sped up realign

[mothur.git] / chimerarealigner.cpp

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);
        }
 }
-//***************************************************************************************************************
+//***************************************************************************************************************/