sped up realign

chimerarealigner.cpp

@@ -12,7 +12,7 @@
 #include "nast.hpp"
 
 //***************************************************************************************************************
-ChimeraReAligner::ChimeraReAligner(vector<Sequence*> t, int ms, int mm) : match(ms), misMatch(mm) {  templateSeqs = t;   m = MothurOut::getInstance(); }
+ChimeraReAligner::ChimeraReAligner()  {  m = MothurOut::getInstance(); }
 //***************************************************************************************************************
 ChimeraReAligner::~ChimeraReAligner() {}	
 //***************************************************************************************************************
@@ -38,15 +38,11 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 				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();
 
+				string p = parents[i].parentAligned;
 				p = p.substr(parents[i].nastRegionStart, length);
-				parent->setAligned(p);
-
+				Sequence* parent = new Sequence(parents[i].parent, p);
 				parentParts.push_back(parent);
 
 				if (queryFrag->getUnaligned().length() > longest)	{ longest = queryFrag->getUnaligned().length(); }
@@ -96,7 +92,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 		exit(1);
 	}
 }
-//***************************************************************************************************************
+/***************************************************************************************************************
 Sequence* ChimeraReAligner::getSequence(string name) {
 	try{
 		Sequence* temp;
@@ -121,4 +117,4 @@ Sequence* ChimeraReAligner::getSequence(string name) {
 		exit(1);
 	}
 }
-//***************************************************************************************************************
+//***************************************************************************************************************/

chimerarealigner.h

@@ -18,17 +18,15 @@
 class ChimeraReAligner  {
 
 	public:
-		ChimeraReAligner(vector<Sequence*>, int, int);	 
+		ChimeraReAligner();	 
 		~ChimeraReAligner();
 
 		void reAlign(Sequence*, vector<results>);
 
 	private:
 		Sequence* querySeq;
-		vector<Sequence*> templateSeqs;
-		int match, misMatch;
 
-		Sequence* getSequence(string);  //find sequence from name
+		//Sequence* getSequence(string);  //find sequence from name
 		MothurOut* m;
 };
 /***********************************************************/

chimeraslayer.cpp

@@ -765,7 +765,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 		if (chimeraFlag == "yes") {
 
 			if (realign) {
-				ChimeraReAligner realigner(thisTemplate, match, misMatch);
+				ChimeraReAligner realigner;
 				realigner.reAlign(query, Results);
 			}