X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerarealigner.cpp;fp=chimerarealigner.cpp;h=57c3641d14f4f2664dd12c3e1a7f89d13722ab91;hb=5a1e62397b91f57d0d3aff635891df04b8999a88;hp=0000000000000000000000000000000000000000;hpb=df92022fc75c08b91cefa2c6ca4fd7b23eb480b0;p=mothur.git

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
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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);
+	}
+}
+//***************************************************************************************************************