pfamHmmer3RawMatch, newLocationStart, finalLocationEnd, fragmentDCStatus); pfMatchRegionTwo.setSplitGroup(splitGroup); pfMatchRegionTwo.setLocFragmentDCStatus(fragmentDCStatus.getSymbol()); newMatchesFromFragment.add(pfMatchRegionTwo); Utilities.verboseLog(verboseLevel," New Match for Region Two :" + pfMatchRegionTwo.toString());
private PfamHmmer3RawMatch getTempPfamHmmer3RawMatch(PfamHmmer3RawMatch rawMatch, int start, int end, DCStatus dcStatus) { final PfamHmmer3RawMatch match = new PfamHmmer3RawMatch( rawMatch.getSequenceIdentifier(), rawMatch.getModelId(), rawMatch.getSignatureLibrary(), rawMatch.getSignatureLibraryRelease(), start, end, rawMatch.getEvalue(), rawMatch.getScore(), rawMatch.getHmmStart(), rawMatch.getHmmEnd(), rawMatch.getHmmBounds(), rawMatch.getScore(), rawMatch.getEnvelopeStart(), rawMatch.getEnvelopeEnd(), rawMatch.getExpectedAccuracy(), rawMatch.getFullSequenceBias(), rawMatch.getDomainCeValue(), rawMatch.getDomainIeValue(), rawMatch.getDomainBias() ); match.setLocFragmentDCStatus(dcStatus.getSymbol()); return match; }