X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=39fb17e47a4e2f72692f5d5be15f19866fca2bef;hb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;hp=41c1db9e678c5890472d9259017a16f6d6b84dc3;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf;p=mothur.git

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 41c1db9..39fb17e 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -17,26 +17,39 @@ ErrorCheck::ErrorCheck() {
 	globaldata = GlobalData::getInstance();
 	validCommand = new ValidCommands();
 	validParameter = new ValidParameters();
-	validCalculator = new ValidCalculators();
-	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();
-	cutoff = globaldata->getCutOff();
-	format = globaldata->getFormat();
-	method = globaldata->getMethod();
+}
+/*******************************************************/
+
+/******************************************************/
+
+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;
+}
 
 /*******************************************************/
 
@@ -45,7 +58,10 @@ 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(')');
@@ -60,26 +76,30 @@ bool ErrorCheck::checkInput(string input) {
 		
 		//is it a valid command
 		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 == "phylipfile" )		{ phylipfile = value; }
-				if (parameter == "columnfile" )		{ columnfile = 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 == "fastafile" )		{ fastafile = 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 == "nexus" )		{ nexusfile = value; }
+				if (parameter == "clustal" )	{ clustalfile = 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; }
@@ -89,65 +109,47 @@ 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 == "trump" )          { trump = value; }
+				if (parameter == "soft" )			{ soft = value; }
+				if (parameter == "filter" )         { filter = value; }
+				if (parameter == "scale" )			{ scale = value;	}
+				if (parameter == "countends" )		{ countends = value; }
+				if (parameter == "processors" )		{ processors = value;	}
+				if (parameter == "size" )			{ size = value; }
+				if (parameter == "candidate")		{ candidatefile = value;	}
+				if (parameter == "search")			{ search = value;		}
+				if (parameter == "ksize")			{ ksize = value;		}
+				if (parameter == "align")		    { align = value;		}
+				if (parameter == "match")			{ match = value;		}
+				if (parameter == "mismatch")		{ mismatch = value;	    }
+				if (parameter == "gapopen")			{ gapopen = value;		}
+				if (parameter == "gapextend" )		{ gapextend = 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 == "phylipfile" )		{ phylipfile = value; }
-				if (parameter == "columnfile" )		{ columnfile = 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 == "fastafile" )		{ fastafile = 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 == "nexus" )		{ nexusfile = value; }
+				if (parameter == "clustal" )	{ clustalfile = value; }
+				if (parameter == "tree" )		{ treefile = value; }
 				if (parameter == "cutoff" )			{ cutoff = value; }
 				if (parameter == "precision" )		{ precision = value; }
 				if (parameter == "iters" )			{ iters = value; }
@@ -157,55 +159,32 @@ 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 == "random" )			{ randomtree = value;	}
+				if (parameter == "abund" )          { abund = value; }
+				if (parameter == "sorted" )			{ sorted = value;	}
+				if (parameter == "trump" )          { trump = value; }
+				if (parameter == "soft" )			{ soft = value; }
+				if (parameter == "filter" )         { filter = value; }
+				if (parameter == "scale" )			{ scale = value;	}
+				if (parameter == "countends" )		{ countends = value; }
+				if (parameter == "processors" )		{ processors = value;	}
+				if (parameter == "size" )			{ size = value; }
+				if (parameter == "candidate")		{ candidatefile = value;	}
+				if (parameter == "search")			{ search = value;		}
+				if (parameter == "ksize")			{ ksize = value;		}
+				if (parameter == "align")		    { align = value;		}
+				if (parameter == "match")			{ match = value;		}
+				if (parameter == "mismatch")		{ mismatch = value;	    }
+				if (parameter == "gapopen")			{ gapopen = value;		}
+				if (parameter == "gapextend" )		{ gapextend = 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; }
-	
 		
+		//check for valid files 
 		if (commandName == "read.dist") { 
 			validateReadFiles();
 			validateReadDist();
@@ -213,37 +192,117 @@ bool ErrorCheck::checkInput(string input) {
 			//you want to do shared commands
 			if ((listfile != "") && (groupfile != ""))	{
 				validateParseFiles(); //checks the listfile and groupfile parameters
-			}else { //you want to do single commands
+			//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();
 		}
 		
-		//are you trying to cluster before you have read something			
-		if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
-			(commandName == "cluster") && (globaldata->getListVector() == NULL)) {
+		//are you trying to cluster before you have read something	
+		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") || (commandName == "concensus")) {
+			if (globaldata->gTree.size() == 0) {//no trees were read
+				cout << "You must execute the read.tree command, before you may execute the unifrac.weighted, unifrac.unweighted or concensus command." << endl; return false;  }
+		}
+		
 		//check for valid method
+		if(commandName == "get.group") {
+			if ((globaldata->getSharedFile() == "")) { cout << "You must read a groupfile or a sharedfile 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 == "bootstrap.shared") || (commandName == "dist.shared")){ 
+			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, tree.shared, bootstrap.shared or dist.shared 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, tree.shared, bootstrap.shared or dist.shared commands." << endl; return false; }
+			}
+		}
+		
+		if  (commandName == "tree.shared")  {
+			//given no files			
+			if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == "")))	{ cout << "You must run the read.otu command or provide a distance file before running the tree.shared command." << endl; return false; }
+			//you want to do single commands
+			else if ((globaldata->getSharedFile() == "") && ((phylipfile != "") || (columnfile != ""))) {
+				validateReadDist();
+			}
+		}
+		
+		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 == "filter.seqs") || (commandName == "dist.seqs")) { 
+			if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) {
+				 cout << "You must enter either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs or dist.seqs command." << endl; return false; 
+			}
+			validateSeqsFiles();
+		}
+		
+		if (commandName == "align.seqs") {
+			if ((fastafile == "") || (candidatefile == "")) {
+				cout << "You must enter fasta and a candidate file to use the align.seqs command." << endl; return false; 
+			}
+			validateSeqsFiles();
 		}
 		
-		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 == "bin.seqs")) { 
+			if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs commands." << 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; }
+			if (fastafile == "") { cout << "fasta is a required parameter for the get.oturep command." << endl; errorFree = false; }
+			validateBinFiles();
+		} 
+
+
 		return errorFree;
 }
 
@@ -265,7 +324,7 @@ void ErrorCheck::validateReadFiles() {
 			//unable to open
 			if (ableToOpen == 1) { errorFree = false; }
 			else { globaldata->inputFileName = phylipfile; }
-		//are we reading a phylipfile
+		//are we reading a columnfile
 		}else if (columnfile != "") {
 			ableToOpen = openInputFile(columnfile, filehandle);
 			filehandle.close();
@@ -299,6 +358,18 @@ void ErrorCheck::validateReadFiles() {
 			//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 if (groupfile != "") {
+			ableToOpen = openInputFile(groupfile, filehandle);
+			filehandle.close();
+			if (ableToOpen == 1) { //unable to open
+				errorFree = false;
+			}
 		}else{ //no file given
 			errorFree = false;
 		}
@@ -323,12 +394,19 @@ void ErrorCheck::validateReadDist() {
 		ifstream filehandle;
 		int ableToOpen;
 		
-		if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylipfile or a columnfile." << endl; errorFree = false; }
-		else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylipfile or columnfile." << endl; errorFree = false; }
+		if (groupfile != "") {
+			ableToOpen = openInputFile(groupfile, filehandle);
+			filehandle.close();
+			//unable to open
+			if (ableToOpen == 1) {  errorFree = false; }
+		}
+		
+		if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist or a tree.shared command with a distance file you must enter a phylip or a column." << endl; errorFree = false; }
+		else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist or a tree.shared command with a distance file 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);
@@ -359,8 +437,8 @@ void ErrorCheck::validateParseFiles() {
 		
 		//checks for valid files
 	
-		if (listfile == "") { cout << "When executing a read.list you must enter a listfile and a groupfile." << endl; errorFree = false; }
-		else if (groupfile == "") { cout << "When executing a read.list 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 != "") {
@@ -373,7 +451,7 @@ void ErrorCheck::validateParseFiles() {
 				ableToOpen = openInputFile(groupfile, filehandle);
 				filehandle.close();
 				if (ableToOpen == 1) { //unable to open
-					errorFree = false;;
+					errorFree = false;
 				}
 			}
 		}
@@ -387,6 +465,46 @@ void ErrorCheck::validateParseFiles() {
 		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);
+	}
+}
 
 /*******************************************************/
 
@@ -401,15 +519,15 @@ void ErrorCheck::validateReadPhil() {
 		//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: listfile, rabundfile or sabundfile." << endl; errorFree = false; }
+				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: listfile, rabundfile or sabundfile." << endl; errorFree = false; }
+				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: listfile, rabundfile or sabundfile." << endl; errorFree = false; }
-		}else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
-			    cout << "When executing a read.otu you must enter one of the following: listfile, rabundfile or sabundfile." << endl; errorFree = false; 
+				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
@@ -432,6 +550,137 @@ void ErrorCheck::validateReadPhil() {
 }
 /*******************************************************/
 
+/******************************************************/
+//This function checks to make sure the user entered appropriate
+// format parameters on a distfile read
+void ErrorCheck::validateSeqsFiles() {
+	try {
+		ifstream filehandle;
+		int ableToOpen;
+		
+		//checks to make sure only one file type is given
+		if (phylipfile != "") { 
+			if ((nexusfile != "") || (fastafile != "") || (clustalfile != "")) { 
+				cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
+			else {
+				ableToOpen = openInputFile(phylipfile, filehandle);
+				filehandle.close();
+				if (ableToOpen == 1) { //unable to open
+					errorFree = false;
+				}
+			}
+		}else if (nexusfile != "") { 
+			if ((phylipfile != "") || (fastafile != "") || (clustalfile != "")) { 
+				cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
+			else {
+				ableToOpen = openInputFile(nexusfile, filehandle);
+				filehandle.close();
+				if (ableToOpen == 1) { //unable to open
+					errorFree = false;
+				}
+			}
+		}else if (fastafile != "") { 
+			if ((phylipfile != "") || (nexusfile != "") || (clustalfile != "")) { 
+				cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
+			else {
+				ableToOpen = openInputFile(fastafile, filehandle);
+				filehandle.close();
+				if (ableToOpen == 1) { //unable to open
+					errorFree = false;
+				}
+			}
+		}else if (clustalfile != "") { 
+			if ((phylipfile != "") || (nexusfile != "") || (fastafile != "")) { 
+				cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
+			else {
+				ableToOpen = openInputFile(clustalfile, filehandle);
+				filehandle.close();
+				if (ableToOpen == 1) { //unable to open
+					errorFree = false;
+				}
+			}
+		}else if (candidatefile != "") {
+			ableToOpen = openInputFile(candidatefile, 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 validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ErrorCheck class function validateSeqsFiles. 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 bin.seq command
+void ErrorCheck::validateBinFiles() {
+	try {
+		ifstream filehandle;
+		int ableToOpen;
+		
+		if (fastafile == "") {
+				cout << "fasta is a required parameter for bin.seqs, get.oturep and get.repseqs 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; }
+		}else if (groupfile != "") {
+			//is it a valid filename'
+			ifstream filehandle;
+			int ableToOpen = openInputFile(groupfile, 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() {
@@ -444,6 +693,11 @@ void ErrorCheck::clear() {
 	namefile		=	"";
 	groupfile		=	""; 
 	orderfile		=	"";
+	sharedfile		=	"";
+	fastafile       =   "";
+	nexusfile       =   "";
+	clustalfile     =   "";
+	candidatefile	=	"";
 	line			=	"";
 	label			=	"";
 	method			=   "furthest";