sped up realign

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index bfd283db0d1b66db7df4606d980cc9d54dad58a7..8615fbb931b1d4d05fd3ae656b59407c91d94939 100644 (file)
--- a/chimerarealigner.cpp
+++ b/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);
        }
 }
-//***************************************************************************************************************
+//***************************************************************************************************************/

diff --git a/chimerarealigner.h b/chimerarealigner.h
index dec41ef716eb9bcd35864bb461ade028786b2133..7ad741800e3b571f4c3b63dd8349bcf2e9e21e47 100644 (file)
--- a/chimerarealigner.h
+++ b/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;
 };
 /***********************************************************/

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 5868a7c721e69a9206a668536f35d02d573c9568..e62c2f047417f29658673493595a5ee1f01e8d29 100644 (file)
--- a/chimeraslayer.cpp
+++ b/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);
                        }