private String getDomainRegion(LocationFragment locationFragment){ String domainRegion = locationFragment.getStart() + "-" + locationFragment.getEnd() + "-" + locationFragment.getDcStatus().getSymbol(); return domainRegion; }
rawDiscontinuousMatch.setLocFragmentDCStatus(fragmentDCStatus.getSymbol()); newMatchesFromFragment.add(rawDiscontinuousMatch); continue; } else if (fragment.getEnd() >= newLocationEnd) { newLocationEnd = fragment.getStart() - 1; fragmentDCStatus = DCStatus.getNewDCStatus(fragmentDCStatus, DCStatus.C_TERMINAL_DISC); } else if (fragment.getStart() > newLocationStart && fragment.getEnd() < newLocationEnd) { fragmentDCStatus = DCStatus.getNewDCStatus(fragmentDCStatus, DCStatus.C_TERMINAL_DISC); 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());
rawMatch.getLocationStart(), rawMatch.getLocationEnd(), DCStatus.parseSymbol(rawMatch.getLocFragmentDCStatus()));
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; }