working on chimeras

[mothur.git] / chimerarealigner.cpp

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
new file mode 100644 (file)
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+++ b/chimerarealigner.cpp
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+/*
+ *  chimerarealigner.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 2/12/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "chimerarealigner.h"
+#include "needlemanoverlap.hpp"
+#include "nast.hpp"
+
+//***************************************************************************************************************
+ChimeraReAligner::ChimeraReAligner(vector<Sequence*> t, int m, int mm) : match(m), misMatch(mm) {  templateSeqs = t;  }
+//***************************************************************************************************************
+ChimeraReAligner::~ChimeraReAligner() {}       
+//***************************************************************************************************************
+void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
+       try {
+               if (parents.size() != 0) {
+                       vector<Sequence*> queryParts;
+                       vector<Sequence*> parentParts;  //queryParts[0] relates to parentParts[0]
+                       
+                       string qAligned = query->getAligned();
+                       string newQuery = "";
+                       
+                       //sort parents by region start
+                       sort(parents.begin(), parents.end(), compareRegionStart);
+
+                       //make sure you don't cutoff beginning of query 
+                       if (parents[0].nastRegionStart > 0) {  newQuery += qAligned.substr(0, parents[0].nastRegionStart+1);  }
+                       int longest = 0;
+                       //take query and break apart into pieces using breakpoints given by results of parents
+                       for (int i = 0; i < parents.size(); i++) {
+                               int length = parents[i].nastRegionEnd - parents[i].nastRegionStart+1;
+                               string q = qAligned.substr(parents[i].nastRegionStart, length);
+                               Sequence* queryFrag = new Sequence(query->getName(), q);
+                               
+                               queryParts.push_back(queryFrag);
+                               
+                               Sequence* parent = getSequence(parents[i].parent);
+                               string p = parent->getAligned();
+                               p = p.substr(parents[i].nastRegionStart, length);
+                               parent->setAligned(p);
+                               
+                               parentParts.push_back(parent);
+                               
+                               if (q.length() > longest)       { longest = q.length(); }
+                               if (p.length() > longest)       { longest = p.length(); }
+                       }
+                                                                                       
+                       //align each peice to correct parent from results
+                       for (int i = 0; i < queryParts.size(); i++) {
+                               alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
+                               Nast nast(alignment, queryParts[i], parentParts[i]);
+                               delete alignment;
+                       }
+                                                                                               
+                       //recombine pieces to form new query sequence
+                       for (int i = 0; i < queryParts.size(); i++) {
+                               newQuery += queryParts[i]->getAligned();
+                       }
+                       
+                       //make sure you don't cutoff end of query 
+                       if (parents[parents.size()-1].nastRegionEnd < qAligned.length()) {  newQuery += qAligned.substr(parents[parents.size()-1].nastRegionEnd-1);  }
+                       
+                       //set query to new aligned string
+                       query->setAligned(newQuery);
+                       
+                       //free memory
+                       for (int i = 0; i < queryParts.size(); i++) { delete queryParts[i];  }
+                       for (int i = 0; i < parentParts.size(); i++) { delete parentParts[i];  }
+                       
+               } //else leave query alone, you have bigger problems...
+               
+       }
+       catch(exception& e) {
+               errorOut(e, "ChimeraReAligner", "reAlign");
+               exit(1);
+       }
+}
+//***************************************************************************************************************
+Sequence* ChimeraReAligner::getSequence(string name) {
+       try{
+               Sequence* temp;
+               
+               //look through templateSeqs til you find it
+               int spot = -1;
+               for (int i = 0; i < templateSeqs.size(); i++) {
+                       if (name == templateSeqs[i]->getName()) {  
+                               spot = i;
+                               break;
+                       }
+               }
+               
+               if(spot == -1) { mothurOut("Error: Could not find sequence."); mothurOutEndLine(); return NULL; }
+               
+               temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
+               
+               return temp;
+       }
+       catch(exception& e) {
+               errorOut(e, "ChimeraReAligner", "getSequence");
+               exit(1);
+       }
+}
+//***************************************************************************************************************