X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=1e7a3388ce4780d369142385cc0b7bf15e96fae9;hb=a4f05f09c250323132a4b9427f41a3ededaec634;hp=f261dd91ff256f953fed82114e42e3d79ff7f5cc;hpb=173a1a82a4e4aa6bef8e4ba77bce342fb9c6563e;p=mothur.git

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index f261dd9..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"
@@ -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"; 
 			}