X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=caf7f73dc31cf02bd48ac7352f339e41b4f6cb96;hb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;hp=54465729f5e04c36c6a0e2bed16064a5ea32b9a2;hpb=ec43347d04dbb2a7d9d9ecfb5fc556e21ad8c2bc;p=mothur.git

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 5446572..caf7f73 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -8,7 +8,6 @@
  */
 
 #include "errorchecking.h"
-#include <math.h>
 
 /*******************************************************/
 
@@ -24,149 +23,33 @@ ErrorCheck::ErrorCheck() {
 /******************************************************/
 
 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();
 
-	
-	string p[] = {
-		"phylip",              //0
-		"column",             //1
-		"list",               //2
-		"rabund",             //3
-		"sabund",             //4
-		"name",               //5
-		"order",              //6
-		"group",              //7
-		"fasta",              //8
-		"treefile",           //9
-		"cutoff",             //10
-		"precision",          //11
-		"iters",              //12
-		"jumble",             //13
-		"freq",               //14
-		"method",             //15
-		"fileroot",           //16
-		"line",               //17
-		"label",              //18
-		"single",             //19
-		"rarefaction",        //20
-		"shared",             //21
-		"summary",            //22
-		"sharedrarefaction",  //23
-		"sharedsummary",      //24
-		"comparegroups",      //25
-		"abund",              //26
-		};
-	
-	string c0[] = {p[0],p[5],p[10],p[11]};
-	string c1[] = {p[2],p[6],p[7]}; 
-	string c2[] = {p[10],p[11],p[15]}; 
-	string c3[] = {p[8]};  
-	string c4[] = {p[14],p[17],p[18],p[19],p[26]};
-	string c5[] = {p[13],p[14],p[17],p[18],p[21],p[25]};
-	string c6[] = {""}; 
-	string c7[] = {""}; 
-	string c8[] = {""}; 
-	string c9[] = {p[12],p[14],p[17],p[18],p[20],p[26]};
-	string c10[] = {p[12],p[13],p[17],p[18],p[23]};
-	string c11[] = {p[17],p[18],p[22],p[26]};   
-	string c12[] =  {p[13],p[17],p[18],p[24]}; 
-	string c13[] = {""}; 	
-	
-	vector<string> v0 (c0, c0+sizeof(c0)/sizeof(string)); 
-	vector<string> v1 (c1, c1+sizeof(c1)/sizeof(string));
-	vector<string> v2 (c2, c2+sizeof(c2)/sizeof(string));
-	vector<string> v3 (c3, c3+sizeof(c3)/sizeof(string));
-	vector<string> v4 (c4, c4+sizeof(c4)/sizeof(string));
-	vector<string> v5 (c5, c5+sizeof(c5)/sizeof(string));
-	vector<string> v6 (c6, c6+sizeof(c6)/sizeof(string));
-	vector<string> v7 (c7, c7+sizeof(c7)/sizeof(string));
-	vector<string> v8 (c8, c8+sizeof(c8)/sizeof(string));
-	vector<string> v9 (c9, c9+sizeof(c9)/sizeof(string));
-	vector<string> v10 (c10, c10+sizeof(c10)/sizeof(string));
-	vector<string> v11 (c11, c11+sizeof(c11)/sizeof(string));
-	vector<string> v12 (c12, c12+sizeof(c12)/sizeof(string));
-	vector<string> v13 (c13, c13+sizeof(c13)/sizeof(string));
-	
-	vector<vector<string> > allCommands;
-	allCommands.push_back(v0);
-	allCommands.push_back(v1);
-	allCommands.push_back(v2);
-	allCommands.push_back(v3);
-	allCommands.push_back(v4);
-	allCommands.push_back(v5);
-	allCommands.push_back(v6);
-	allCommands.push_back(v7);
-	allCommands.push_back(v8);
-	allCommands.push_back(v9);
-	allCommands.push_back(v10);
-	allCommands.push_back(v11);
-	allCommands.push_back(v12);
-	allCommands.push_back(v13);
-	
-	string commands[] = {
-	"read.dist",          //0
-	"read.otu",           //1
-	"cluster",            //2
-	"deconvolute",        //3
-	"collect.single",     //4
-	"collect.shared",     //5
-	"get.group",          //6
-	"get.label",          //7
-	"get.line",           //8
-	"rarefaction.single", //9
-	"rarefaction.shared", //10
-	"summary.single",     //11
-	"summary.shared",     //12
-	"quit"                //13
-	};
-	
-	for(int i = 0; i < allCommands.size(); i++)
-		commandParameters[commands[i]] = allCommands.at(i);
-	
-	 //{Lowerbound(piSent if no lowerbound), Upperbound(piSent if no upperbound), 1 if only the first 2 values, 0 if greater than, 0 if less than};
-	piSent = 3.14159;
-	double ip0[] = {10, piSent, 0, 1, 0};
-	double ip1[] = {10, piSent, 0, 1, 0};
-	double ip2[] = {0, 1, 1, 0, 0};
-	double ip3[] =  {1, piSent, 0, 0, 0};
-	double ip4[] = {1, piSent, 0, 1, 0};
-	double ip5[] = {5, piSent, 0, 1, 0};
-	
-	vector<double> ipv0 (ip0, ip0+sizeof(ip0)/sizeof(double)); 
-	vector<double> ipv1 (ip1, ip1+sizeof(ip1)/sizeof(double)); 
-	vector<double> ipv2 (ip2, ip2+sizeof(ip2)/sizeof(double)); 
-	vector<double> ipv3 (ip3, ip3+sizeof(ip3)/sizeof(double)); 
-	vector<double> ipv4 (ip4, ip4+sizeof(ip4)/sizeof(double)); 
-	vector<double> ipv5 (ip5, ip5+sizeof(ip5)/sizeof(double));
-
-	intParams[p[11]] = ipv0;
-	intParams[p[12]] = ipv1;
-	intParams[p[13]] = ipv2;
-	intParams[p[14]] = ipv3;
-	intParams[p[17]] = ipv4;
-	intParams[p[26]] = ipv5;
-	
-	randomtree = globaldata->getRandomTree();
-	sharedfile = globaldata->getSharedFile();
+	//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;
+}
 
 /*******************************************************/
 
@@ -193,7 +76,6 @@ 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
@@ -203,49 +85,8 @@ bool ErrorCheck::checkInput(string input) {
 				splitAtEquals(parameter, value);
 				
 				//is it a valid parameter
-				if (validParameter->isValidParameter(parameter) != true) { return false; }
-				if(!validCommandParameter(parameter,commandName)) { 
-					cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
-					return false; 
-				}
-				if(!validParameterValue(value, parameter)) {
-					if(parameter.compare("precision") == 0)
-						cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
-					else {
-					vector<double> bounds = intParams[parameter];
-					double a = bounds.at(0);
-					double b = bounds.at(1);
-					double c = bounds.at(2);
-					double d = bounds.at(3);
-					double e = bounds.at(4);
-					cout << "The '" << parameter << "' parameter needs to be ";
-					if(c == 1)
-							cout << "either '" << a << "' or '" << b << "'.\n";
-					else
-					{
-						if(a != piSent)
-						{
-							cout << ">";
-							if(d != 0)
-								cout << "=";
-							cout << " '" << a << "'";
-						}
-						if(b == piSent)
-							cout << ".\n";
-						else if(a != piSent)
-							cout << " and ";
-						if(b != piSent)
-						{
-							cout << "<";
-							if(e != 0)
-								cout << "=";
-							cout << " '" << b << ".\n";
-						}
-					}
-					}
-					return false;
-				}
-
+				if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
+				
 				if (parameter == "phylip" )		{ phylipfile = value; }
 				if (parameter == "column" )		{ columnfile = value; }
 				if (parameter == "list" )		{ listfile = value; }
@@ -254,9 +95,11 @@ bool ErrorCheck::checkInput(string input) {
 				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 == "group" )			{ groupfile = value; }
+				if (parameter == "shared" )			{ sharedfile = value; }
 				if (parameter == "cutoff" )			{ cutoff = value; }
 				if (parameter == "precision" )		{ precision = value; }
 				if (parameter == "iters" )			{ iters = value; }
@@ -267,7 +110,23 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "line" )			{ line = value; }
 				if (parameter == "label" )			{ label = value; }
 				if (parameter == "abund" )          { abund = value; }
-				if (parameter == "random" )			{ randomtree = 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
@@ -275,48 +134,9 @@ bool ErrorCheck::checkInput(string input) {
 				value = optionText;
 				splitAtEquals(parameter, value);
 				//is it a valid parameter
-				if (validParameter->isValidParameter(parameter) != true) { return false; }
-				if(!validCommandParameter(parameter,commandName)) { 
-					cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
-					return false; 
-				}
-				if(!validParameterValue(value, parameter)) {
-					if(parameter.compare("precision") == 0)
-						cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
-					else {
-					vector<double> bounds = intParams[parameter];
-					double a = bounds.at(0);
-					double b = bounds.at(1);
-					double c = bounds.at(2);
-					double d = bounds.at(3);
-					double e = bounds.at(4);
-					cout << "The '" << parameter << "' parameter needs to be ";
-					if(c == 1)
-							cout << "either '" << a << "' or '" << b << "'.\n";
-					else
-					{
-						if(a != piSent)
-						{
-							cout << ">";
-							if(d != 0)
-								cout << "=";
-							cout << " '" << a << "'";
-						}
-						if(b == piSent)
-							cout << ".\n";
-						else if(a != piSent)
-							cout << " and ";
-						if(b != piSent)
-						{
-							cout << "<";
-							if(e != 0)
-								cout << "=";
-							cout << " '" << b << ".\n";
-						}
-					}
-					}
-					return false;
-				}
+				if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
+	
+				
 				if (parameter == "phylip" )		{ phylipfile = value; }
 				if (parameter == "column" )		{ columnfile = value; }				
 				if (parameter == "list" )		{ listfile = value; }
@@ -327,6 +147,8 @@ bool ErrorCheck::checkInput(string input) {
 				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; }
@@ -339,12 +161,30 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "label" )			{ label = value; }
 				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();
@@ -352,27 +192,35 @@ 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.shared") { 
-			//you want to do shared commands with just the 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; }
+		}else if (commandName == "unique.seqs") {
+			if (fastafile == "") { cout << "You must enter a fastafile with the unique.seqs() 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 == "")  {
@@ -381,14 +229,14 @@ bool ErrorCheck::checkInput(string input) {
 			}
 		}
 		
-		if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
+		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 or unifrac.unweighted command." << endl; return false;  }
+				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->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
+			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; }
@@ -398,16 +246,70 @@ bool ErrorCheck::checkInput(string input) {
 			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 ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")){ 
 			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") ){ 
+		if (commandName == "get.rabund") {
+			if (globaldata->getListFile() == "") { cout << "You must read a listfile before you can use the get.rabund command." << endl; return false; }
+		}
+		
+		if (commandName == "get.sabund") {
+			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << 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 or summary.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 or summary.shared commands." << endl; return false; }
+				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 == "") {
+				 cout << "You must enter either a fasta 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 == "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;
 }
@@ -430,7 +332,7 @@ 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();
@@ -470,6 +372,12 @@ void ErrorCheck::validateReadFiles() {
 			//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;
 		}
@@ -486,113 +394,6 @@ void ErrorCheck::validateReadFiles() {
 }
 /*******************************************************/
 
-/******************************************************/
-//This function checks to see if the given paramter
-//is a valid paramter for the given command.
-bool ErrorCheck::validCommandParameter(string parameter, string commandName) {
-	try {
-		for(int i = 0; i < commandParameters[commandName].size(); i++)
-			if(parameter.compare(commandParameters[commandName][i]) == 0)
-				return true;
-		return false;
-	}
-		
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-}
-/*******************************************************/
-
-/******************************************************/
-//This function checks to see if the given paramter value
-//is convertable into an int if that parameter requires it.
-bool ErrorCheck::validParameterValue(string value, string parameter) {
-	try {
-		int pVal;
-		if(intParams.count(parameter) == 1)
-		{
-			vector<double> bounds = intParams[parameter];
-			bool valid = convertTest(value, pVal);
-			if(!valid)
-				return false;
-			if(parameter.compare("precision") == 0)
-			{
-				double logNum = log10((double)pVal);
-				double diff = (double)((int)logNum - logNum);
-				if(diff != 0)
-					return false;
-			}
-			double a = bounds.at(0);
-			double b = bounds.at(1);
-			double c = bounds.at(2);
-			double d = bounds.at(3);
-			double e = bounds.at(4);
-			bool a0 = pVal > a;
-			bool a1 = pVal >= a;
-			bool b0 = pVal < b;
-			bool b1 = pVal <= b;
-			
-			if(c != 1)
-			{
-				if(a == piSent && b == piSent)
-					return true;
-				if(a != piSent && b == piSent)
-				{
-					if(d == 0)
-						return a0;
-					else
-						return a1;
-				}
-				else if(a == piSent && b != piSent)
-				{
-					if(e == 0)
-						return b0;
-					else
-						return b1;
-				}
-				else
-				{
-					if(d == 0 && e == 0)
-						return (a0 && b0);
-					else if(d == 0 && e == 1)
-						return (a0 && b1);
-					else if(d == 1 && e == 0)
-						return (a1 && b0);
-					else
-						return (a1 && b1);
-				}
-			}
-			else
-			{
-				if(a == piSent && b == piSent)
-					return true;
-				if(a != piSent && b == piSent)
-					return (pVal == a);
-				else if(a == piSent && b != piSent)
-					return (pVal == b);
-				else
-					return (pVal == a || pVal == b);
-			}
-		}
-		return true;
-	}
-		
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. 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
@@ -601,8 +402,15 @@ void ErrorCheck::validateReadDist() {
 		ifstream filehandle;
 		int ableToOpen;
 		
-		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 (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 == "") {
@@ -651,7 +459,7 @@ void ErrorCheck::validateParseFiles() {
 				ableToOpen = openInputFile(groupfile, filehandle);
 				filehandle.close();
 				if (ableToOpen == 1) { //unable to open
-					errorFree = false;;
+					errorFree = false;
 				}
 			}
 		}
@@ -726,7 +534,7 @@ void ErrorCheck::validateReadPhil() {
 		}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 == "")) {
+		}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; 
 		}
 		
@@ -750,6 +558,137 @@ 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() {
@@ -763,6 +702,10 @@ void ErrorCheck::clear() {
 	groupfile		=	""; 
 	orderfile		=	"";
 	sharedfile		=	"";
+	fastafile       =   "";
+	nexusfile       =   "";
+	clustalfile     =   "";
+	candidatefile	=	"";
 	line			=	"";
 	label			=	"";
 	method			=   "furthest";