X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=841cad2ddddea905faaf91dca54f193b0221a6ea;hb=c5c7502f435e1413c19e373dab1dfebcaa67588d;hp=78b082d3e2b3c76108845a3bd15a749d4ff465b6;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 78b082d..841cad2 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -17,24 +17,37 @@ ErrorCheck::ErrorCheck() {
 	globaldata = GlobalData::getInstance();
 	validCommand = new ValidCommands();
 	validParameter = new ValidParameters();
-	validCalculator = new ValidCalculators();
-	distfile = globaldata->getDistFile();
+}
+/*******************************************************/
+
+/******************************************************/
+
+void ErrorCheck::refresh() {
+	columnfile = globaldata->getColumnFile();
+	phylipfile = globaldata->getPhylipFile();
 	listfile = globaldata->getListFile();
 	rabundfile = globaldata->getRabundFile();
 	sabundfile = globaldata->getSabundFile();
 	namefile = globaldata->getNameFile();
 	groupfile = globaldata->getGroupFile();
 	orderfile = globaldata->getOrderFile();
+	fastafile = globaldata->getFastaFile();
+	treefile = globaldata->getTreeFile();
 	cutoff = globaldata->getCutOff();
 	format = globaldata->getFormat();
 	method = globaldata->getMethod();
-
+	randomtree = globaldata->getRandomTree();
+	sharedfile = globaldata->getSharedFile();
 }
+
 /*******************************************************/
 
 /******************************************************/
 
-ErrorCheck::~ErrorCheck() {}
+ErrorCheck::~ErrorCheck() {
+	delete validCommand;
+	delete validParameter;
+}
 
 /*******************************************************/
 
@@ -43,7 +56,10 @@ ErrorCheck::~ErrorCheck() {}
 bool ErrorCheck::checkInput(string input) {
 		errorFree = true;
 		clear();
-
+		
+		//refresh variable
+		refresh();
+		
 		//get command name and parameters
 		int openParen = input.find_first_of('(');
 		int closeParen = input.find_last_of(')');
@@ -60,22 +76,29 @@ bool ErrorCheck::checkInput(string input) {
 		if (validCommand->isValidCommand(commandName) != true) { return false; }
 		
 		string parameter, value;
+		
 		//reads in parameters and values
 		if((optionText != "") && (commandName != "help")){
 			while((optionText.find_first_of(',') != -1) && (errorFree)) {  //while there are parameters
-				globaldata->splitAtComma(value, optionText);
-				globaldata->splitAtEquals(parameter, value);
+				splitAtComma(value, optionText);
+				splitAtEquals(parameter, value);
 				
 				//is it a valid parameter
-				if (validParameter->isValidParameter(parameter) != true) { return false; }
+				if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
+
+
 				
-				if (parameter == "distfile" )		{ distfile = value; }
-				if (parameter == "listfile" )		{ listfile = value; }
-				if (parameter == "rabundfile" )		{ rabundfile = value; }
-				if (parameter == "sabundfile" )		{ sabundfile = value; }
-				if (parameter == "namefile" )		{ namefile = value; }
-				if (parameter == "orderfile" )		{ orderfile = value; }
-				if (parameter == "groupfile" )		{ groupfile = value; }
+				if (parameter == "phylip" )		{ phylipfile = value; }
+				if (parameter == "column" )		{ columnfile = value; }
+				if (parameter == "list" )		{ listfile = value; }
+				if (parameter == "rabund" )		{ rabundfile = value; }
+				if (parameter == "sabund" )		{ sabundfile = value; }
+				if (parameter == "name" )		{ namefile = value; }
+				if (parameter == "order" )		{ orderfile = value; }
+				if (parameter == "fasta" )		{ fastafile = value; }
+				if (parameter == "tree" )		{ treefile = value; }
+				if (parameter == "group" )		{ groupfile = value; }
+				if (parameter == "shared" )		{ sharedfile = value; }
 				if (parameter == "cutoff" )			{ cutoff = value; }
 				if (parameter == "precision" )		{ precision = value; }
 				if (parameter == "iters" )			{ iters = value; }
@@ -85,63 +108,32 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "fileroot" )		{ fileroot = value; }
 				if (parameter == "line" )			{ line = value; }
 				if (parameter == "label" )			{ label = value; }
-
-				if (parameter == "single") {//stores estimators in a vector
-					singleEsimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, singleEsimators);
-					for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; }
-					}
-				}
-				if (parameter == "rarefaction") {//stores estimators in a vector
-					rareEstimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, rareEstimators);
-					for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; }
-					}
-				}
-				if (parameter == "shared") {//stores estimators in a vector
-					sharedEstimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, sharedEstimators);
-					for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; }
-					}
-				}
-				if (parameter == "summary") { //stores summaries to be used in a vector
-					summaryEstimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, summaryEstimators);
-					for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; }
-					}
-				}
-				if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector
-					sharedRareEstimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, sharedRareEstimators);
-					for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; }
-					}
-				}
+				if (parameter == "abund" )          { abund = value; }
+				if (parameter == "random" )			{ randomtree = value;	}
+				if (parameter == "sorted" )			{ sorted = value;	}
+				if (parameter == "scaler" )			{ scaler = value;	}
+				
 			}
 			
 			//gets the last parameter and value
 			if (errorFree)  { //gets the last parameter and value
 				value = optionText;
-				globaldata->splitAtEquals(parameter, value);
+				splitAtEquals(parameter, value);
 				//is it a valid parameter
-				if (validParameter->isValidParameter(parameter) != true) { return false; }
+				if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
+	
 				
-				if (parameter == "distfile" )		{ distfile = value; }
-				if (parameter == "listfile" )		{ listfile = value; }
-				if (parameter == "rabundfile" )		{ rabundfile = value; }
-				if (parameter == "sabundfile" )		{ sabundfile = value; }
-				if (parameter == "namefile" )		{ namefile = value; }
-				if (parameter == "orderfile" )		{ orderfile = value; }
-				if (parameter == "groupfile" )		{ groupfile = value; }
+				if (parameter == "phylip" )		{ phylipfile = value; }
+				if (parameter == "column" )		{ columnfile = value; }				
+				if (parameter == "list" )		{ listfile = value; }
+				if (parameter == "rabund" )		{ rabundfile = value; }
+				if (parameter == "sabund" )		{ sabundfile = value; }
+				if (parameter == "name" )		{ namefile = value; }
+				if (parameter == "order" )		{ orderfile = value; }
+				if (parameter == "group" )		{ groupfile = value; }
+				if (parameter == "shared" )		{ sharedfile = value; }
+				if (parameter == "fasta" )		{ fastafile = value; }
+				if (parameter == "tree" )		{ treefile = value; }
 				if (parameter == "cutoff" )			{ cutoff = value; }
 				if (parameter == "precision" )		{ precision = value; }
 				if (parameter == "iters" )			{ iters = value; }
@@ -151,92 +143,110 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "fileroot" )		{ fileroot = value; }
 				if (parameter == "line" )			{ line = value; }
 				if (parameter == "label" )			{ label = value; }
-
-				if (parameter == "single") {//stores estimators in a vector
-					singleEsimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, singleEsimators);
-					for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; }
-					}
-				}
-				if (parameter == "rarefaction") {//stores estimators in a vector
-					rareEstimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, rareEstimators);
-					for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; }
-					}
-				}
-				if (parameter == "shared") {//stores estimators in a vector
-					sharedEstimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, sharedEstimators);
-					for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; }
-					}
-				}
-				if (parameter == "summary") { //stores summaries to be used in a vector
-					summaryEstimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, summaryEstimators);
-					for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; }
-					}
-				}
-				if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector
-					sharedRareEstimators.clear(); //clears out old values
-					globaldata->splitAtDash(value, sharedRareEstimators);
-					for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators
-						//is it a valid calculator
-						if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; }
-					}
-				}
-
+				if (parameter == "random" )			{ randomtree = value;	}
+				if (parameter == "abund" )          { abund = value; }
+				if (parameter == "sorted" )			{ sorted = value;	}
+				if (parameter == "scaler" )			{ scaler = value;	}
 			}
 		}
 		
 		//make sure the user does not use both the line and label parameters
 		if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
 		
-		//validate files
-		if (commandName == "parselist") {
-			validateParseFiles(commandName);
-		}
-		if ((commandName == "read.phylip") || (commandName == "read.column")) { 
+		//check for valid files 
+		if (commandName == "read.dist") { 
 			validateReadFiles();
 			validateReadDist();
-		}else if ((commandName == "read.list") || (commandName == "read.rabund") || (commandName == "read.sabund")){ 
-			validateReadFiles();
-			validateReadPhil(commandName);	
-		}else if (commandName == "read.shared") { 
+		}else if (commandName == "read.otu") { 
+			//you want to do shared commands
+			if ((listfile != "") && (groupfile != ""))	{
+				validateParseFiles(); //checks the listfile and groupfile parameters
+			//you want to do single commands
+			}else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){ 
+				validateReadFiles();
+				validateReadPhil();
+			//you have not given a file
+			}else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
+				cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false; 
+			//you want to do shared commands with a shared file
+			}else if (sharedfile != "") {//you are reading a shared file
+				validateReadFiles();
+			}
+		}else if (commandName == "read.tree") { 
+			validateTreeFiles(); //checks the treefile and groupfile parameters
+		}else if (commandName == "deconvolute") {
+			if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
 			validateReadFiles();
-			validateParseFiles(commandName); //checks the listfile and groupfile parameters
 		}
 		
 		//are you trying to cluster before you have read something			
-		if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
-			(commandName == "cluster") && (globaldata->getListVector() == NULL)) {
+		if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
+			((commandName == "cluster") && (globaldata->gListVector == NULL))) {
 				cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; 
 				errorFree = false;
 		} 
 		
+		if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
+			 cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false; 
+		}
+		
+		if (commandName == "parsimony") {
+			//are you trying to use parsimony without reading a tree or saying you want random distribution
+			if (randomtree == "")  {
+				if (globaldata->gTree.size() == 0) {
+					cout << "You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command." << endl; return false;  }
+			}
+		}
+		
+		if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
+			if (globaldata->gTree.size() == 0) {//no trees were read
+				cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false;  }
+		}
+		
 		//check for valid method
+		if(commandName == "get.group") {
+			if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
+		}
+		if (commandName == "get.label" || commandName == "get.line") {
+			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label or get.line command." << endl; return false; }
+		}
 		if (commandName == "cluster") {
 			if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 			else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
 		}
 		
 		if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){ 
-			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a listfile, sabundfile or rabundfile before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
+			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
 		}
 		
-		if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "shared") ){ 
-			if (globaldata->getListFile() == "") { cout << "You must read a listfile and a groupfile before you can use the collect.shared, rarefaction.shared, summary.shared or shared commands." << endl; return false; }
-			else if (globaldata->getGroupFile() == "") { cout << "You must read a listfile and a groupfile before you can use the collect.shared, rarefaction.shared, summary.shared or shared commands." << endl; return false; }
+		if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.groups") ){ 
+			if (globaldata->getSharedFile() == "") {
+				if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared or tree.groups commands." << endl; return false; }
+				else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared or tree.groups commands." << endl; return false; }
+			}
 		}
- 
 		
+		if ((commandName == "heatmap") || (commandName == "venn")) { 
+			if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
+				 cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap or venn commands." << endl; return false; 
+			}
+		}
+		
+		if ((commandName == "bin.seqs")) { 
+			if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
+			validateBinFiles();
+		}
+		
+		if ((commandName == "get.oturep")) { 
+			if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
+				cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl; 
+				errorFree = false;
+			}
+			if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
+			validateBinFiles();
+		} 
+
+
 		return errorFree;
 }
 
@@ -251,13 +261,20 @@ void ErrorCheck::validateReadFiles() {
 		ifstream filehandle;
 		int ableToOpen;
 	
-		//are we reading a distfile
-		if (distfile != "") {
-			ableToOpen = openInputFile(distfile, filehandle);
+		//are we reading a phylipfile
+		if (phylipfile != "") {
+			ableToOpen = openInputFile(phylipfile, filehandle);
 			filehandle.close();
 			//unable to open
 			if (ableToOpen == 1) { errorFree = false; }
-			else { globaldata->inputFileName = distfile; }
+			else { globaldata->inputFileName = phylipfile; }
+		//are we reading a columnfile
+		}else if (columnfile != "") {
+			ableToOpen = openInputFile(columnfile, filehandle);
+			filehandle.close();
+			//unable to open
+			if (ableToOpen == 1) { errorFree = false; }
+			else { globaldata->inputFileName = columnfile; }
 		//are we reading a listfile
 		}else if (listfile!= "") {
 			ableToOpen = openInputFile(listfile, filehandle);
@@ -279,6 +296,18 @@ void ErrorCheck::validateReadFiles() {
 			//unable to open
 			if (ableToOpen == 1) {  errorFree = false; }
 			else { globaldata->inputFileName = sabundfile; }
+		}else if (fastafile != "") {
+			ableToOpen = openInputFile(fastafile, filehandle);
+			filehandle.close();
+			//unable to open
+			if (ableToOpen == 1) {  errorFree = false; }
+			else { globaldata->inputFileName = fastafile; }
+		}else if (sharedfile != "") {
+			ableToOpen = openInputFile(sharedfile, filehandle);
+			filehandle.close();
+			//unable to open
+			if (ableToOpen == 1) {  errorFree = false; }
+			else { globaldata->inputFileName = sharedfile; }
 		}else{ //no file given
 			errorFree = false;
 		}
@@ -303,11 +332,19 @@ void ErrorCheck::validateReadDist() {
 		ifstream filehandle;
 		int ableToOpen;
 		
-		if (distfile == "") { cout << "When executing a read.phylip or read.column you must enter a distfile." << endl; errorFree = false; }
+		if (groupfile != "") {
+			ableToOpen = openInputFile(groupfile, filehandle);
+			filehandle.close();
+			//unable to open
+			if (ableToOpen == 1) {  errorFree = false; }
+		}
 		
-		if (commandName == "read.column") {
+		if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
+		else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
+		
+		if (columnfile != "") {
 			if (namefile == "") {
-				cout << "You need to provide a namefile name if you are going to use the column format." << endl;
+				cout << "You need to provide a namefile if you are going to use the column format." << endl;
 				errorFree = false; 
 			}else {
 				ableToOpen = openInputFile(namefile, filehandle);
@@ -331,20 +368,16 @@ void ErrorCheck::validateReadDist() {
 /******************************************************/
 //This function checks to make sure the user entered appropriate
 // format parameters on a parselistcommand
-void ErrorCheck::validateParseFiles(string command) {
+void ErrorCheck::validateParseFiles() {
 	try {
 		ifstream filehandle;
 		int ableToOpen;
 		
 		//checks for valid files
-		if (command == "read.shared" ) {
-			if (listfile == "") { cout << "When executing a read.shared you must enter a listfile and a groupfile." << endl; errorFree = false; }
-			else if (groupfile == "") { cout << "When executing a read.shared you must enter a listfile and a groupfile." << endl; errorFree = false; }
-		}else if (command == "parselist" ) {
-			if (listfile == "") { cout << "When executing a parselist you must enter a listfile and a groupfile." << endl; errorFree = false; }
-			else if (groupfile == "") { cout << "When executing a parselist you must enter a listfile and a groupfile." << endl; errorFree = false; }
-		}
-		
+	
+		if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
+		else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
+	
 		//checks parameters on the read command
 		if (listfile != "") {
 			ableToOpen = openInputFile(listfile, filehandle);
@@ -370,24 +403,69 @@ void ErrorCheck::validateParseFiles(string command) {
 		exit(1);
 	}
 }
+/*******************************************************/
+
+/******************************************************/
+//This function checks to make sure the user entered appropriate
+// format parameters on a parselistcommand
+void ErrorCheck::validateTreeFiles() {
+	try {
+		ifstream filehandle;
+		int ableToOpen;
+		
+		//checks for valid files
+	
+		if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
+		else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
+	
+		//checks parameters on the read command
+		if (treefile != "") {
+			ableToOpen = openInputFile(treefile, filehandle);
+			filehandle.close();
+			if (ableToOpen == 1) { //unable to open
+				errorFree = false;
+			}
+			if (groupfile != "") {
+				ableToOpen = openInputFile(groupfile, filehandle);
+				filehandle.close();
+				if (ableToOpen == 1) { //unable to open
+					errorFree = false;;
+				}
+			}
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
 
 /*******************************************************/
 
 /******************************************************/
 //This function checks to make sure the user entered appropriate
 // format parameters on a distfile read
-void ErrorCheck::validateReadPhil(string command) {
+void ErrorCheck::validateReadPhil() {
 	try {
 		ifstream filehandle;
 		int ableToOpen;
 		
-		//checks for valid files
-		if (command == "read.list" ) {
-			if (listfile == "") { cout << "When executing a read.list you must enter a listfile." << endl; errorFree = false; }
-		}else if (command == "read.sabund" ) {
-			if (sabundfile == "") { cout << "When executing a read.sabund you must enter a sabundfile." << endl; errorFree = false; }
-		}else if (command == "read.rabund" ) {
-			if (rabundfile == "") { cout << "When executing a read.rabund you must enter a rabundfile." << endl; errorFree = false; }
+		//checks to make sure only one file type is given
+		if (listfile != "") { 
+			if ((rabundfile != "") || (sabundfile != "")) { 
+				cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
+		}else if (rabundfile != "") { 
+			if ((listfile != "") || (sabundfile != "")) { 
+				cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
+		}else if (sabundfile != "") { 
+			if ((listfile != "") || (rabundfile != "")) { 
+				cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
+		}else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
+			    cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false; 
 		}
 		
 		//checks parameters on the read command
@@ -410,17 +488,71 @@ void ErrorCheck::validateReadPhil(string command) {
 }
 /*******************************************************/
 
+/******************************************************/
+//This function checks to make sure the user entered appropriate
+// format parameters on a bin.seq command
+void ErrorCheck::validateBinFiles() {
+	try {
+		ifstream filehandle;
+		int ableToOpen;
+		
+		if (fastafile == "") {
+				cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false; 
+		}else if (fastafile != "") {
+			//is it a valid filename'
+			ableToOpen = openInputFile(fastafile, filehandle);
+			filehandle.close();
+			//unable to open
+			if (ableToOpen == 1) {  errorFree = false; }
+		}else if (listfile != "") {
+			//is it a valid filename'
+			ableToOpen = openInputFile(listfile, filehandle);
+			filehandle.close();
+			//unable to open
+			if (ableToOpen == 1) {  errorFree = false; }
+		}else if (globaldata->getNameFile() != "") {
+			//is it a valid filename'
+			ifstream filehandle;
+			int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
+			filehandle.close();
+			//unable to open
+			if (ableToOpen == 1) {  errorFree = false; }
+		}else if (namefile != "") {
+			//is it a valid filename'
+			ifstream filehandle;
+			int ableToOpen = openInputFile(namefile, filehandle);
+			filehandle.close();
+			//unable to open
+			if (ableToOpen == 1) {  errorFree = false; }
+		}
+
+
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/*******************************************************/
+
 /******************************************************/
 
 void ErrorCheck::clear() {
 	//option definitions should go here...
-	distfile		=	"";
+	phylipfile		=	"";
+	columnfile		=	"";
 	listfile		=	"";
 	rabundfile		=	"";
 	sabundfile		=	"";
 	namefile		=	"";
 	groupfile		=	""; 
 	orderfile		=	"";
+	sharedfile		=	"";
 	line			=	"";
 	label			=	"";
 	method			=   "furthest";