From: pschloss <pschloss>
Date: Sun, 24 May 2009 16:39:16 +0000 (+0000)
Subject: This contains Pat's bug fixes and updates.  It represents mothur v.1.3.0
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=cdcf99b7760701e6869ca8e4e6e91c8e8c4ae186

This contains Pat's bug fixes and updates.  It represents mothur v.1.3.0
---

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 1b52eee..6c86778 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -174,327 +174,327 @@
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-		EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = "<group>"; };
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+		EB72FE250FC1F5CA0051AC11 /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = SOURCE_ROOT; };
+		EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = SOURCE_ROOT; };
+		EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = SOURCE_ROOT; };
+		EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = SOURCE_ROOT; };
+		EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = SOURCE_ROOT; };
 /* End PBXFileReference section */
 
 /* Begin PBXFrameworksBuildPhase section */
diff --git a/boneh.cpp b/boneh.cpp
index 2025ae7..f5c8f90 100644
--- a/boneh.cpp
+++ b/boneh.cpp
@@ -11,11 +11,10 @@
 #include <math.h>
 
 /***********************************************************************/
+
 //This solves for the value of 'v' using a binary search.
 double Boneh::getV(double f1, double n, double rs) {
 
-	//cout << "f1 = " << f1 << "\nn = " << n << "\nrs = " << rs << "\n\n";
-	
 	if(rs == 0)
 		return 0;
 	
@@ -24,56 +23,53 @@ double Boneh::getV(double f1, double n, double rs) {
 	double step = v/2;
 	double ls = v * (1 - pow((1 - f1/(n*v)), n));
 	
-	//cout << "ls = " << ls << "\n";
-	
 	while(abs(ls - rs) > accuracy) {
-		if(ls > rs)
-			v -= step;
-		else
-			v += step;
+		if(ls > rs)	{	v -= step;	}
+		else		{	v += step;	}
 		
-		ls = v* (1 - pow((1 - f1/(n*v)), n));
+		ls = v * (1 - pow((1 - f1/(n * v)), n));
 		step /= 2;
-		
-		//cout << "ls = " << ls << "\n";
 	}
-	
+
 	return v;
 }
 	
 /***********************************************************************/	
-EstOutput Boneh::getValues(SAbundVector* rank){
+EstOutput Boneh::getValues(SAbundVector* sabund){
 
 	try {
 		data.resize(1,0);
 		
+
 		bool valid = false;
 		double sum = 0;
-		double n = (double)rank->getNumSeqs();
-		double f1 = (double)rank->get(1);
+		double n = (double)sabund->getNumSeqs();
+		if(m==0){	m=n;	}
 		
-		for(int i = 1; i < rank->size(); i++)
-			sum += (double)rank->get(i) * exp(-i);
+		double f1 = (double)sabund->get(1);
 		
-		if(rank->get(1) > sum)
+		for(int i = 1; i < sabund->size(); i++){
+			sum += (double)sabund->get(i) * exp(-i);
+		}
+
+		if(sabund->get(1) > sum)
 			valid = true;
 		
 		sum = 0;
 		if(valid) {
-			for(int j = 1; j < rank->size(); j++)
-				sum += rank->get(j) * pow((1 - (double)j / n), n);
+			for(int j = 1; j < sabund->size(); j++){
+				sum += sabund->get(j) * pow((1 - (double)j / n), n);
+			}
 			
 			double v = getV(f1, n, sum);
 			
-			//cout << "v = " << v << "\n";
-			
-			
 			sum = 0;
-			for(int j = 1; j < rank->size(); j++) {
-				for (int i = 0; i < rank->get(j); i++) {
-					sum += pow(1 - j / n, n) * (1 - pow(1 - j / n, m)) + v * pow(1 - f1/(n*v), n) * (1 - pow(1 - f1/(n*v), m));
+			for(int j = 1; j < sabund->size(); j++) {
+				for (int i = 0; i < sabund->get(j); i++) {
+					sum += pow(1 - j / n, n) * (1 - pow(1 - j / n, m));
 				}
 			}
+			sum +=  v * pow(1 - f1/(n*v), n) * (1 - pow(1 - f1/(n*v), m));
 		}
 
 		data[0] = sum;
diff --git a/bootstrap.h b/bootstrap.h
index e54d985..70fdf05 100644
--- a/bootstrap.h
+++ b/bootstrap.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class Bootstrap : public Calculator  {
 	
 public:
-	Bootstrap() : Calculator("Bootstrap", 1, false) {};
+	Bootstrap() : Calculator("bootstrap", 1, false) {};
 	EstOutput getValues(SAbundVector*);
 	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
 	
diff --git a/chao1.h b/chao1.h
index 27b7827..1322aac 100644
--- a/chao1.h
+++ b/chao1.h
@@ -19,7 +19,7 @@ It is a child of the calculator class. */
 class Chao1 : public Calculator  {
 	
 public: 
-	Chao1() : Calculator("Chao", 3, false) {};
+	Chao1() : Calculator("chao", 3, false) {};
 	EstOutput getValues(SAbundVector*);	
 	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
 };
diff --git a/distancecommand.cpp b/distancecommand.cpp
index 7d1f6a0..6fee651 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -20,12 +20,12 @@ DistanceCommand::DistanceCommand(){
 	try {
 		globaldata = GlobalData::getInstance();
 		validCalculator = new ValidCalculators();
-		ends = globaldata->getEnds();
+		countends = globaldata->getCountEnds();
 		convert(globaldata->getProcessors(), processors);
 		convert(globaldata->getCutOff(), cutoff);
 		
 		int i;
-		if (ends != "T") {
+		if (countends == "T") {
 			for (i=0; i<globaldata->Estimators.size(); i++) {
 				if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) { 
 					if (globaldata->Estimators[i] == "nogaps") { 
@@ -83,7 +83,8 @@ int DistanceCommand::execute(){
 		seqDB = readSeqs->getDB();
 	
 		int numSeqs = seqDB->getNumSeqs();
-		
+		cutoff += 0.005;
+
 		string distFile = getRootName(globaldata->getFastaFile()) + "dist";
 		
 		remove(distFile.c_str());
@@ -201,10 +202,6 @@ int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLi
 		for(int i=startLine;i<endLine;i++){
 		
 			for(int j=0;j<i;j++){
-//cout << "unaligned" << endl;
-//cout << align->get(i).getUnaligned() << "  " << align->get(j).getUnaligned() << endl;
-//cout << "aligned" << endl;
-//cout << align->get(i).getAligned() << "  " << align->get(j).getAligned() << endl;
 				distCalculator->calcDist(align->get(i), align->get(j));
 				double dist = distCalculator->getDist();
 
diff --git a/distancecommand.h b/distancecommand.h
index 34dd65e..6bd7572 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -39,7 +39,7 @@ private:
 	ReadSeqs* readSeqs;
 	ofstream out;
 	string outputFileName;
-	string ends;
+	string countends;
 	int processors;
 	float cutoff;
 	
diff --git a/eachgapdist.h b/eachgapdist.h
index 767c4bf..d21e55c 100644
--- a/eachgapdist.h
+++ b/eachgapdist.h
@@ -21,28 +21,28 @@ public:
 		int length = 0;
 		int start = 0;
 		
-		for(int i=0; i<A.getLength(); i++){
-			if(A.getAligned()[i] != '.' || B.getAligned()[i] != '.'){
+		string seqA = A.getAligned();
+		string seqB = B.getAligned();
+		int alignLength = seqA.length();
+		
+		for(int i=0; i<alignLength; i++){
+			if(seqA[i] != '.' || seqB[i] != '.'){
 				start = i;
 				break;
 			}
 		}
-		
-		for(int i=start;i<A.getLength();i++){
-			if((A.getAligned()[i] == '-' || B.getAligned()[i] == '-') && (A.getAligned()[i] == '.' || B.getAligned()[i] == '.')){}
-			else if(A.getAligned()[i] == '.' && B.getAligned()[i] == '.'){
+
+		for(int i=start;i<alignLength;i++){
+			if(seqA[i] == '.' && seqB[i] == '.'){
 				break;	
 			}
-			else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
-				if(A.getAligned()[i] != B.getAligned()[i]){
+			else if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.') || (seqA[i] == '.' && seqB[i] == '-')){;}
+			else{
+				if(seqA[i] != seqB[i]){
 					diff++;
 				}
 				length++;
 			}
-			else if(A.getAligned()[i] != '-' || B.getAligned()[i] != '-'){
-				diff++;
-				length++;
-			}
 		}
 		
 		if(length == 0)	{	dist = 1.0000;								}
@@ -53,4 +53,4 @@ public:
 
 /**************************************************************************************************/
 
-#endif
\ No newline at end of file
+#endif
diff --git a/eachgapignore.h b/eachgapignore.h
index 9b9d167..9763a6d 100644
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -22,40 +22,28 @@ public:
 		int diff = 0;
 		int length = 0;
 		int start = 0;
-		int end = 0;
 		
-		for(int i=0;i<A.getLength();i++){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-			}
-			else{
+		string seqA = A.getAligned();
+		string seqB = B.getAligned();
+		int alignLength = seqA.length();
+		
+		for(int i=0; i<alignLength; i++){
+			if(seqA[i] != '.' && seqB[i] != '.'){
 				start = i;
 				break;
 			}
 		}
-		for(int i=A.getLength()-1;i>=0;i--){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-			}
-			else{
-				end = i;
-				break;
-			}
-		}
 		
-		for(int i=start;i<=end;i++){
-			if(A.getAligned()[i] == '-' && B.getAligned()[i] == '-'){}
-			else if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.'){
+		for(int i=start;i<alignLength;i++){
+			if(seqA[i] == '.' || seqB[i] == '.'){
 				break;	
 			}
-			else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
-				if(A.getAligned()[i] != B.getAligned()[i]){
+			else if(seqA[i] != '-' || seqB[i] != '-'){
+				if(seqA[i] != seqB[i]){
 					diff++;
 				}
 				length++;
 			}
-			else if(A.getAligned()[i] != '-' || B.getAligned()[i] != '-'){
-				diff++;
-				length++;
-			}
 		}
 		
 		if(length == 0)	{	dist = 1.0000;								}
diff --git a/efron.cpp b/efron.cpp
index aeeb4c2..e88b025 100644
--- a/efron.cpp
+++ b/efron.cpp
@@ -17,16 +17,12 @@ EstOutput Efron::getValues(SAbundVector* rank){
 		data.resize(1,0);
 		
 		double n = (double)rank->getNumSeqs();
-		if(m > n) {
-			cout << "Error in the 'efron' calculator. 'size' must be less than the length of the smallest sabund vector.\n";
-			data[0] = 0;
-			return data;
-		}
+		if(m > n || m == 0) {	m = n;	}
 		
 		double sum = 0;
-		for(int i = 1; i < rank->size(); i++)
-			sum += pow(-1, (double)(i+1)) * pow(((double)m / n), i) * (double)(rank->get(i));
-
+		for(int i = 1; i < rank->size(); i++){
+			sum += pow(-1., i+1) * pow(((double)m / n), i) * (double)(rank->get(i));
+		}
 		data[0] = sum;
 		
 		return data;
diff --git a/errorchecking.cpp b/errorchecking.cpp
index c5396cf..8b80580 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -116,7 +116,7 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "soft" )			{ soft = value; }
 				if (parameter == "filter" )         { filter = value; }
 				if (parameter == "scale" )			{ scale = value;	}
-				if (parameter == "ends" )			{ ends = value; }
+				if (parameter == "countends" )		{ countends = value; }
 				if (parameter == "processors" )		{ processors = value;	}
 				if (parameter == "size" )			{ size = value; }
 				if (parameter == "candidate")		{ candidatefile = value;	}
@@ -166,7 +166,7 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "soft" )			{ soft = value; }
 				if (parameter == "filter" )         { filter = value; }
 				if (parameter == "scale" )			{ scale = value;	}
-				if (parameter == "ends" )			{ ends = value; }
+				if (parameter == "countends" )		{ countends = value; }
 				if (parameter == "processors" )		{ processors = value;	}
 				if (parameter == "size" )			{ size = value; }
 				if (parameter == "candidate")		{ candidatefile = value;	}
diff --git a/errorchecking.h b/errorchecking.h
index c667167..ac09f6e 100644
--- a/errorchecking.h
+++ b/errorchecking.h
@@ -35,7 +35,7 @@ class ErrorCheck {
 		void clear();
 		void refresh();
 		string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, cutoff, format; 
-		string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund, sorted, trump, soft, filter, scale, ends, processors, size;
+		string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund, sorted, trump, soft, filter, scale, countends, processors, size;
 		string candidatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
 		string commandName, optionText;
 		bool errorFree;
diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index f4cc6d8..6c02242 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -10,158 +10,160 @@
 #include "filterseqscommand.h"
 
 /**************************************************************************************/
-void FilterSeqsCommand::doTrump() {
-	trump = globaldata->getTrump();
-	for(int i = 0; i < db->size(); i++) {
-		Sequence cur = db->get(i);
-		string curAligned = cur.getAligned();
-		for(int j = 0; j < curAligned.length(); j++) {
-			string curChar = curAligned.substr(j, 1);
-			if(curChar.compare(trump) == 0) 
-				columnsToRemove[j] = true;
-		}
-	}
+
+FilterSeqsCommand::FilterSeqsCommand(){
+	globaldata = GlobalData::getInstance();
+	
+	if(globaldata->getFastaFile() != "")		{	readSeqs =  new ReadFasta(globaldata->inputFileName);	}
+	else if(globaldata->getNexusFile() != "")	{	readSeqs = new ReadNexus(globaldata->inputFileName);	}
+	else if(globaldata->getClustalFile() != "") {	readSeqs = new ReadClustal(globaldata->inputFileName);	}
+	else if(globaldata->getPhylipFile() != "")	{	readSeqs = new ReadPhylip(globaldata->inputFileName);	}
+	
+	readSeqs->read();
+	db = readSeqs->getDB();
+	numSeqs = db->size();
+	
+	alignmentLength = db->get(0).getLength();
+
+	filter = string(alignmentLength, '1');
 }
 
 /**************************************************************************************/
-void FilterSeqsCommand::doSoft() {
-	soft = atoi(globaldata->getSoft().c_str());
-	vector<vector<int> > columnSymbolSums;
-	vector<vector<string> > columnSymbols;
-	for(int i = 0; i < db->get(0).getLength(); i++) {
-		vector<string> symbols;
-		vector<int> sums;
-		columnSymbols.push_back(symbols);
-		columnSymbolSums.push_back(sums);
-	}
+
+void FilterSeqsCommand::doHard() {
 	
-	for(int i = 0; i < db->size(); i++) {
-		Sequence cur = db->get(i);
-		string curAligned = cur.getAligned();
+	string hardName = globaldata->getHard();
+	string hardFilter = "";
 		
-		for(int j = 0; j < curAligned.length(); j++) {
-			string curChar = curAligned.substr(j, 1);
-			vector<string> curColumnSymbols = columnSymbols[j];
-			bool newSymbol = true;
-			
-			for(int k = 0; k < curColumnSymbols.size(); k++) 
-				if(curChar.compare(curColumnSymbols[k]) == 0) {
-					newSymbol = false;
-					columnSymbolSums[j][k]++;
-				}
-			
-			if(newSymbol) {
-				columnSymbols[j].push_back(curChar);
-				columnSymbolSums[j].push_back(1);
+	ifstream fileHandle;
+	openInputFile(hardName, fileHandle);
+	
+	fileHandle >> hardFilter;
+	
+	if(hardFilter.length() != filter.length()){
+		cout << "The hard filter is not the same length as the alignment: Hard filter will not be applied." << endl;
+	}
+	else{
+		filter = hardFilter;
+	}
+	
+}
+
+/**************************************************************************************/
+
+void FilterSeqsCommand::doTrump() {
+
+	char trump = globaldata->getTrump()[0];
+	
+	for(int i = 0; i < numSeqs; i++) {
+		string curAligned = db->get(i).getAligned();;
+
+		for(int j = 0; j < alignmentLength; j++) {
+			if(curAligned[j] == trump){
+				filter[j] = '0';
 			}
 		}
 	}
+
+}
+
+/**************************************************************************************/
+
+void FilterSeqsCommand::doVertical() {
+
+	vector<int> counts(alignmentLength, 0);
 	
-	
-	for(int i = 0; i < columnSymbolSums.size(); i++) {
-		int totalSum = 0;
-		int max = 0;
-		vector<int> curColumnSymbols = columnSymbolSums[i];
+	for(int i = 0; i < numSeqs; i++) {
+		string curAligned = db->get(i).getAligned();;
 		
-		for(int j = 0; j < curColumnSymbols.size(); j++) {
-			int curSum = curColumnSymbols[j];
-			//cout << columnSymbols[i][j] << ": " << curSum << "\n";
-			if(curSum > max)
-				max = curSum;
-			totalSum += curSum;
+		for(int j = 0; j < alignmentLength; j++) {
+			if(curAligned[j] == '-' || curAligned[j] == '.'){
+				counts[j]++;
+			}
 		}
-		//cout << "\n";
-		
-		if((double)max/(double)totalSum * 100 < soft)
-			columnsToRemove[i] = true;
+	}
+	for(int i=0;i<alignmentLength;i++){
+		if(counts[i] == numSeqs)	{	filter[i] = '0';		}
 	}
 }
 
 /**************************************************************************************/
-void FilterSeqsCommand::doFilter() {
-	filter = globaldata->getFilter();
-	ifstream filehandle;
-	openInputFile(filter, filehandle);
+
+void FilterSeqsCommand::doSoft() {
+
+	int softThreshold = numSeqs * (float)atoi(globaldata->getSoft().c_str()) / 100.0;
+
+	vector<int> a(alignmentLength, 0);
+	vector<int> t(alignmentLength, 0);
+	vector<int> g(alignmentLength, 0);
+	vector<int> c(alignmentLength, 0);
+	vector<int> x(alignmentLength, 0);
 	
-	char c;
-	int count = 0;
-	while(!filehandle.eof()) {
-		c = filehandle.get();
-		if(c == '0') 
-			columnsToRemove[count] = true;
-		count++;
+	for(int i=0;i<numSeqs;i++){
+		string curAligned = db->get(i).getAligned();;
+
+		for(int j=0;j<alignmentLength;j++){
+			if(toupper(curAligned[j]) == 'A')										{	a[j]++;	}
+			else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[i]) == 'U')	{	t[j]++;	}
+			else if(toupper(curAligned[j]) == 'G')									{	g[j]++;	}
+			else if(toupper(curAligned[j]) == 'C')									{	c[j]++;	}
+		}
+	}
+
+	for(int i=0;i<alignmentLength;i++){
+		if(a[i] < softThreshold && t[i] < softThreshold && g[i] < softThreshold && c[i] < softThreshold){
+			filter[i] = '0';			
+		}
 	}
 }
 
 /**************************************************************************************/
+
 int FilterSeqsCommand::execute() {	
 	try {
-		globaldata = GlobalData::getInstance();
-		filename = globaldata->inputFileName;
-		
-		if(globaldata->getFastaFile() != "") {
-			readSeqs =  new ReadFasta(filename); }
-		else if(globaldata->getNexusFile() != "") {
-			readSeqs = new ReadNexus(filename); }
-		else if(globaldata->getClustalFile() != "") {
-			readSeqs = new ReadClustal(filename); }
-		else if(globaldata->getPhylipFile() != "") {
-			readSeqs = new ReadPhylip(filename); }
-			
-		readSeqs->read();
-		db = readSeqs->getDB();
-		
-		//for(int i = 0; i < db->size(); i++) {
-//			cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getAligned() << "\n\n";
-//		}
+						
+		if(globaldata->getHard().compare("") != 0)		{	doHard();		}	//	has to be applied first!
+		if(globaldata->getTrump().compare("") != 0)		{	doTrump();		}
+		if(globaldata->getVertical() == "T")			{	doVertical();	}
+		if(globaldata->getSoft().compare("") != 0)		{	doSoft();		}
 
-		for(int i = 0; i < db->get(0).getLength(); i++) 
-			columnsToRemove.push_back(false);
+		ofstream outfile;
+		string filterFile = getRootName(globaldata->inputFileName) + "filter";
+		openOutputFile(filterFile, outfile);
+
+		outfile << filter << endl;
+		outfile.close();
 		
-				
-		if(globaldata->getTrump().compare("") != 0) 
-			doTrump();
-		else if(globaldata->getSoft().compare("") != 0)
-			doSoft();
-		else if(globaldata->getFilter().compare("") != 0) 
-			doFilter();
+		string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta";
+		openOutputFile(filteredFasta, outfile);
+
+		for(int i=0;i<numSeqs;i++){
+			string curAligned = db->get(i).getAligned();
+			outfile << '>' << db->get(i).getName() << endl;
+			for(int j=0;j<alignmentLength;j++){
+				if(filter[j] == '1'){
+					outfile << curAligned[j];
+				}
+			}
+			outfile << endl;
+		}
+		outfile.close();
 		
-		//for(int i = 0; i < columnsToRemove.size(); i++)
-//		{
-//			cout << "Remove Column " << i << " = ";
-//			if(columnsToRemove[i])
-//				cout << "true\n";
-//			else
-//				cout << "false\n";
-//		}
-
-
-		//Creating the new SequenceDB 
-		SequenceDB newDB;
-		for(int i = 0; i < db->size(); i++) {
-			Sequence curSeq = db->get(i);
-			string curAligned = curSeq.getAligned();
-			string curName = curSeq.getName();
-			string newAligned = "";
-			for(int j = 0; j < curAligned.length(); j++) 
-				if(!columnsToRemove[j]) 
-					newAligned += curAligned.substr(j, 1);
-			
-			Sequence newSeq(curName, newAligned);
-			newDB.add(newSeq);
+		int filteredLength = 0;
+		for(int i=0;i<alignmentLength;i++){
+			if(filter[i] == '1'){	filteredLength++;	}
 		}
 		
-		string newFileName = getRootName(filename) + "filter.fa";
-		ofstream outfile;
-		outfile.open(newFileName.c_str());
-		newDB.print(outfile);
-		outfile.close();
-			
+		cout << endl;
+		cout << "Length of filtered alignment: " << filteredLength << endl;
+		cout << "Number of columns removed: " << alignmentLength-filteredLength << endl;
+		cout << "Length of the original alignment: " << alignmentLength << endl;
+		cout << "Number of sequences used to construct filter: " << numSeqs << endl;
+		
 		globaldata->clear();
-		//delete db;
-		//delete newDB;
 		
 		return 0;
+		
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -171,4 +173,6 @@ int FilterSeqsCommand::execute() {
 		cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		exit(1);
 	}
-}
\ No newline at end of file
+}
+
+/**************************************************************************************/
diff --git a/filterseqscommand.h b/filterseqscommand.h
index 06eaa6d..2279689 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -23,23 +23,25 @@ using namespace std;
 class FilterSeqsCommand : public Command {
 
 public:
-	FilterSeqsCommand() {};
+	FilterSeqsCommand();
 	~FilterSeqsCommand() {};
 	int execute();	
 	
 private:
 	void doTrump();
 	void doSoft();
-	void doFilter();
+	void doHard();
+	void doVertical();
 	
-	GlobalData* globaldata;
-	string filename, trump, filter;
+	int alignmentLength;
+	int numSeqs;
 	
+	GlobalData* globaldata;	
 	ReadSeqs* readSeqs;
-	
-	vector<bool> columnsToRemove;
 	SequenceDB* db;
-	double soft;
+	
+	string filter;
+
 };
 
 #endif
\ No newline at end of file
diff --git a/globaldata.cpp b/globaldata.cpp
index 7d30401..1be2c6e 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -80,10 +80,10 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "sorted")		{ sorted = value;		}
 				if (key == "vertical")		{ vertical = value;		}
 				if (key == "trump")		    { trump = value;		}
-				if (key == "filter")		{ filter = value;		}
+				if (key == "hard")			{ hard = value;		}
 				if (key == "soft")		    { soft = value;		    }
 				if (key == "scale")			{ scale = value;		}
-				if (key == "ends" )			{ ends = value;			}
+				if (key == "countends" )	{ countends = value;	}
 				if (key == "processors" )	{ processors = value;	}
 				if (key == "size" )         { size = value;         }
 				if (key == "candidate")		{ candidatefile = value;	}
@@ -151,10 +151,10 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "sorted")		{ sorted = value;		}
 			if (key == "vertical")		{ vertical = value;		}
 			if (key == "trump")		    { trump = value;		}
-			if (key == "filter")		{ filter = value;		}
+			if (key == "hard")			{ hard = value;		}
 			if (key == "soft")		    { soft = value;		    }
 			if (key == "scale")			{ scale = value;		}
-			if (key == "ends" )			{ ends = value;			}
+			if (key == "countends" )	{ countends = value;	}
 			if (key == "processors" )	{ processors = value;	}
 			if (key == "size" )         { size = value;         }
 			if (key == "candidate")		{ candidatefile = value;	}
@@ -229,7 +229,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "dist.seqs") {
-			if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
+			if ((calc == "default") || (calc == "")) {  calc = "onegap";	}
+			if (countends == "")	{ countends = "T"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -242,12 +243,17 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			splitAtDash(calc, Estimators); 
 		}
 		if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
-			if (calc != "") { 
-				Estimators.clear();
-				splitAtDash(calc, Estimators);			
-			}else { cout << "You have not specified any calculators." << endl; }
+			if ((calc == "default") || (calc == "")) { 
+				calc = "jclass-thetayc";
+			}
+			Estimators.clear();
+			splitAtDash(calc, Estimators); 
+		}
+		if(commandName == "filter.seqs"){
+			if(trump == "" && vertical == "" && hard == "" && soft == ""){
+				trump = '.';
+			}
 		}
-
 
 		//if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
 		if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
@@ -296,11 +302,12 @@ string GlobalData::getGroups()			{	return groups;		}
 string GlobalData::getStep()			{	return step;		}
 string GlobalData::getForm()			{	return form;		}
 string GlobalData::getSorted()			{	return sorted;		}
+string GlobalData::getVertical()		{   return vertical;    }
 string GlobalData::getTrump()			{   return trump;       }
 string GlobalData::getSoft()			{   return soft;		}
-string GlobalData::getFilter()			{   return filter;		}
+string GlobalData::getHard()			{   return hard;		}
 string GlobalData::getScale()			{	return scale;		}
-string GlobalData::getEnds()			{   return ends;		}
+string GlobalData::getCountEnds()		{   return countends;	}
 string GlobalData::getProcessors()		{	return processors;	}
 string GlobalData::getSize()            {   return size;        }
 string GlobalData::getCandidateFile()	{	return candidatefile;}
@@ -313,19 +320,19 @@ string GlobalData::getGapopen()			{	return gapopen;		}
 string GlobalData::getGapextend()		{	return gapextend;	}
 
 
-void GlobalData::setListFile(string file)	{	listfile = file;	inputFileName = file;}
-void GlobalData::setRabundFile(string file)	{	rabundfile = file;	inputFileName = file;}
-void GlobalData::setSabundFile(string file)	{	sabundfile = file;	inputFileName = file;}
-void GlobalData::setPhylipFile(string file)	{	phylipfile = file;    inputFileName = file;}
-void GlobalData::setColumnFile(string file)	{	columnfile = file;    inputFileName = file;}
-void GlobalData::setGroupFile(string file)		{	groupfile = file;	}
-void GlobalData::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file; fileroot = file;}
+void GlobalData::setListFile(string file)		{	listfile = file;	inputFileName = file;					}
+void GlobalData::setRabundFile(string file)		{	rabundfile = file;	inputFileName = file;					}
+void GlobalData::setSabundFile(string file)		{	sabundfile = file;	inputFileName = file;					}
+void GlobalData::setPhylipFile(string file)		{	phylipfile = file;    inputFileName = file;					}
+void GlobalData::setColumnFile(string file)		{	columnfile = file;    inputFileName = file;					}
+void GlobalData::setGroupFile(string file)		{	groupfile = file;											}
+void GlobalData::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file; fileroot = file;	}
 void GlobalData::setNameFile(string file)		{	namefile = file;		}
 void GlobalData::setFormat(string Format)		{	format = Format;		}
 void GlobalData::setRandomTree(string Random)	{	randomtree = Random;	}
 void GlobalData::setGroups(string g)			{	groups = g;				}
 void GlobalData::setCalc(string Calc)			{	calc = Calc;			}
-void GlobalData::setEnds(string e)				{   ends = e;				}
+void GlobalData::setCountEnds(string e)			{   countends = e;			}
 void GlobalData::setProcessors(string p)		{	processors = p;			}
 
 
@@ -375,13 +382,13 @@ void GlobalData::clear() {
 	form			=	"integral";
 	sorted			=	"T";  //F means don't sort, T means sort.
 	vertical        =   "";		
-	trump           =   ".";		
-	filter          =   "";		
+	trump           =	"";		
+	hard			=   "";		
 	soft            =   "";	
 	scale			=	"log10";
-	ends			=   "T";  //yes
+	countends		=   "T";  //yes
 	processors		=	"1";
-	size            =   "1000";
+	size            =   "0";
 	search			=	"kmer";
 	ksize			=	"7";
 	align			=	"needleman";
@@ -408,9 +415,9 @@ void GlobalData::reset() {
 	abund			=   "10";
 	step			=	"0.01";
 	form			=	"integral";
-	ends			=   "T";
+	countends		=   "T";
 	processors		=	"1";
-	size            =   "1000";
+	size            =   "0";
 	search			=	"kmer";
 	ksize			=	"7";
 	align			=	"needleman";
@@ -419,8 +426,8 @@ void GlobalData::reset() {
 	gapopen			=	"-1.0";
 	gapextend		=	"-2.0";
 	vertical        =   "";		
-	trump           =   ".";		
-	filter          =   "";		
+	trump           =   "";		
+	hard			=   "";		
 	soft            =   "";	
 
 }
diff --git a/globaldata.hpp b/globaldata.hpp
index b3b0798..6d1b3f3 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -75,7 +75,7 @@ public:
 	string getStep();
 	string getForm();
 	string getSorted();
-	string getEnds();
+	string getCountEnds();
 	string getProcessors();
 	string getSize();
 	string getCandidateFile();
@@ -86,9 +86,10 @@ public:
 	string getMismatch();
 	string getGapopen();
 	string getGapextend();
+	string getVertical();
 	string getTrump();
 	string getSoft();
-	string getFilter();
+	string getHard();
 	string getScale();
 
 
@@ -104,7 +105,7 @@ public:
 	void setRandomTree(string);
 	void setGroups(string);
 	void setCalc(string);
-	void setEnds(string);
+	void setCountEnds(string);
 	void setProcessors(string);
 
 	void clear(); 
@@ -122,7 +123,7 @@ public:
 private:
 
 	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
-	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors, candidatefile, search, ksize, align, match, size;
+	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, hard, scale, countends, processors, candidatefile, search, ksize, align, match, size;
 	string mismatch, gapopen, gapextend;
 
 
diff --git a/heatmap.cpp b/heatmap.cpp
index 90b1115..4bb9385 100644
--- a/heatmap.cpp
+++ b/heatmap.cpp
@@ -105,7 +105,6 @@ void HeatMap::getPic(RAbundVector* rabund) {
 
 void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
 	try {
-		
 		//sort lookup so shared bins are on top
 		if (sorted == "T") {  sortSharedVectors(lookup);  }
 		
@@ -141,10 +140,10 @@ void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
 						scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i]))))  + "0000"; 
 					} 
 				}else { scaleRelAbund[i][j] = "FFFFFF";  }
-				
+
 			}
 		}
-		
+
 		string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.svg";
 		openOutputFile(filenamesvg, outsvg);
 		
@@ -180,7 +179,7 @@ void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
 		
 		outsvg << "</g>\n</svg>\n";
 		outsvg.close();
-		
+
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -217,11 +216,11 @@ void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
 			looktemp.push_back(temp);
 		}
 		
-		//clear out lookup to create sorted lookup
+		//clear out lookup to create sorted lookup -- Sarah look at - this is causing segmentation faults
 		for (int j = 0; j < lookup.size(); j++) {
-			delete lookup[j];
+//			delete lookup[j];
 		}
-		lookup.clear();
+		lookup.clear();  //doesn't this do the job?
 		
 		//create and initialize lookup to empty vectors
 		for (int i = 0; i < looktemp.size(); i++) { 
@@ -260,9 +259,9 @@ void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
 			}
 		}
 		
-		//delete looktemp
+		//delete looktemp -- Sarah look at - this is causing segmentation faults
 		for (int j = 0; j < looktemp.size(); j++) {
-			delete looktemp[j];
+//			delete looktemp[j];
 		}
 		
 	}
diff --git a/helpcommand.cpp b/helpcommand.cpp
index b890c99..b480dcb 100644
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -72,15 +72,15 @@ int HelpCommand::execute(){
 		cout << "deconvolute(fasta=yourFastaFile) " << "\n";
 	}else if (globaldata->helpRequest == "dist.seqs") {
 		cout << "The dist.seqs command reads a file containing sequences and creates a distance file." << "\n";
-		cout << "The dist.seqs command parameters are fasta, phylip, clustal, nexus, calc, ends, cutoff and processors.  " << "\n";
+		cout << "The dist.seqs command parameters are fasta, phylip, clustal, nexus, calc, countends, cutoff and processors.  " << "\n";
 		cout << "You must use one of the following parameters for your filename: fasta, phylip, clustal or nexus. " << "\n";
 		cout << "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";
-		cout << "The ends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T." << "\n";
+		cout << "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";
 		cout << "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0." << "\n";
 		cout << "The processors parameter allows you to specify number of processors to use.  The default is 1, but you can use up to 4 processors." << "\n";
 		cout << "The dist.seqs command should be in the following format: " << "\n";
-		cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, ends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
-		cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, ends=F, cutoff= 2.0, processors=3)." << "\n";
+		cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
+		cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3)." << "\n";
 		cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n";
 	}else if (globaldata->helpRequest == "align.seqs") {
 		cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n";
@@ -273,9 +273,9 @@ int HelpCommand::execute(){
 		cout << "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
 		cout << "Example dist.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
 		cout << "The default value for groups is all the groups in your groupfile." << "\n";
-		cout << "There is no default value for calc." << "\n";
+		cout << "The default value for calc is jclass and thetayc." << "\n";
 		validCalcs->printCalc("matrix", cout);
-		cout << "The dist.shared command outputs a .matrix file for each calculator you specify at each distance you choose." << "\n";
+		cout << "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose." << "\n";
 		cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
 	}else if (globaldata->helpRequest == "bootstrap.shared") { 
 		cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
diff --git a/ignoregaps.h b/ignoregaps.h
index 8127b62..e81ab92 100644
--- a/ignoregaps.h
+++ b/ignoregaps.h
@@ -24,37 +24,30 @@ public:
 		int diff = 0;
 		int length = 0;
 		int start = 0;
-		int end = 0;
 		
-		for(int i=0;i<A.getLength();i++){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-			}
-			else{
+		string seqA = A.getAligned();
+		string seqB = B.getAligned();
+		int alignLength = seqA.length();
+		
+		for(int i=0;i<alignLength;i++){
+			if(seqA[i] != '.' && seqB[i] != '.'){
 				start = i;
 				break;
 			}
 		}
-		for(int i=A.getLength()-1;i>=0;i--){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-			}
-			else{
-				end = i;
-				break;
-			}
-		}
 		
-		for(int i=start; i<=end; i++){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.'){
+		for(int i=start; i<alignLength; i++){
+			if(seqA[i] == '.' || seqB[i] == '.'){
 				break;
 			}
-			else if((A.getAligned()[i] != '-' && B.getAligned()[i] != '-')){
-				if(A.getAligned()[i] != B.getAligned()[i]){
+			else if((seqA[i] != '-' && seqB[i] != '-')){
+				if(seqA[i] != seqB[i]){
 					diff++;
 				}
 				length++;
 			}
 		}
-		
+
 		if(length == 0)		{	dist = 1.0000;								}
 		else				{	dist = ((double)diff  / (double)length);	}
 		
diff --git a/jackknife.h b/jackknife.h
index 70f1dca..ce9497b 100644
--- a/jackknife.h
+++ b/jackknife.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class Jackknife : public Calculator  {
 	
 public:
-	Jackknife() : Calculator("Jackknife", 3, false) {	getAMatrix(); };
+	Jackknife() : Calculator("jackknife", 3, false) {	getAMatrix(); };
 	EstOutput getValues(SAbundVector*);
 	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
 
diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index a5e7a4e..c792cc9 100644
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -131,7 +131,7 @@ int MatrixOutputCommand::execute(){
 						}
 					}
 					
-					exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".matrix";
+					exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".dist";
 					openOutputFile(exportFileName, out);
 					printSims(out);
 					out.close();
@@ -166,14 +166,11 @@ void MatrixOutputCommand::printSims(ostream& out) {
 	try {
 		
 		//output column headers
-		out << '\t';
-		for (int i = 0; i < lookup.size(); i++) {	out << lookup[i]->getGroup() << '\t';		}
-		out << endl;
-		
+		out << simMatrix.size() << endl;
 		
 		for (int m = 0; m < simMatrix.size(); m++)	{
 			out << lookup[m]->getGroup() << '\t';
-			for (int n = 0; n < simMatrix.size(); n++)	{
+			for (int n = 0; n < m; n++)	{
 				out << simMatrix[m][n] << '\t'; 
 			}
 			out << endl;
diff --git a/npshannon.h b/npshannon.h
index dc137ed..2e9578b 100644
--- a/npshannon.h
+++ b/npshannon.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class NPShannon : public Calculator  {
 	
 public:
-	NPShannon() : Calculator("NPShannon", 1, false) {};
+	NPShannon() : Calculator("npshannon", 1, false) {};
 	EstOutput getValues(SAbundVector*);
 	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
 private:
diff --git a/nseqs.h b/nseqs.h
index 1382add..42a1f57 100644
--- a/nseqs.h
+++ b/nseqs.h
@@ -19,7 +19,7 @@
 class NSeqs : public Calculator {
 
 public:
-	NSeqs() : Calculator("NSeqs", 1, false) {};
+	NSeqs() : Calculator("nseqs", 1, false) {};
 	EstOutput getValues(SAbundVector* rank){
 		data.resize(1,0);
 		data[0] = (double)rank->getNumSeqs();
diff --git a/onegapdist.h b/onegapdist.h
index b6b257c..c466c53 100644
--- a/onegapdist.h
+++ b/onegapdist.h
@@ -20,22 +20,25 @@ public:
 	void calcDist(Sequence A, Sequence B){
 		
 		int difference = 0;
+		int minLength = 0;
 		int openGapA = 0;
 		int openGapB = 0;
-		int minLength = 0;
 		int start = 0;
 		
-		for(int i=0;i<A.getLength();i++){
-			if(A.getAligned()[i] == '.' && B.getAligned()[i] == '.'){
-			}
-			else{
+		string seqA = A.getAligned();
+		string seqB = B.getAligned();
+		int alignLength = seqA.length();
+		
+		for(int i=0;i<alignLength;i++){
+			if((seqA[i] != '.' || seqB[i] != '.')){
 				start = i;
 				break;
 			}
 		}
-		for(int i=start;i<A.getLength();i++){
-			if((A.getAligned()[i] == '-' || B.getAligned()[i] == '-') && (A.getAligned()[i] == '.' || B.getAligned()[i] == '.')){}
-			else if(A.getAligned()[i] == '-' && B.getAligned()[i] != '-' && B.getAligned()[i] != '.'){
+
+		for(int i=start;i<alignLength;i++){
+			if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '.' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.')){	;	}
+			else if(seqB[i] != '-' && (seqA[i] == '-' || seqA[i] == '.')){
 				if(openGapA == 0){
 					difference++;
 					minLength++;
@@ -43,7 +46,7 @@ public:
 					openGapB = 0;
 				}
 			}
-			else if(A.getAligned()[i] != '-' && B.getAligned()[i] == '-' && A.getAligned()[i] != '.'){
+			else if(seqA[i] != '-' && (seqB[i] == '-' || seqB[i] == '.')){
 				if(openGapB == 0){
 					difference++;
 					minLength++;
@@ -51,8 +54,8 @@ public:
 					openGapB = 1;
 				}
 			}
-			else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
-				if(A.getAligned()[i] != B.getAligned()[i]){
+			else if(seqA[i] != '-' && seqB[i] != '-'){
+				if(seqA[i] != seqB[i]){
 					difference++;
 					minLength++;
 					openGapA = 0;
@@ -64,10 +67,12 @@ public:
 					openGapB = 0;
 				}
 			}
-			else if(A.getAligned()[i] == '.' && B.getAligned()[i] == '.'){
+
+			else if(seqA[i] == '.' && seqB[i] == '.'){
 				break;
 			}
 		}
+	
 		if(minLength == 0)	{	dist = 1.0000;							}
 		else				{	dist = (double)difference / minLength;	}
 	}
@@ -76,4 +81,4 @@ public:
 
 /**************************************************************************************************/
 
-#endif
\ No newline at end of file
+#endif
diff --git a/onegapignore.h b/onegapignore.h
index ee6cc52..6421741 100644
--- a/onegapignore.h
+++ b/onegapignore.h
@@ -25,27 +25,27 @@ public:
 		int start = 0;
 		int end = 0;
 		
-		for(int i=0;i<A.getLength();i++){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-			}
-			else{
+		string seqA = A.getAligned();
+		string seqB = B.getAligned();
+		int alignLength = seqA.length();
+		
+		// this assumes that sequences start and end with '.'s instead of'-'s.
+		for(int i=0;i<alignLength;i++){
+			if(seqA[i] != '.' && seqB[i] != '.'){
 				start = i;
 				break;
 			}
 		}
-		for(int i=A.getLength()-1;i>=0;i--){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-			}
-			else{
+		for(int i=alignLength-1;i>=0;i--){
+			if(seqA[i] != '.' && seqB[i] != '.'){
 				end = i;
 				break;
 			}
 		}
 		
-		
 		for(int i=start;i<=end;i++){
-			if(A.getAligned()[i] == '-' && B.getAligned()[i] == '-'){}
-			else if(A.getAligned()[i] == '-' && B.getAligned()[i] != '-'){
+			if(seqA[i] == '-' && seqB[i] == '-'){	;	}
+			else if(seqB[i] != '-' && seqA[i] == '-'){
 				if(openGapA == 0){
 					difference++;
 					minLength++;
@@ -53,7 +53,7 @@ public:
 					openGapB = 0;
 				}
 			}
-			else if(A.getAligned()[i] != '-' && B.getAligned()[i] == '-'){
+			else if(seqA[i] != '-' && seqB[i] == '-'){
 				if(openGapB == 0){
 					difference++;
 					minLength++;
@@ -61,20 +61,16 @@ public:
 					openGapB = 1;
 				}
 			}
-			else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
-				if(A.getAligned()[i] != B.getAligned()[i]){
+			else if(seqA[i] != '-' && seqB[i] != '-'){
+				if(seqA[i] != seqB[i]){
 					difference++;
-					minLength++;
-					openGapA = 0;
-					openGapB = 0;
-				}
-				else{
-					minLength++;
-					openGapA = 0;
-					openGapB = 0;
 				}
+				minLength++;
+				openGapA = 0;
+				openGapB = 0;
 			}
 		}
+
 		if(minLength == 0)	{	dist = 1.0000;							}
 		else				{	dist = (double)difference / minLength;	}
 	}
diff --git a/rarecalc.h b/rarecalc.h
index 99964ec..a7ad2b7 100644
--- a/rarecalc.h
+++ b/rarecalc.h
@@ -19,7 +19,7 @@ class RareCalc {
 public:
 	RareCalc(RAbundVector* b) : bins(b), numSeqs(b->getNumSeqs()), maxRank(b->getMaxRank()), numBins(b->getNumBins()) {	bMatrix = binomial(numSeqs+1);	};
 	EstOutput getValues(int);
-	string getName()	{	return "RareCalc";	}
+	string getName()	{	return "rarecalc";	}
 private:
 	RAbundVector* bins;
 	vector<vector<double> > bMatrix;
diff --git a/sequence.cpp b/sequence.cpp
index f136426..2f167c5 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -64,7 +64,7 @@ string Sequence::convert2ints() {
 	string processed;
 	
 	for(int i=0;i<unaligned.length();i++) {
-		if(toupper(unaligned[i]) == 'A')			{	processed += '0';	}
+		if(toupper(unaligned[i]) == 'A')		{	processed += '0';	}
 		else if(toupper(unaligned[i]) == 'C')	{	processed += '1';	}
 		else if(toupper(unaligned[i]) == 'G')	{	processed += '2';	}
 		else if(toupper(unaligned[i]) == 'T')	{	processed += '3';	}
@@ -101,6 +101,27 @@ void Sequence::setUnaligned(string sequence){
 //********************************************************************************************************************
 
 void Sequence::setAligned(string sequence){
+	
+	//if the alignment starts or ends with a gap, replace it with a period to indicate missing data
+	
+	if(sequence[0] == '-'){
+		for(int i=0;i<sequence.length();i++){
+			if(sequence[i] == '-'){
+				sequence[i] = '.';
+			}
+			else{
+				break;
+			}
+		}
+		for(int i=sequence.length()-1;i>=0;i--){
+			if(sequence[i] == '-'){
+				sequence[i] = '.';
+			}
+			else{
+				break;
+			}
+		}
+	}
 	aligned = sequence;
 }
 
diff --git a/shannon.h b/shannon.h
index 1930239..7fbcafc 100644
--- a/shannon.h
+++ b/shannon.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class Shannon : public Calculator  {
 	
 public:
-	Shannon() : Calculator("Shannon", 3, false) {};
+	Shannon() : Calculator("shannon", 3, false) {};
 	EstOutput getValues(SAbundVector* rank);
 	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
 private:
diff --git a/sharedanderberg.h b/sharedanderberg.h
index 44a1e6d..4de5ca2 100644
--- a/sharedanderberg.h
+++ b/sharedanderberg.h
@@ -16,7 +16,7 @@
 class SharedAnderberg : public Calculator  {
 	
 public:
-	SharedAnderberg() :  Calculator("SharedAnderberg", 1) {};
+	SharedAnderberg() :  Calculator("anderberg", 1) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
 private:
diff --git a/sharedanderbergs.h b/sharedanderbergs.h
index f17e5fa..2460cfe 100644
--- a/sharedanderbergs.h
+++ b/sharedanderbergs.h
@@ -16,7 +16,7 @@
 class Anderberg : public Calculator  {
 	
 	public:
-		Anderberg() :  Calculator("Anderberg", 1, false) {};
+		Anderberg() :  Calculator("anderberg", 1, false) {};
 		EstOutput getValues(SAbundVector*) {return data;};
 		EstOutput getValues(vector<SharedRAbundVector*>);
 	private:
diff --git a/sharedbraycurtis.h b/sharedbraycurtis.h
index 446b3eb..7a8ef11 100644
--- a/sharedbraycurtis.h
+++ b/sharedbraycurtis.h
@@ -15,7 +15,7 @@
 class BrayCurtis : public Calculator  {
 	
 public:
-	BrayCurtis() :  Calculator("BrayCurtis", 1, false) {};
+	BrayCurtis() :  Calculator("braycurtis", 1, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedchao1.cpp b/sharedchao1.cpp
index c3388fd..7c617c5 100644
--- a/sharedchao1.cpp
+++ b/sharedchao1.cpp
@@ -42,7 +42,6 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
 			
 			//they are shared
 			if (sharedByAll == true) { 
-				 
 				// cout << "temp = ";
 				// for (int h = 0; h < temp.size(); h++) { cout << temp[h] << " "; } cout << endl;
 				//find f1 and f2values
@@ -53,29 +52,35 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
 			
 		//cout << "Entering " << endl;
 		//calculate chao1, (numleaves-1) because numleaves contains the ++ values.
-		for (int i = 0; i < numLeaves; i++) {
-			//divide by zero error
-			if (f2leaves[i]->lvalue == 0) { f2leaves[i]->lvalue++; }
-			if (f2leaves[i]->rvalue == 0) { f2leaves[i]->rvalue++; }
-			
-			//cout << "f2 leaves ";
-			//cout << f2leaves[i]->lvalue << f2leaves[i]->rvalue << endl;
-			
-		//	cout << "f2 leaf coef ";
-			//cout << f2leaves[i]->lcoef << '\t' << f2leaves[i]->rcoef << endl;
-			
-		//	cout << "f1 leaves ";
-		//	cout << f1leaves[i]->lvalue << f1leaves[i]->rvalue << endl;
-			
+		bool bias;
+		for(int i=0;i<numLeaves;i++){
+			if (f2leaves[i]->lvalue == 0) { bias = true;}// break;}
+		}
+
+		if(bias){
+			for (int i = 0; i < numLeaves; i++) {
+				
+				leftvalue = (float)(f1leaves[i]->lvalue * (f1leaves[i]->lvalue - 1)) / (float)((pow(2, (float)f2leaves[i]->lcoef)) * (f2leaves[i]->lvalue + 1));
+				if (i != (numLeaves-1)) {
+					rightvalue = (float)(f1leaves[i]->rvalue * (f1leaves[i]->rvalue - 1)) / (float)((pow(2, (float)f2leaves[i]->rcoef)) * (f2leaves[i]->rvalue + 1));
+				}else{
+					rightvalue = (float)(f1leaves[i]->rvalue);
+				}
+				Chao += leftvalue + rightvalue;
+			}
+		}
+		else{
 			
-			leftvalue = (float)(f1leaves[i]->lvalue * f1leaves[i]->lvalue) / (float)((pow(2, (float)f2leaves[i]->lcoef)) * f2leaves[i]->lvalue);
-			if (i != (numLeaves-1)) {
-				rightvalue = (float)(f1leaves[i]->rvalue * f1leaves[i]->rvalue) / (float)((pow(2, (float)f2leaves[i]->rcoef)) * f2leaves[i]->rvalue);
-			}else{
-				rightvalue = (float)(f1leaves[i]->rvalue);
+			for (int i = 0; i < numLeaves; i++) {
+				
+				leftvalue = (float)(f1leaves[i]->lvalue * f1leaves[i]->lvalue) / (float)((pow(2, (float)f2leaves[i]->lcoef)) * f2leaves[i]->lvalue);
+				if (i != (numLeaves-1)) {
+					rightvalue = (float)(f1leaves[i]->rvalue * f1leaves[i]->rvalue) / (float)((pow(2, (float)f2leaves[i]->rcoef)) * f2leaves[i]->rvalue);
+				}else{
+					rightvalue = (float)(f1leaves[i]->rvalue);
+				}
+				Chao += leftvalue + rightvalue;
 			}
-			//cout << "left = " << leftvalue << " right = " << rightvalue << endl;
-			Chao += leftvalue + rightvalue;
 		}
 		
 		for (int i = 0; i < numNodes; i++) {
diff --git a/sharedjabund.cpp b/sharedjabund.cpp
index b969e24..bedec32 100644
--- a/sharedjabund.cpp
+++ b/sharedjabund.cpp
@@ -21,7 +21,7 @@ EstOutput JAbund::getValues(vector<SharedRAbundVector*> shared) {
 		
 		//UVest[0] is Uest UVest[1] is Vest
 		data[0] = (UVest[0] * UVest[1]) / ((float)(UVest[0] + UVest[1] - (UVest[0] * UVest[1])));
-		
+		if(data[0] > 1){data[0] = 1;	}
 		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
 		
 		return data;
diff --git a/sharedjabund.h b/sharedjabund.h
index f01d616..a5fab2f 100644
--- a/sharedjabund.h
+++ b/sharedjabund.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class JAbund : public Calculator  {
 	
 public:
-	JAbund() :  Calculator("JAbund", 3, false) {};
+	JAbund() :  Calculator("jabund", 3, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedjclass.h b/sharedjclass.h
index 45302ef..d18dfee 100644
--- a/sharedjclass.h
+++ b/sharedjclass.h
@@ -19,7 +19,7 @@ It is a child of the calculator class. */
 class Jclass : public Calculator  {
 	
 public:
-	Jclass() :  Calculator("Jclass", 3, false) {};
+	Jclass() :  Calculator("jclass", 3, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedjest.h b/sharedjest.h
index 8a943c9..8eaf70f 100644
--- a/sharedjest.h
+++ b/sharedjest.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class Jest : public Calculator  {
 	
 public:
-	Jest() :  Calculator("Jest", 3, false) {};
+	Jest() :  Calculator("jest", 3, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedkulczynski.h b/sharedkulczynski.h
index aad69fe..58594c6 100644
--- a/sharedkulczynski.h
+++ b/sharedkulczynski.h
@@ -17,7 +17,7 @@
 class Kulczynski : public Calculator  {
 	
 public:
-	Kulczynski() :  Calculator("Kulczynski", 1, false) {};
+	Kulczynski() :  Calculator("kulczynski", 1, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedkulczynskicody.h b/sharedkulczynskicody.h
index b91dee9..c09be3a 100644
--- a/sharedkulczynskicody.h
+++ b/sharedkulczynskicody.h
@@ -18,7 +18,7 @@
 class KulczynskiCody : public Calculator  {
 	
 public:
-	KulczynskiCody() :  Calculator("KulczynskiCody", 1, false) {};
+	KulczynskiCody() :  Calculator("kulczynskicody", 1, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedlennon.h b/sharedlennon.h
index 0aba6a9..cd2ebf6 100644
--- a/sharedlennon.h
+++ b/sharedlennon.h
@@ -18,7 +18,7 @@
 class Lennon : public Calculator  {
 	
 public:
-	Lennon() :  Calculator("Lennon", 1, false) {};
+	Lennon() :  Calculator("lennon", 1, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedmorisitahorn.h b/sharedmorisitahorn.h
index e771139..a7980d0 100644
--- a/sharedmorisitahorn.h
+++ b/sharedmorisitahorn.h
@@ -17,7 +17,7 @@
 class MorHorn : public Calculator  {
 	
 public:
-	MorHorn() :  Calculator("MorisitaHorn", 1, false) {};
+	MorHorn() :  Calculator("morisitahorn", 1, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharednseqs.h b/sharednseqs.h
index 1809d97..aa989bc 100644
--- a/sharednseqs.h
+++ b/sharednseqs.h
@@ -16,7 +16,7 @@
 class SharedNSeqs : public Calculator {
 
 public:
-	SharedNSeqs() : Calculator("SharedNSeqs", 1, false) {};
+	SharedNSeqs() : Calculator("sharednseqs", 1, false) {};
 	EstOutput getValues(SAbundVector* rank){ return data; };
 	EstOutput getValues(vector<SharedRAbundVector*> shared) {
 		data.resize(1,0);
diff --git a/sharedochiai.h b/sharedochiai.h
index 61d9df3..99003e6 100644
--- a/sharedochiai.h
+++ b/sharedochiai.h
@@ -16,7 +16,7 @@
 class Ochiai : public Calculator  {
 	
 public:
-	Ochiai() :  Calculator("Ochiai", 1, false) {};
+	Ochiai() :  Calculator("ochiai", 1, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedsorabund.h b/sharedsorabund.h
index 032dbda..0dbf4a4 100644
--- a/sharedsorabund.h
+++ b/sharedsorabund.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class SorAbund : public Calculator  {
 	
 public:
-	SorAbund() :  Calculator("SorAbund", 3, false) {};
+	SorAbund() :  Calculator("sorabund", 3, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedsorclass.h b/sharedsorclass.h
index 16fbed0..75df657 100644
--- a/sharedsorclass.h
+++ b/sharedsorclass.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class SorClass : public Calculator  {
 	
 public:
-	SorClass() :  Calculator("SorClass", 3, false) {};
+	SorClass() :  Calculator("sorclass", 3, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedsorest.h b/sharedsorest.h
index a38cbae..8e044aa 100644
--- a/sharedsorest.h
+++ b/sharedsorest.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class SorEst : public Calculator  {
 	
 public:
-	SorEst() :  Calculator("SorEst", 3, false) {};
+	SorEst() :  Calculator("sorest", 3, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedthetan.h b/sharedthetan.h
index 48e816d..4637b97 100644
--- a/sharedthetan.h
+++ b/sharedthetan.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class ThetaN : public Calculator  {
 	
 public:
-	ThetaN() :  Calculator("ThetaN", 3, false) {};
+	ThetaN() :  Calculator("thetan", 3, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/sharedthetayc.h b/sharedthetayc.h
index 0d9f4a0..536306c 100644
--- a/sharedthetayc.h
+++ b/sharedthetayc.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class ThetaYC : public Calculator  {
 	
 public:
-	ThetaYC() :  Calculator("ThetaYC", 3, false) {};
+	ThetaYC() :  Calculator("thetayc", 3, false) {};
 	EstOutput getValues(SAbundVector*) {return data;};
 	EstOutput getValues(vector<SharedRAbundVector*>);
 private:
diff --git a/shen.cpp b/shen.cpp
index 61291a6..a2f6188 100644
--- a/shen.cpp
+++ b/shen.cpp
@@ -28,7 +28,7 @@ EstOutput Shen::getValues(SAbundVector* rank){
 		Ace* calc = new Ace(abund);
 		EstOutput ace = calc->getValues(rank);
 		
-		double f0 = n - ace[0];
+		double f0 = ace[0]-rank->getNumBins();
 		
 		data[0] = f0 * (1 - pow(1 - f1/n/f0, m));
 
diff --git a/simpson.h b/simpson.h
index 3006e86..0214217 100644
--- a/simpson.h
+++ b/simpson.h
@@ -20,7 +20,7 @@ It is a child of the calculator class. */
 class Simpson : public Calculator  {
 
 public:
-	Simpson() : Calculator("Simpson", 3, false) {};
+	Simpson() : Calculator("simpson", 3, false) {};
 	EstOutput getValues(SAbundVector*);
 	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
 };
diff --git a/validcommands.cpp b/validcommands.cpp
index 230d800..6f2790d 100644
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -22,7 +22,7 @@ ValidCommands::ValidCommands() {
 		commands["cluster"]				= "cluster"; 
 		commands["deconvolute"]			= "deconvolute"; 
 		commands["dist.seqs"]			= "dist.seqs";
-		commands["dist.shared"]			= "dist.shared";  //matrix output
+		commands["dist.shared"]			= "dist.shared";
 		commands["collect.single"]		= "collect.single"; 
 		commands["collect.shared"]		= "collect.shared"; 
 		commands["rarefaction.single"]	= "rarefaction.single"; 
diff --git a/validparameter.cpp b/validparameter.cpp
index ddec9d1..650ef1f 100644
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -267,7 +267,7 @@ void ValidParameters::initCommandParameters() {
 		string heatmapArray[] =  {"groups","line","label","sorted","scale"};
 		commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
 		
-		string filterseqsArray[] =  {"fasta","phylip","clustal","nexus", "trump", "soft", "filter"};
+		string filterseqsArray[] =  {"fasta","phylip","clustal","nexus", "trump", "soft", "hard", "vertical"};
 		commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
 
 		string vennArray[] =  {"groups","line","label","calc"};
@@ -291,7 +291,7 @@ void ValidParameters::initCommandParameters() {
 		string concensusArray[] =  {};
 		commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
 		
-		string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
+		string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "countends", "cutoff", "processors"};
 		commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
 		
 		string AlignArray[] =  {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};