fixed get.lienage and remove.lineage bug with confidence scores that are floats....

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index e3f8852203b21640567a725aa10af3d68eb6fbef..1e7a3388ce4780d369142385cc0b7bf15e96fae9 100644 (file)
--- 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"; 
                        }