MASTERARBEIT - Fachhochschule Salzburg

DQuelltexteD.1 amodseq: Alignment voralignierter Sequenzenin das Profil-HMMpublic int AlignSequenceToModel( ModelSequences modelSeq,AlignedSequence algSeq )throws AlignmentException{String seqID = algSeq.getName();int seqOffset = 0;int modelOffset = 0;int matchOffset = 0;int insertlen, endins;↩→↩→StringBuilder seq = new StringBuilder(50000);StringBuilder mask = new StringBuilder(50000);seq.append(algSeq.getSequenceString());mask.append(algSeq.getMaskString());for(int i=0; i < mask.length(); i++){switch( mask.charAt(i) ){case ’D’:case ’M’:matchOffset = modelSeq.getNextMatch(modelOffset);if( matchOffset == modelOffset ){modelOffset++;seqOffset++;} else {insertlen = matchOffset - modelOffset;mask.insert(i, StringUtils.RepeatChar(gapChar, insertlen));124