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 f261dd91ff256f953fed82114e42e3d79ff7f5cc..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"
@@ -61,8 +60,7 @@ vector<string> PairwiseSeqsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;
                outputTypes["column"] = tempOutNames;
@@ -75,10 +73,10 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(){
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
        
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        
@@ -268,7 +266,7 @@ void PairwiseSeqsCommand::help(){
 
 int PairwiseSeqsCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                int longestBase = 2000; //will need to update this in driver if we find sequences with more bases.  hardcoded so we don't have the pre-read user fasta file.
                
@@ -495,6 +493,19 @@ int PairwiseSeqsCommand::execute(){
                        
                delete distCalculator;
                
+               //set phylip file as new current phylipfile
+               string current = "";
+               itTypes = outputTypes.find("phylip");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+               }
+               
+               //set column file as new current columnfile
+               itTypes = outputTypes.find("column");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
@@ -593,16 +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; }
                                }
@@ -661,15 +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'; 
                        }
@@ -716,16 +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'); 
                                }
@@ -770,7 +781,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 
                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 
-               int startTime = time(NULL);
+               
                
                string outputString = "";
                size = 0;
@@ -797,16 +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"; 
                        }
                        
@@ -846,7 +857,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 
                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
                
-               int startTime = time(NULL);
+               
                
                string outputString = "";
                size = 0;
@@ -873,16 +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"; 
                        }