X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=1e7a3388ce4780d369142385cc0b7bf15e96fae9;hb=a4f05f09c250323132a4b9427f41a3ededaec634;hp=e3f8852203b21640567a725aa10af3d68eb6fbef;hpb=264c8a3c759d9a999c485236e98dac98d4f0db5f;p=mothur.git

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index e3f8852..1e7a338 100644
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -14,7 +14,6 @@
 #include "needlemanoverlap.hpp"
 #include "blastalign.hpp"
 #include "noalign.hpp"
-#include "nast.hpp"
 
 #include "ignoregaps.h"
 #include "eachgapdist.h"
@@ -605,16 +604,16 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
 					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 				}
 				
-				Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
-				Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 				
-				Nast(alignment, seqI, seqJ);
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
 				
-				distCalculator->calcDist(*seqI, *seqJ);
+				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
 				
-				delete seqI; delete seqJ;
-				
 				if(dist <= cutoff){
 					if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 				}
@@ -673,15 +672,15 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st
 					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 				}
 				
-				Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
-				Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 				
-				Nast(alignment, seqI, seqJ);
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
 				
-				distCalculator->calcDist(*seqI, *seqJ);
+				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
-				
-				delete seqI; delete seqJ;
 								
 				outFile << dist << '\t'; 
 			}
@@ -728,16 +727,16 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI,
 					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 				}
 				
-				Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
-				Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 				
-				Nast(alignment, seqI, seqJ);
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
 				
-				distCalculator->calcDist(*seqI, *seqJ);
+				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
 				
-				delete seqI; delete seqJ;
-				
 				if(dist <= cutoff){
 					 outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); 
 				}
@@ -809,16 +808,16 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 				}
 				
-				Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
-				Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 				
-				Nast(alignment, seqI, seqJ);
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
 				
-				distCalculator->calcDist(*seqI, *seqJ);
+				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
 				
-				delete seqI; delete seqJ;
-				
 				outputString += toString(dist) + "\t"; 
 			}
 			
@@ -885,16 +884,16 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 				}
 				
-				Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
-				Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 				
-				Nast(alignment, seqI, seqJ);
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
 				
-				distCalculator->calcDist(*seqI, *seqJ);
+				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
 				
-				delete seqI; delete seqJ;
-				
 				outputString += toString(dist) + "\t"; 
 			}