X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sensspeccommand.cpp;h=12786ca41c848d967ffda72e2d06f382881d8eed;hp=213a2ca99da988257a46ba8e91cb5e4123b5bb0e;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 213a2ca..12786ca 100644
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -12,16 +12,15 @@
 //**********************************************************************************************************************
 vector<string> SensSpecCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-		CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
-		//CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
-		CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pcolumn);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
-		CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-		CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","sensspec",false,true,true); parameters.push_back(plist);
+		CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pphylip);
+		CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pcolumn);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "","",false,false); parameters.push_back(pcutoff);
+		CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+		CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+		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);		}
@@ -45,6 +44,21 @@ string SensSpecCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string SensSpecCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "sensspec") {  pattern = "[filename],sensspec"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "SensSpecCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 SensSpecCommand::SensSpecCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -62,7 +76,8 @@ SensSpecCommand::SensSpecCommand(){
 SensSpecCommand::SensSpecCommand(string option)  {
 	try {
 		
-		abort = false; calledHelp = false;   
+		abort = false; calledHelp = false;  
+		allLines = 1;
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
@@ -115,16 +130,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
 					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["column"] = inputDir + it->second;		}
-				}
-				
-				//it = parameters.find("name");
-				//user has given a template file
-				//if(it != parameters.end()){ 
-					//path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					//if (path == "") {	parameters["name"] = inputDir + it->second;		}
-				//}
-				
+				}				
 			}
 			//check for required parameters
 			listFile = validParameter.validFile(parameters, "list", true);
@@ -134,16 +140,17 @@ SensSpecCommand::SensSpecCommand(string option)  {
 				else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (listFile == "not open") { abort = true; }	
+			else { m->setListFile(listFile); }
 			
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not found") { phylipfile = "";  }
 			else if (phylipfile == "not open") { abort = true; }	
-			else { distFile = phylipfile; format = "phylip";   }
+			else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile);  }
 			
 			columnfile = validParameter.validFile(parameters, "column", true);
 			if (columnfile == "not found") { columnfile = ""; }
 			else if (columnfile == "not open") { abort = true; }	
-			else { distFile = columnfile; format = "column";   }
+			else { distFile = columnfile; format = "column";   m->setColumnFile(columnfile); }
 			
 			if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
 				//give priority to column, then phylip
@@ -174,23 +181,24 @@ SensSpecCommand::SensSpecCommand(string option)  {
 			else if(!m->isTrue(temp))	{	hard = 0;	}
 			else if(m->isTrue(temp))	{	hard = 1;	}
 			
-//			temp = validParameter.validFile(parameters, "name", true);
-//			if (temp == "not found")	{	nameFile = "";		}
-//			else if(temp == "not open")	{	abort = true;		}
-//			else						{	nameFile = temp;	}
-//			cout << "name:\t" << nameFile << endl;
-
 			temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found") { temp = "-1.00"; }
-			convert(temp, cutoff);  
+			m->mothurConvert(temp, cutoff);  
 //			cout << cutoff << endl;
 			
 			temp = validParameter.validFile(parameters, "precision", false);	if (temp == "not found") { temp = "100"; }
-			convert(temp, precision);  
+			m->mothurConvert(temp, precision);  
 //			cout << precision << endl;
 			
-			lineLabel = validParameter.validFile(parameters, "label", false);	if (lineLabel == "not found") { lineLabel = ""; }
+			string label = validParameter.validFile(parameters, "label", false);			
+			if (label == "not found") { label = ""; }
+			else { 
+				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
+				else { allLines = 1;  }
+			}
 			
-			sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + ".sensspec";
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+			sensSpecFileName = getOutputFileName("sensspec",variables);
 		}
 	}
 	catch(exception& e) {
@@ -203,14 +211,27 @@ SensSpecCommand::SensSpecCommand(string option)  {
 int SensSpecCommand::execute(){
 	try{
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
-
+        
+        int startTime = time(NULL);
+        
+        //create list file with only unique names, saves time and memory by removing redundant names from list file that are not in the distance file.
+        string newListFile = preProcessList();
+        if (newListFile != "") { listFile = newListFile; }
+        
 		setUpOutput();
 		outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
 		if(format == "phylip")		{	processPhylip();	}
 		else if(format == "column")	{	processColumn();	}
 		
+        //remove temp file if created
+        if (newListFile != "") { m->mothurRemove(newListFile); }
+        
+		if (m->control_pressed) { m->mothurRemove(sensSpecFileName); return 0; }
+        
+        m->mothurOut("It took " + toString(time(NULL) - startTime) + " to run sens.spec."); m->mothurOutEndLine();
+        
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(sensSpecFileName); m->mothurOutEndLine();	
 		m->mothurOutEndLine();
 		
@@ -222,219 +243,421 @@ int SensSpecCommand::execute(){
 		exit(1);
 	}
 }
+//***************************************************************************************************************
+bool SensSpecCommand::testFile(){
+	try{
+        ifstream fileHandle;
+        m->openInputFile(phylipfile, fileHandle);
+        
+        bool square = false;
+        string numTest, name;
+        fileHandle >> numTest >> name;
+
+        if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+
+        char d;
+        while((d=fileHandle.get()) != EOF){
+            if(isalnum(d)){
+                square = true;
+                break;
+            }
+            if(d == '\n'){
+                square = false;
+                break;
+            }
+        }
+        fileHandle.close();
+        
+        return square;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "testFile");
+		exit(1);
+	}
+}
 
 //***************************************************************************************************************
 
-void SensSpecCommand::processPhylip(){
+int SensSpecCommand::processPhylip(){
 	try{
 		//probably need some checking to confirm that the names in the distance matrix are the same as those in the list file
-		
-		ifstream inputListFile;
-		m->openInputFile(listFile, inputListFile);
-		
-		string origCutoff = "";
+        square = testFile();
+ 		string origCutoff = "";
 		bool getCutoff = 0;
 		if(cutoff == -1.00)	{	getCutoff = 1;															}
 		else				{	origCutoff = toString(cutoff);	cutoff += (0.49 / double(precision));	}
 		
-		string label;
-		int numOTUs;
-
 		map<string, int> seqMap;
 		string seqList;
 		
-		while(inputListFile){
-			inputListFile >> label >> numOTUs;
-			for(int i=0;i<numOTUs;i++){
-				inputListFile >> seqList;
-				int seqListLength = seqList.length();
-				string seqName = "";
-				for(int j=0;j<seqListLength;j++){
-					
-					if(seqList[j] == ','){
-						seqMap[seqName] = i;
-						seqName = "";
-					}
-					else{
-						seqName += seqList[j];
-					}
-					
-				}
-				seqMap[seqName] = i;
+		InputData input(listFile, "list");
+		ListVector* list = input.getListVector();
+		string lastLabel = list->getLabel();
+		
+		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+		set<string> processedLabels;
+		set<string> userLabels = labels;
+		
+		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+			
+			if(m->control_pressed){
+                for (int i = 0; i < outputNames.size(); i++){	m->mothurRemove(outputNames[i]);  }  delete list;  return 0;
+            }
+			
+			if(allLines == 1 || labels.count(list->getLabel()) == 1){			
+				
+				processedLabels.insert(list->getLabel());
+				userLabels.erase(list->getLabel());
+				
+				//process
+				fillSeqMap(seqMap, list);
+				process(seqMap, list->getLabel(), getCutoff, origCutoff);
 			}
-			m->gobble(inputListFile);
+			
+			if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+				string saveLabel = list->getLabel();
+				
+				delete list;
+				list = input.getListVector(lastLabel);
+				
+				processedLabels.insert(list->getLabel());
+				userLabels.erase(list->getLabel());
+				
+				//process
+				fillSeqMap(seqMap, list);
+				process(seqMap, list->getLabel(), getCutoff, origCutoff);
+				
+				//restore real lastlabel to save below
+				list->setLabel(saveLabel);
+			}		
+			
+			lastLabel = list->getLabel();			
+			
+			delete list;
+			list = input.getListVector();
+		}
+		
+		
+		//output error messages about any remaining user labels
+		set<string>::iterator it;
+		bool needToRun = false;
+		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+			m->mothurOut("Your file does not include the label " + *it); 
+			if (processedLabels.count(lastLabel) != 1) {
+				m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+				needToRun = true;
+			}else {
+				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+			}
+		}
+		
+		//run last label if you need to
+		if (needToRun == true)  {
+			if (list != NULL) {	delete list;	}
+			list = input.getListVector(lastLabel);
+			
+			//process
+			fillSeqMap(seqMap, list);
+			process(seqMap, list->getLabel(), getCutoff, origCutoff);
+			
+			delete list;
+		}
 		
-			int lNumSeqs = seqMap.size();
-			int pNumSeqs = 0;
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "processPhylip");
+		exit(1);
+	}
+}
 
-			ifstream phylipFile;
-			m->openInputFile(distFile, phylipFile);
-			phylipFile >> pNumSeqs;
-			if(pNumSeqs != lNumSeqs){	cout << "numSeq mismatch!" << endl;	}
-			
-			string seqName;
-			double distance;
-			vector<int> otuIndices(lNumSeqs, -1);
+//***************************************************************************************************************
+
+int SensSpecCommand::fillSeqMap(map<string, int>& seqMap, ListVector*& list){
+	try {
+		//for each otu
+		for(int i=0;i<list->getNumBins();i++){
+			
+			if (m->control_pressed) { return 0; }
+			
+			string seqList = list->get(i);
+			int seqListLength = seqList.length();
+			string seqName = "";
+			
+			//parse bin by name, mapping each name to its otu number
+			for(int j=0;j<seqListLength;j++){
 				
-			truePositives = 0;
-			falsePositives = 0;
-			trueNegatives = 0;
-			falseNegatives = 0;
-			
-			if(getCutoff == 1){
-				if(label != "unique"){
-					origCutoff = label;
-					convert(label, cutoff);
-					if(hard == 0){	cutoff += (0.49 / double(precision));	}		
+				if(seqList[j] == ','){
+					seqMap[seqName] = i;
+					seqName = "";
 				}
 				else{
-					origCutoff = "unique";
-					cutoff = 0.0000;
+					seqName += seqList[j];
+				}
+				
+			}
+			seqMap[seqName] = i;
+		}
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "fillSeqMap");
+		exit(1);
+	}
+}
+//***************************************************************************************************************
+int SensSpecCommand::fillSeqPairSet(set<string>& seqPairSet, ListVector*& list){
+	try {
+		int numSeqs = 0;
+		
+		//for each otu
+		for(int i=0;i<list->getNumBins();i++){
+			
+			if (m->control_pressed) { return 0; }
+			
+			vector<string> seqNameVector;
+			string bin = list->get(i);
+			m->splitAtComma(bin, seqNameVector);
+			
+			numSeqs += seqNameVector.size();
+			
+			for(int j=0;j<seqNameVector.size();j++){
+				string seqPairString = "";				
+				for(int k=0;k<j;k++){
+					if(seqNameVector[j] < seqNameVector[k])	{	seqPairString = seqNameVector[j] + '\t' + seqNameVector[k];	}
+					else									{	seqPairString = seqNameVector[k] + '\t' + seqNameVector[j];	}
+					seqPairSet.insert(seqPairString);
 				}
 			}
-				   
-			cout << label << endl;
+		}
+		
+		return numSeqs;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "fillSeqPairSet");
+		exit(1);
+	}
+}
+//***************************************************************************************************************
+int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCutoff, string& origCutoff){
+	try {
+						
+		int lNumSeqs = seqMap.size();
+		int pNumSeqs = 0;
+		
+		ifstream phylipFile;
+		m->openInputFile(distFile, phylipFile);
+		phylipFile >> pNumSeqs;
+		if(pNumSeqs != lNumSeqs){	m->mothurOut("numSeq mismatch!\n"); /*m->control_pressed = true;*/ }
+		
+		string seqName;
+		double distance;
+		vector<int> otuIndices(lNumSeqs, -1);
+		
+		truePositives = 0;
+		falsePositives = 0;
+		trueNegatives = 0;
+		falseNegatives = 0;
+		
+		if(getCutoff == 1){
+			if(label != "unique"){
+				origCutoff = label;
+				convert(label, cutoff);
+				if(hard == 0){	cutoff += (0.49 / double(precision));	}		
+			}
+			else{
+				origCutoff = "unique";
+				cutoff = 0.0000;
+			}
+		}
+		
+		m->mothurOut(label); m->mothurOutEndLine();
+		
+		for(int i=0;i<pNumSeqs;i++){
+			
+			if (m->control_pressed) { return 0; }
+			
+			phylipFile >> seqName;
+			otuIndices[i] = seqMap[seqName];
 			
-			for(int i=0;i<lNumSeqs;i++){
-				phylipFile >> seqName;
-				otuIndices[i] = seqMap[seqName];
+			for(int j=0;j<i;j++){
+				phylipFile >> distance;
 				
-				for(int j=0;j<i;j++){
-					phylipFile >> distance;
-					
-					if(distance <= cutoff){
-						if(otuIndices[i] == otuIndices[j])	{	truePositives++;	}
-						else								{	falseNegatives++;	}
-					}
-					else{
-						if(otuIndices[i] == otuIndices[j])	{	falsePositives++;	}
-						else								{	trueNegatives++;	}
-					}
+				if(distance <= cutoff){
+					if(otuIndices[i] == otuIndices[j])	{	truePositives++;	}
+					else								{	falseNegatives++;	}
 				}
+				else{
+					if(otuIndices[i] == otuIndices[j])	{	falsePositives++;	}
+					else								{	trueNegatives++;	}
+				}
+			}
+            
+            if (square) { m->getline(phylipFile); } //get rest of line - redundant distances
+            m->gobble(phylipFile);
+		}
+		phylipFile.close();
+		
+		outputStatistics(label, origCutoff);
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "process");
+		exit(1);
+	}
+}
+//***************************************************************************************************************
+int SensSpecCommand::process(set<string>& seqPairSet, string label, bool& getCutoff, string& origCutoff, int numSeqs){
+	try {
+		int numDists = (numSeqs * (numSeqs-1) / 2);
+		
+		ifstream columnFile;
+		m->openInputFile(distFile, columnFile);
+		string seqNameA, seqNameB, seqPairString;
+		double distance;
+		
+		truePositives = 0;
+		falsePositives = 0;
+		trueNegatives = numDists;
+		falseNegatives = 0;
+		
+		if(getCutoff == 1){
+			if(label != "unique"){
+				origCutoff = label;
+				convert(label, cutoff);
+				if(hard == 0){	cutoff += (0.49 / double(precision));	}		
+			}
+			else{
+				origCutoff = "unique";
+				cutoff = 0.0000;
+			}
+		}
+		
+		m->mothurOut(label); m->mothurOutEndLine();
+		
+		while(columnFile){
+			columnFile >> seqNameA >> seqNameB >> distance;
+			if(seqNameA < seqNameB)	{	seqPairString = seqNameA + '\t' + seqNameB;	}
+			else					{	seqPairString = seqNameB + '\t' + seqNameA;	}
+			
+			set<string>::iterator it = seqPairSet.find(seqPairString);
+			
+			if(distance <= cutoff){
+				if(it != seqPairSet.end()){
+					truePositives++;
+					seqPairSet.erase(it);	
+				}
+				else{
+					falseNegatives++;
+				}
+				trueNegatives--;
+			}
+			else if(it != seqPairSet.end()){	
+				falsePositives++;
+				trueNegatives--;
+				seqPairSet.erase(it);	
 			}
-			phylipFile.close();
 			
-			outputStatistics(label, origCutoff);
+			m->gobble(columnFile);
 		}
-		inputListFile.close();
-
+		falsePositives += seqPairSet.size();
+		
+		outputStatistics(label, origCutoff);
+		
+				
+		return 0;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "SensSpecCommand", "processPhylip");
+		m->errorOut(e, "SensSpecCommand", "process");
 		exit(1);
 	}
 }
-
 //***************************************************************************************************************
 
-void SensSpecCommand::processColumn(){
+int SensSpecCommand::processColumn(){
 	try{		
-		ifstream inputListFile;
-		m->openInputFile(listFile, inputListFile);
-		
 		string origCutoff = "";
 		bool getCutoff = 0;
 		if(cutoff == -1.00)	{	getCutoff = 1;															}
 		else				{	origCutoff = toString(cutoff);	cutoff += (0.49 / double(precision));	}
 		
 		set<string> seqPairSet;
+		int numSeqs = 0;
+		
+		InputData input(listFile, "list");
+		ListVector* list = input.getListVector();
+		string lastLabel = list->getLabel();
 		
-		string label, seqList;
-		int numOTUs;
-		int numSeqs;
+		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+		set<string> processedLabels;
+		set<string> userLabels = labels;
 		
-		while(inputListFile){
-			numSeqs = 0;
+		
+		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+			
+			if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  }  delete list;  return 0;  }
 			
-			inputListFile >> label >> numOTUs;
-			for(int i=0;i<numOTUs;i++){
+			if(allLines == 1 || labels.count(list->getLabel()) == 1){			
 				
-				vector<string> seqNameVector;
+				processedLabels.insert(list->getLabel());
+				userLabels.erase(list->getLabel());
 				
-				inputListFile >> seqList;
-				int seqListLength = seqList.length();
-				string seqName = "";
-				for(int j=0;j<seqListLength;j++){
-					
-					if(seqList[j] == ','){
-						seqNameVector.push_back(seqName);
-						seqName = "";
-					}
-					else{
-						seqName += seqList[j];
-					}
-				}
-				seqNameVector.push_back(seqName);
-
-				numSeqs += seqNameVector.size();
-				
-				int numSeqsInOTU = seqNameVector.size();
-				for(int j=0;j<numSeqsInOTU;j++){
-					string seqPairString = "";				
-					for(int k=0;k<j;k++){
-						if(seqNameVector[j] < seqNameVector[k])	{	seqPairString = seqNameVector[j] + '\t' + seqNameVector[k];	}
-						else									{	seqPairString = seqNameVector[k] + '\t' + seqNameVector[j];	}
-						seqPairSet.insert(seqPairString);
-					}
-				}
-			}
-			m->gobble(inputListFile);
-			
-			int numDists = (numSeqs * (numSeqs-1) / 2);
-
-			ifstream columnFile;
-			m->openInputFile(distFile, columnFile);
-			string seqNameA, seqNameB, seqPairString;
-			double distance;
-			
-			truePositives = 0;
-			falsePositives = 0;
-			trueNegatives = numDists;
-			falseNegatives = 0;
-			
-			if(getCutoff == 1){
-				if(label != "unique"){
-					origCutoff = label;
-					convert(label, cutoff);
-					if(hard == 0){	cutoff += (0.49 / double(precision));	}		
-				}
-				else{
-					origCutoff = "unique";
-					cutoff = 0.0000;
-				}
+				//process
+				numSeqs = fillSeqPairSet(seqPairSet, list);
+				process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 			}
 			
-			cout << label << endl;
+			if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+				string saveLabel = list->getLabel();
+				
+				delete list;
+				list = input.getListVector(lastLabel);
+				
+				processedLabels.insert(list->getLabel());
+				userLabels.erase(list->getLabel());
+				
+				//process
+				numSeqs = fillSeqPairSet(seqPairSet, list);
+				process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
+				
+				//restore real lastlabel to save below
+				list->setLabel(saveLabel);
+			}		
 			
-			while(columnFile){
-				columnFile >> seqNameA >> seqNameB >> distance;
-				if(seqNameA < seqNameB)	{	seqPairString = seqNameA + '\t' + seqNameB;	}
-				else					{	seqPairString = seqNameB + '\t' + seqNameA;	}
-
-				set<string>::iterator it = seqPairSet.find(seqPairString);
+			lastLabel = list->getLabel();			
 			
-				if(distance <= cutoff){
-					if(it != seqPairSet.end()){
-						truePositives++;
-						seqPairSet.erase(it);	
-					}
-					else{
-						falseNegatives++;
-					}
-					trueNegatives--;
-				}
-				else if(it != seqPairSet.end()){	
-					falsePositives++;
-					trueNegatives--;
-					seqPairSet.erase(it);	
-				}
-				
-				m->gobble(columnFile);
+			delete list;
+			list = input.getListVector();
+		}
+		
+		
+		//output error messages about any remaining user labels
+		set<string>::iterator it;
+		bool needToRun = false;
+		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+			m->mothurOut("Your file does not include the label " + *it); 
+			if (processedLabels.count(lastLabel) != 1) {
+				m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+				needToRun = true;
+			}else {
+				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 			}
-			falsePositives += seqPairSet.size();
+		}
+		
+		//run last label if you need to
+		if (needToRun == true)  {
+			if (list != NULL) {	delete list;	}
+			list = input.getListVector(lastLabel);
 			
-			outputStatistics(label, origCutoff);
+			//process
+			numSeqs = fillSeqPairSet(seqPairSet, list);
+			delete list;
+			process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 		}
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SensSpecCommand", "processColumn");
@@ -507,6 +730,114 @@ void SensSpecCommand::outputStatistics(string label, string cutoff){
 		exit(1);
 	}
 }
+//***************************************************************************************************************
+
+string SensSpecCommand::preProcessList(){
+    try {
+        set<string> uniqueNames;
+        //get unique names from distance file
+        if (format == "phylip") {
+            
+            ifstream phylipFile;
+            m->openInputFile(distFile, phylipFile);
+            string numTest;
+            int pNumSeqs;
+			phylipFile >> numTest; m->gobble(phylipFile);
+			
+			if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+            else {
+                m->mothurConvert(numTest, pNumSeqs);
+            }
+            
+            string seqName;
+            for(int i=0;i<pNumSeqs;i++){
+                if (m->control_pressed) { return ""; }
+                phylipFile >> seqName;  m->getline(phylipFile);  m->gobble(phylipFile);
+                uniqueNames.insert(seqName);
+            }
+            phylipFile.close();
+        }else {
+            ifstream columnFile;
+            m->openInputFile(distFile, columnFile);
+            string seqNameA, seqNameB;
+            double distance;
+            
+            while(columnFile){
+                if (m->control_pressed) { return ""; }
+                columnFile >> seqNameA >> seqNameB >> distance;
+                uniqueNames.insert(seqNameA); uniqueNames.insert(seqNameB);
+                m->gobble(columnFile);
+            }
+            columnFile.close();
+        }
+        
+        //read list file, if numSeqs > unique names then remove redundant names
+        string newListFile = listFile + ".temp";
+        ofstream out;
+        m->openOutputFile(newListFile, out);
+        ifstream in;
+		m->openInputFile(listFile, in);
+		
+		bool wroteSomething = false;
+		
+		while(!in.eof()){
+			
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(newListFile);  return ""; }
+            
+			//read in list vector
+			ListVector list(in);
+            
+            //listfile is already unique
+            if (list.getNumSeqs() == uniqueNames.size()) { in.close(); out.close(); m->mothurRemove(newListFile);  return ""; }
+			
+			//make a new list vector
+			ListVector newList;
+			newList.setLabel(list.getLabel());
+			
+			//for each bin
+			for (int i = 0; i < list.getNumBins(); i++) {
+                
+				//parse out names that are in accnos file
+				string binnames = list.get(i);
+                vector<string> bnames;
+                m->splitAtComma(binnames, bnames);
+				
+				string newNames = "";
+                for (int j = 0; j < bnames.size(); j++) {
+					string name = bnames[j];
+					//if that name is in the .accnos file, add it
+					if (uniqueNames.count(name) != 0) {  newNames += name + ",";  }
+				}
+                
+				//if there are names in this bin add to new list
+				if (newNames != "") { 
+					newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+					newList.push_back(newNames);	
+				}
+			}
+            
+			//print new listvector
+			if (newList.getNumBins() != 0) {
+				wroteSomething = true;
+				newList.print(out);
+			}
+			
+			m->gobble(in);
+		}
+		in.close();	
+		out.close();
+
+        if (wroteSomething) { return newListFile; }
+        else { m->mothurRemove(newListFile); }
+        
+        return ""; 
+    }
+    catch(exception& e) {
+        m->errorOut(e, "SensSpecCommand", "preProcessList");
+        exit(1);
+    }
+}
+
 
 //***************************************************************************************************************