Examples of edu.msu.cme.rdp.alignment.pairwise.PairwiseAlignment

                if ( lowestCommonRank == null){  // not the rank we care
                    continue;
                }


                // we need to use overlap_trim mode and calculate distance as metric to count insertions, deletions and mismatches.
                PairwiseAlignment result = PairwiseAligner.align(seq.getSeqString().replaceAll("U", "T"), trainSeq.getSeqString().replaceAll("U", "T"), scoringMatrix, mode);
                short sab = (short) (100 - 100*dist.getDistance(result.getAlignedSeqj().getBytes(), result.getAlignedSeqi().getBytes(), 0));
                sabCoutMap.get(lowestCommonRank)[sab]++; 
                                
            }           
        }
        parser.close();

            for ( int j = i+1; j < seqList.size(); j++){
                LineageSequence seqy = seqList.get(j);
                HierarchyTree treey = nodeMap.get((String) seqy.getAncestors().get(seqy.getAncestors().size() - 1));
                
                Taxonomy lowestCommonAnc = findLowestCommonAncestor(treex, treey);               
                PairwiseAlignment result = PairwiseAligner.align(seqx.getSeqString().replaceAll("U", "T"), seqy.getSeqString().replaceAll("U", "T"), scoringMatrix, mode);
                double distance = dist.getDistance(result.getAlignedSeqj().getBytes(), result.getAlignedSeqi().getBytes(), 0);


                if ( show_alignment){
                    System.out.println(">\t" + seqx.getSeqName() + "\t" + seqy.getSeqName() + "\t" + String.format("%.3f", distance) + "\t" + lowestCommonAnc.getHierLevel());
                    System.out.println(result.getAlignedSeqi() + "\n");
                    System.out.println(result.getAlignedSeqj() + "\n");
                }
        
                ArrayList<Double> distList = distanceMap.get(lowestCommonAnc);
                if ( distList == null){
                    distList = new ArrayList<Double>();

Examples of edu.msu.cme.rdp.alignment.pairwise.PairwiseAlignment

Related Classes of edu.msu.cme.rdp.alignment.pairwise.PairwiseAlignment