X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=c9e5ecfdfda727427793e98aaed0270cdcd6e046;hp=733c47063bad878d8a54b061cc06e28fa2c7618c;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=df41d90a9611eab75d0516e2654ed8580f8df24c

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 733c470..c9e5ecf 100644
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -8,60 +8,83 @@
  */
 
 #include "pairwiseseqscommand.h"
-#include "sequence.hpp"
-
-#include "gotohoverlap.hpp"
-#include "needlemanoverlap.hpp"
-#include "blastalign.hpp"
-#include "noalign.hpp"
-#include "nast.hpp"
-
-#include "ignoregaps.h"
-#include "eachgapdist.h"
-#include "eachgapignore.h"
-#include "onegapdist.h"
-#include "onegapignore.h"
-
 
 //**********************************************************************************************************************
-vector<string> PairwiseSeqsCommand::getValidParameters(){	
+vector<string> PairwiseSeqsCommand::setParameters(){	
 	try {
-		string AlignArray[] =  {"fasta","align","match","mismatch","gapopen","gapextend", "processors","calc","compress","cutoff","countends","output","outputdir","inputdir"};
-		vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","phylip-column",false,true,true); parameters.push_back(pfasta);
+		CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false); parameters.push_back(palign);
+		CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
+		CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+		CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+		CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+		CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false,true); parameters.push_back(poutput);
+		CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "","",false,false); parameters.push_back(pcalc);
+		CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcountends);
+		CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcompress);
+		CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+		
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
 		return myArray;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "PairwiseSeqsCommand", "getValidParameters");
+		m->errorOut(e, "PairwiseSeqsCommand", "setParameters");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-vector<string> PairwiseSeqsCommand::getRequiredParameters(){	
+string PairwiseSeqsCommand::getHelpString(){	
 	try {
-		string AlignArray[] =  {"fasta"};
-		vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
-		return myArray;
+		string helpString = "";
+		helpString += "The pairwise.seqs command reads a fasta file and creates distance matrix.\n";
+		helpString += "The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n";
+		helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
+		helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n";
+		helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
+		helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
+		helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
+		helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
+		helpString += "The calc parameter allows you to specify the method of calculating the distances.  Your options are: nogaps, onegap or eachgap. The default is onegap.\n";
+		helpString += "The countends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T.\n";
+		helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
+		helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
+		helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n";
+		helpString += "The pairwise.seqs command should be in the following format: \n";
+		helpString += "pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n";
+		helpString += "Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+		return helpString;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "PairwiseSeqsCommand", "getRequiredParameters");
+		m->errorOut(e, "PairwiseSeqsCommand", "getHelpString");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-vector<string> PairwiseSeqsCommand::getRequiredFiles(){	
-	try {
-		vector<string> myArray;
-		return myArray;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PairwiseSeqsCommand", "getRequiredFiles");
-		exit(1);
-	}
+string PairwiseSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "phylip") {  pattern = "[filename],[outputtag],dist"; } 
+        else if (type == "column") { pattern = "[filename],dist"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "PairwiseSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
+		setParameters();
 		vector<string> tempOutNames;
 		outputTypes["phylip"] = tempOutNames;
 		outputTypes["column"] = tempOutNames;
@@ -74,16 +97,14 @@ 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 if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
-			
-			//valid paramters for this command
-			string AlignArray[] =  {"fasta","align","match","mismatch","gapopen","gapextend", "processors","cutoff","compress","calc","countends","output","outputdir","inputdir"};
-			vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string, string> parameters = parser.getParameters(); 
@@ -111,55 +132,77 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
 			if (inputDir == "not found"){	inputDir = "";		}
 
 			fastaFileName = validParameter.validFile(parameters, "fasta", false);
-			if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the pairwise.seqs command."); m->mothurOutEndLine(); abort = true;  }
+			if (fastaFileName == "not found") { 				
+				//if there is a current fasta file, use it
+				string filename = m->getFastaFile(); 
+				if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+			}
 			else { 
 				m->splitAtDash(fastaFileName, fastaFileNames);
 				
 				//go through files and make sure they are good, if not, then disregard them
 				for (int i = 0; i < fastaFileNames.size(); i++) {
 					
-					if (inputDir != "") {
-						string path = m->hasPath(fastaFileNames[i]);
-						//if the user has not given a path then, add inputdir. else leave path alone.
-						if (path == "") {	fastaFileNames[i] = inputDir + fastaFileNames[i];		}
-					}
-	
-					int ableToOpen;
-					ifstream in;
-
-					ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
-				
-					//if you can't open it, try default location
-					if (ableToOpen == 1) {
-						if (m->getDefaultPath() != "") { //default path is set
-							string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
-							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-							ifstream in2;
-							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-							in2.close();
-							fastaFileNames[i] = tryPath;
+					bool ignore = false;
+					if (fastaFileNames[i] == "current") { 
+						fastaFileNames[i] = m->getFastaFile(); 
+						if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+						else { 	
+							m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; 
+							//erase from file list
+							fastaFileNames.erase(fastaFileNames.begin()+i);
+							i--;
 						}
 					}
 					
-					//if you can't open it, try output location
-					if (ableToOpen == 1) {
-						if (m->getOutputDir() != "") { //default path is set
-							string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
-							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-							ifstream in2;
-							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-							in2.close();
-							fastaFileNames[i] = tryPath;
+					if (!ignore) {
+					
+						if (inputDir != "") {
+							string path = m->hasPath(fastaFileNames[i]);
+							//if the user has not given a path then, add inputdir. else leave path alone.
+							if (path == "") {	fastaFileNames[i] = inputDir + fastaFileNames[i];		}
 						}
-					}
+		
+						int ableToOpen;
+						ifstream in;
+
+						ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 					
-					in.close();					
+						//if you can't open it, try default location
+						if (ableToOpen == 1) {
+							if (m->getDefaultPath() != "") { //default path is set
+								string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+								m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+								ifstream in2;
+								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+								in2.close();
+								fastaFileNames[i] = tryPath;
+							}
+						}
+						
+						//if you can't open it, try output location
+						if (ableToOpen == 1) {
+							if (m->getOutputDir() != "") { //default path is set
+								string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+								m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+								ifstream in2;
+								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+								in2.close();
+								fastaFileNames[i] = tryPath;
+							}
+						}
+						
+						in.close();					
 
-					if (ableToOpen == 1) { 
-						m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
-						//erase from file list
-						fastaFileNames.erase(fastaFileNames.begin()+i);
-						i--;
+						if (ableToOpen == 1) { 
+							m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
+							//erase from file list
+							fastaFileNames.erase(fastaFileNames.begin()+i);
+							i--;
+						}else {
+							m->setFastaFile(fastaFileNames[i]);
+						}
 					}
 				}
 				
@@ -171,22 +214,26 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
 			// ...at some point should added some additional type checking...
 			string temp;
 			temp = validParameter.validFile(parameters, "match", false);		if (temp == "not found"){	temp = "1.0";			}
-			convert(temp, match);  
+			m->mothurConvert(temp, match);  
 			
 			temp = validParameter.validFile(parameters, "mismatch", false);		if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, misMatch);  
+			m->mothurConvert(temp, misMatch);  
+            if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 			
 			temp = validParameter.validFile(parameters, "gapopen", false);		if (temp == "not found"){	temp = "-2.0";			}
-			convert(temp, gapOpen);  
+			m->mothurConvert(temp, gapOpen);  
+            if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 			
 			temp = validParameter.validFile(parameters, "gapextend", false);	if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, gapExtend); 
+			m->mothurConvert(temp, gapExtend); 
+            if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 			
-			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = "1";				}
-			convert(temp, processors); 
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
+			m->setProcessors(temp);
+			m->mothurConvert(temp, processors);
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);		if(temp == "not found"){	temp = "1.0"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			temp = validParameter.validFile(parameters, "countends", false);	if(temp == "not found"){	temp = "T";	}
 			countends = m->isTrue(temp); 
@@ -197,6 +244,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
 			align = validParameter.validFile(parameters, "align", false);		if (align == "not found"){	align = "needleman";	}
 			
 			output = validParameter.validFile(parameters, "output", false);		if(output == "not found"){	output = "column"; }
+            if (output=="phylip") { output = "lt"; }
 			if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
 			
 			calc = validParameter.validFile(parameters, "calc", false);			
@@ -205,25 +253,6 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
 				 if (calc == "default")  {  calc = "onegap";  }
 			}
 			m->splitAtDash(calc, Estimators);
-			
-			ValidCalculators validCalculator;
-			if (countends) {
-				for (int i=0; i<Estimators.size(); i++) {
-					if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
-						if (Estimators[i] == "nogaps")			{	distCalculator = new ignoreGaps();	}
-						else if (Estimators[i] == "eachgap")	{	distCalculator = new eachGapDist();	}
-						else if (Estimators[i] == "onegap")		{	distCalculator = new oneGapDist();	}
-					}
-				}
-			}else {
-				for (int i=0; i<Estimators.size(); i++) {
-					if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
-						if (Estimators[i] == "nogaps")		{	distCalculator = new ignoreGaps();					}
-						else if (Estimators[i] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
-						else if (Estimators[i] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
-					}
-				}
-			}
 		}
 		
 	}
@@ -232,54 +261,13 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
 		exit(1);
 	}
 }
-//**********************************************************************************************************************
-PairwiseSeqsCommand::~PairwiseSeqsCommand(){}
-//**********************************************************************************************************************
-
-void PairwiseSeqsCommand::help(){
-	try {
-		m->mothurOut("The pairwise.seqs command reads a fasta file and creates distance matrix.\n");
-		m->mothurOut("The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n");
-		m->mothurOut("The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
-		m->mothurOut("The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
-		m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
-		m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
-		m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
-		m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
-		m->mothurOut("The calc parameter allows you to specify the method of calculating the distances.  Your options are: nogaps, onegap or eachgap. The default is onegap.\n");
-		m->mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T.\n");
-		m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
-		m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
-		m->mothurOut("The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n");
-		m->mothurOut("The pairwise.seqs command should be in the following format: \n");
-		m->mothurOut("pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n");
-		m->mothurOut("Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n");
-		m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PairwiseSeqsCommand", "help");
-		exit(1);
-	}
-}
-
-
 //**********************************************************************************************************************
 
 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.
-		
-		if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
-		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
-		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
-		else if(align == "noalign")		{	alignment = new NoAlign();													}
-		else {
-			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
-			m->mothurOutEndLine();
-			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
-		}
+		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.
 		
 		cutoff += 0.005;
 		
@@ -298,17 +286,21 @@ int PairwiseSeqsCommand::execute(){
 			int numSeqs = alignDB.getNumSeqs();
 			int startTime = time(NULL);
 			string outputFile = "";
-				
+			
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
 			if (output == "lt") { //does the user want lower triangle phylip formatted file 
-				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
-				remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
+				variables["[outputtag]"] = "phylip";
+                outputFile = getOutputFileName("phylip", variables);
+				m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
 			}else if (output == "column") { //user wants column format
-				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
+				outputFile = getOutputFileName("column", variables);
 				outputTypes["column"].push_back(outputFile);
-				remove(outputFile.c_str());
+				m->mothurRemove(outputFile);
 			}else { //assume square
-				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
-				remove(outputFile.c_str());
+                variables["[outputtag]"] = "square";
+                outputFile = getOutputFileName("phylip", variables);
+				m->mothurRemove(outputFile);
 				outputTypes["phylip"].push_back(outputFile);
 			}
 			
@@ -346,11 +338,11 @@ int PairwiseSeqsCommand::execute(){
 					
 					driverMPI(start, end, outMPI, cutoff); 
 					
-					if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);  remove(outputFile.c_str()); delete distCalculator;  return 0; }
+					if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);  m->mothurRemove(outputFile); return 0; }
 				
 					//wait on chidren
 					for(int i = 1; i < processors; i++) { 
-						if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   remove(outputFile.c_str()); delete distCalculator;  return 0; }
+						if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   m->mothurRemove(outputFile);  return 0; }
 						
 						char buf[5];
 						MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
@@ -359,7 +351,7 @@ int PairwiseSeqsCommand::execute(){
 					//do your part
 					driverMPI(start, end, outMPI, cutoff); 
 					
-					if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  remove(outputFile.c_str()); delete distCalculator;  return 0; }
+					if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  m->mothurRemove(outputFile);  return 0; }
 				
 					char buf[5];
 					strcpy(buf, "done"); 
@@ -374,12 +366,12 @@ int PairwiseSeqsCommand::execute(){
 				
 					//do your part
 					string outputMyPart;
-					unsigned long int mySize;
+					unsigned long long mySize;
 					
 					if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 					else { driverMPI(start, end, outputFile, mySize, output); }
 		
-					if (m->control_pressed) {  outputTypes.clear();   remove(outputFile.c_str()); delete distCalculator;  return 0; }
+					if (m->control_pressed) {  outputTypes.clear();   m->mothurRemove(outputFile);   return 0; }
 					
 					int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 					MPI_File outMPI;
@@ -392,9 +384,9 @@ int PairwiseSeqsCommand::execute(){
 
 					//wait on chidren
 					for(int b = 1; b < processors; b++) { 
-						unsigned long int fileSize;
+						unsigned long long fileSize;
 						
-						if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  remove(outputFile.c_str());  delete distCalculator;  return 0; }
+						if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  m->mothurRemove(outputFile);   return 0; }
 						
 						MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status); 
 						
@@ -420,11 +412,11 @@ int PairwiseSeqsCommand::execute(){
 					MPI_File_close(&outMPI);
 				}else { //you are a child process
 					//do your part
-					unsigned long int size;
+					unsigned long long size;
 					if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 					else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 					
-					if (m->control_pressed) { delete distCalculator;  return 0; }
+					if (m->control_pressed) {  return 0; }
 				
 					//tell parent you are done.
 					MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
@@ -433,7 +425,7 @@ int PairwiseSeqsCommand::execute(){
 			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 	#else		
 					
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			//if you don't need to fork anything
 			if(processors == 1){
 				if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
@@ -441,36 +433,27 @@ int PairwiseSeqsCommand::execute(){
 			}else{ //you have multiple processors
 				
 				for (int i = 0; i < processors; i++) {
-					lines.push_back(new linePair());
+					distlinePair tempLine;
+					lines.push_back(tempLine);
 					if (output != "square") {
-						lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
-						lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
+						lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
+						lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 					}else{
-						lines[i]->start = int ((float(i)/float(processors)) * numSeqs);
-						lines[i]->end = int ((float(i+1)/float(processors)) * numSeqs);
+						lines[i].start = int ((float(i)/float(processors)) * numSeqs);
+						lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 					}
 				}
-
-				createProcesses(outputFile); 
-			
-				map<int, int>::iterator it = processIDS.begin();
-				rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
-				it++;
 				
-				//append and remove temp files
-				for (; it != processIDS.end(); it++) {
-					m->appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
-					remove((outputFile + toString(it->second) + ".temp").c_str());
-				}
+				createProcesses(outputFile); 
 			}
-		#else
+		//#else
 			//ifstream inFASTA;
-			if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
-			else { driver(0, numSeqs, outputFile, "square");  }
-		#endif
+			//if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
+			//else { driver(0, numSeqs, outputFile, "square");  }
+		//#endif
 		
 	#endif
-			if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
+			if (m->control_pressed) { outputTypes.clear();   m->mothurRemove(outputFile); return 0; }
 			
 			#ifdef USE_MPI
 				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
@@ -498,13 +481,24 @@ int PairwiseSeqsCommand::execute(){
 			
 			m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 			
-			if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
+			if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
+		}
+		
+		//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); }
 		}
-			
-		delete distCalculator;
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
 		m->mothurOutEndLine();
 		
@@ -520,30 +514,88 @@ int PairwiseSeqsCommand::execute(){
 /**************************************************************************************************/
 void PairwiseSeqsCommand::createProcesses(string filename) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-		int process = 0;
+        int process = 1;
 		processIDS.clear();
+        
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+		
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
 			int pid = fork();
 			
 			if (pid > 0) {
-				processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
+				processIDS.push_back(pid); 
 				process++;
 			}else if (pid == 0){
-				if (output != "square") {  driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff); }
-				else { driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", "square"); }
+				if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
+				else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
+				exit(0);
+			}else { 
+				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
 				exit(0);
-			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+			}
 		}
-	
+		
+		//parent do my part
+		if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
+		else { driver(lines[0].start, lines[0].end, filename, "square"); }
+
+		
 		//force parent to wait until all the processes are done
-		for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) { 
-			int temp = it->second;
+		for (int i=0;i<processIDS.size();i++) { 
+			int temp = processIDS[i];
 			wait(&temp);
 		}
+#else     
+        //////////////////////////////////////////////////////////////////////////////////////////////////////
+		//Windows version shared memory, so be careful when passing variables through the distanceData struct. 
+		//Above fork() will clone, so memory is separate, but that's not the case with windows, 
+		//that's why the distance calculator was moved inside of the driver to make separate copies.
+		//////////////////////////////////////////////////////////////////////////////////////////////////////
+		
+		vector<pairwiseData*> pDataArray; //[processors-1];
+		DWORD   dwThreadIdArray[processors-1];
+		HANDLE  hThreadArray[processors-1]; 
+		
+		//Create processor-1 worker threads.
+		for( int i=0; i<processors-1; i++ ){
+			string extension = toString(i) + ".temp";
+
+			// Allocate memory for thread data.
+			pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, cutoff, i);
+			pDataArray.push_back(tempDist);
+			processIDS.push_back(i);
+			
+			if (output != "square") { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);  } 
+            else { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseSquareThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);  }
+		}
+		
+		//do your part
+		if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
+		else { driver(lines[0].start, lines[0].end, filename, "square"); }
+		
+		//Wait until all threads have terminated.
+		WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+		
+		//Close all thread handles and free memory allocations.
+		for(int i=0; i < pDataArray.size(); i++){
+            if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
+			CloseHandle(hThreadArray[i]);
+			delete pDataArray[i];
+		}
+
 #endif
+        
+        //append and remove temp files
+		for (int i=0;i<processIDS.size();i++) { 
+			m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
+			m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
+		}
+        
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
@@ -557,6 +609,33 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
 	try {
 
 		int startTime = time(NULL);
+        
+        Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
+        
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
 		
 		//column file
 		ofstream outFile(dFileName.c_str(), ios::trunc);
@@ -576,7 +655,7 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
 			
 			for(int j=0;j<i;j++){
 				
-				if (m->control_pressed) { outFile.close(); return 0;  }
+				if (m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0;  }
 				
 				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
@@ -586,16 +665,21 @@ 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);
-				
-				distCalculator->calcDist(*seqI, *seqJ);
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
+
+				//cout << seqI.getName() << '\t' << seqJ.getName() << endl;
+                //cout << alignment->getSeqAAln() << endl << alignment->getSeqBAln() << endl;
+                
+				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
-				
-				delete seqI; delete seqJ;
-				
+                
+                //cout << "dist = " << dist << endl;
+				                
 				if(dist <= cutoff){
 					if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 				}
@@ -612,6 +696,8 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
 		m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 		
 		outFile.close();
+        delete alignment;
+        delete distCalculator;
 		
 		return 1;
 	}
@@ -626,7 +712,34 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st
 	try {
 
 		int startTime = time(NULL);
+        
+        Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
 		
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+
 		//column file
 		ofstream outFile(dFileName.c_str(), ios::trunc);
 		outFile.setf(ios::fixed, ios::showpoint);
@@ -644,7 +757,7 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st
 			
 			for(int j=0;j<alignDB.getNumSeqs();j++){
 				
-				if (m->control_pressed) { outFile.close(); return 0;  }
+				if (m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0;  }
 				
 				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
@@ -654,15 +767,15 @@ 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'; 
 			}
@@ -677,6 +790,8 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st
 		m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 		
 		outFile.close();
+        delete alignment;
+        delete distCalculator;
 		
 		return 1;
 	}
@@ -692,14 +807,41 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI,
 	try {
 		MPI_Status status;
 		int startTime = time(NULL);
+        
+        Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
 		
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+
 		string outputString = "";
 		
 		for(int i=startLine;i<endLine;i++){
 	
 			for(int j=0;j<i;j++){
 				
-				if (m->control_pressed) {  return 0;  }
+				if (m->control_pressed) { delete alignment; delete distCalculator; return 0;  }
 				
 				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
@@ -709,16 +851,16 @@ 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'); 
 				}
@@ -741,7 +883,8 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI,
 			delete buf;
 			
 		}
-		
+		delete alignment;
+        delete distCalculator;
 		return 1;
 	}
 	catch(exception& e) {
@@ -751,7 +894,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI,
 }
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
 	try {
 		MPI_Status status;
 		
@@ -763,7 +906,33 @@ 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);
+		Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
+        
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+
 		
 		string outputString = "";
 		size = 0;
@@ -780,7 +949,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 			
 			for(int j=0;j<i;j++){
 				
-				if (m->control_pressed) {  return 0;  }
+				if (m->control_pressed) { delete alignment; delete distCalculator; return 0;  }
 				
 				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
@@ -790,16 +959,16 @@ 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"; 
 			}
 			
@@ -817,6 +986,8 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 		}
 		
 		MPI_File_close(&outMPI);
+        delete alignment;
+        delete distCalculator;
 		
 		return 1;
 	}
@@ -827,7 +998,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 }
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
 	try {
 		MPI_Status status;
 		
@@ -839,8 +1010,33 @@ 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);
+		Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
 		
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+        
 		string outputString = "";
 		size = 0;
 		
@@ -856,7 +1052,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 			
 			for(int j=0;j<alignDB.getNumSeqs();j++){
 				
-				if (m->control_pressed) {  return 0;  }
+				if (m->control_pressed) {  delete alignment; return 0;  }
 				
 				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
@@ -866,16 +1062,16 @@ 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"; 
 			}
 			
@@ -894,6 +1090,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 		
 		MPI_File_close(&outMPI);
 		
+        delete alignment;
 		return 1;
 	}
 	catch(exception& e) {