5 * Created by westcott on 2/12/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "chimerarealigner.h"
11 #include "needlemanoverlap.hpp"
14 //***************************************************************************************************************
15 ChimeraReAligner::ChimeraReAligner(vector<Sequence*> t, int ms, int mm) : match(ms), misMatch(mm) { templateSeqs = t; m = MothurOut::getInstance(); }
16 //***************************************************************************************************************
17 ChimeraReAligner::~ChimeraReAligner() {}
18 //***************************************************************************************************************
19 void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
21 if (parents.size() != 0) {
22 vector<Sequence*> queryParts;
23 vector<Sequence*> parentParts; //queryParts[0] relates to parentParts[0]
25 string qAligned = query->getAligned();
28 //sort parents by region start
29 sort(parents.begin(), parents.end(), compareRegionStart);
31 //make sure you don't cutoff beginning of query
32 if (parents[0].nastRegionStart > 0) { newQuery += qAligned.substr(0, parents[0].nastRegionStart); }
35 //take query and break apart into pieces using breakpoints given by results of parents
36 for (int i = 0; i < parents.size(); i++) {
37 int length = parents[i].nastRegionEnd - parents[i].nastRegionStart+1;
38 string q = qAligned.substr(parents[i].nastRegionStart, length);
40 Sequence* queryFrag = new Sequence(query->getName(), q);
42 queryParts.push_back(queryFrag);
44 Sequence* parent = getSequence(parents[i].parent);
45 string p = parent->getAligned();
47 p = p.substr(parents[i].nastRegionStart, length);
48 parent->setAligned(p);
50 parentParts.push_back(parent);
52 if (q.length() > longest) { longest = q.length(); }
53 if (p.length() > longest) { longest = p.length(); }
56 //align each peice to correct parent from results
57 for (int i = 0; i < queryParts.size(); i++) {
58 if ((queryParts[i]->getUnaligned() == "") || (parentParts[i]->getUnaligned() == "")) {;}
60 alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
62 Nast nast(alignment, queryParts[i], parentParts[i]);
67 //recombine pieces to form new query sequence
68 for (int i = 0; i < queryParts.size(); i++) {
69 //sometimes the parent regions do not meet, for example region 1 may end at 1000 and region 2 starts at 1100.
70 //we don't want to loose length so in this case we will leave query alone
72 int space = parents[i].nastRegionStart - parents[i-1].nastRegionEnd - 1;
73 if (space > 0) { //they don't meet and we need to add query piece
74 string q = qAligned.substr(parents[i-1].nastRegionEnd+1, space);
79 newQuery += queryParts[i]->getAligned();
82 //make sure you don't cutoff end of query
83 if (parents[parents.size()-1].nastRegionEnd < (qAligned.length()-1)) { newQuery += qAligned.substr(parents[parents.size()-1].nastRegionEnd+1); }
85 //set query to new aligned string
86 query->setAligned(newQuery);
89 for (int i = 0; i < queryParts.size(); i++) { delete queryParts[i]; }
90 for (int i = 0; i < parentParts.size(); i++) { delete parentParts[i]; }
92 } //else leave query alone, you have bigger problems...
96 m->errorOut(e, "ChimeraReAligner", "reAlign");
100 //***************************************************************************************************************
101 Sequence* ChimeraReAligner::getSequence(string name) {
105 //look through templateSeqs til you find it
107 for (int i = 0; i < templateSeqs.size(); i++) {
108 if (name == templateSeqs[i]->getName()) {
114 if(spot == -1) { m->mothurOut("Error: Could not find sequence."); m->mothurOutEndLine(); return NULL; }
116 temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
120 catch(exception& e) {
121 m->errorOut(e, "ChimeraReAligner", "getSequence");
125 //***************************************************************************************************************