chimerarealigner.cpp

   1 /*
   2  *  chimerarealigner.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 2/12/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimerarealigner.h"
  11 #include "needlemanoverlap.hpp"
  12 #include "nast.hpp"
  13
  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) {
  20         try {
  21                 if (parents.size() != 0) {
  22                         vector<Sequence*> queryParts;
  23                         vector<Sequence*> parentParts;  //queryParts[0] relates to parentParts[0]
  24
  25                         string qAligned = query->getAligned();
  26                         string newQuery = "";
  27
  28                         //sort parents by region start
  29                         sort(parents.begin(), parents.end(), compareRegionStart);
  30
  31                         //make sure you don't cutoff beginning of query
  32                         if (parents[0].nastRegionStart > 0) {  newQuery += qAligned.substr(0, parents[0].nastRegionStart);  }
  33                         int longest = 0;
  34                         //take query and break apart into pieces using breakpoints given by results of parents
  35                         for (int i = 0; i < parents.size(); i++) {
  36                                 int length = parents[i].nastRegionEnd - parents[i].nastRegionStart+1;
  37                                 string q = qAligned.substr(parents[i].nastRegionStart, length);
  38                                 Sequence* queryFrag = new Sequence(query->getName(), q);
  39
  40                                 queryParts.push_back(queryFrag);
  41
  42                                 Sequence* parent = getSequence(parents[i].parent);
  43                                 string p = parent->getAligned();
  44
  45                                 p = p.substr(parents[i].nastRegionStart, length);
  46                                 parent->setAligned(p);
  47
  48                                 parentParts.push_back(parent);
  49
  50                                 if (q.length() > longest)       { longest = q.length(); }
  51                                 if (p.length() > longest)       { longest = p.length(); }
  52                         }
  53
  54                         //align each peice to correct parent from results
  55                         for (int i = 0; i < queryParts.size(); i++) {
  56                                 alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
  57                                 Nast nast(alignment, queryParts[i], parentParts[i]);
  58                                 delete alignment;
  59                         }
  60
  61                         //recombine pieces to form new query sequence
  62                         for (int i = 0; i < queryParts.size(); i++) {
  63                                 newQuery += queryParts[i]->getAligned();
  64                         }
  65
  66
  67                         //make sure you don't cutoff end of query
  68                         if (parents[parents.size()-1].nastRegionEnd < qAligned.length()) {  newQuery += qAligned.substr(parents[parents.size()-1].nastRegionEnd);  }
  69
  70                         //set query to new aligned string
  71                         query->setAligned(newQuery);
  72
  73                         //free memory
  74                         for (int i = 0; i < queryParts.size(); i++) { delete queryParts[i];  }
  75                         for (int i = 0; i < parentParts.size(); i++) { delete parentParts[i];  }
  76
  77                 } //else leave query alone, you have bigger problems...
  78
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "ChimeraReAligner", "reAlign");
  82                 exit(1);
  83         }
  84 }
  85 //***************************************************************************************************************
  86 Sequence* ChimeraReAligner::getSequence(string name) {
  87         try{
  88                 Sequence* temp;
  89
  90                 //look through templateSeqs til you find it
  91                 int spot = -1;
  92                 for (int i = 0; i < templateSeqs.size(); i++) {
  93                         if (name == templateSeqs[i]->getName()) {
  94                                 spot = i;
  95                                 break;
  96                         }
  97                 }
  98
  99                 if(spot == -1) { m->mothurOut("Error: Could not find sequence."); m->mothurOutEndLine(); return NULL; }
 100
 101                 temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
 102
 103                 return temp;
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "ChimeraReAligner", "getSequence");
 107                 exit(1);
 108         }
 109 }
 110 //***************************************************************************************************************