X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=aa223a20379d1fd590908fbb5aa92c7a38cbf03b;hb=fe342304a0fdff3ab48226e1dcfdab95d3a94a64;hp=1d60a4a35a8e7252e8f318a4997f91abdf102a51;hpb=16bea3130e36addc54e2116dfbcd02d706ebee45;p=mothur.git

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 1d60a4a..aa223a2 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -23,28 +23,31 @@ 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();
-	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;
+}
 
 /*******************************************************/
 
@@ -73,6 +76,7 @@ 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
@@ -80,7 +84,7 @@ bool ErrorCheck::checkInput(string input) {
 				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 == "phylip" )		{ phylipfile = value; }
 				if (parameter == "column" )		{ columnfile = value; }
@@ -102,8 +106,11 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "fileroot" )		{ fileroot = value; }
 				if (parameter == "line" )			{ line = value; }
 				if (parameter == "label" )			{ label = value; }
+				if (parameter == "abund" )          { abund = value; }
 				if (parameter == "random" )			{ randomtree = value;	}
-
+				if (parameter == "sorted" )			{ sorted = value;	}
+				if (parameter == "scale" )			{ scale = value;	}
+				
 			}
 			
 			//gets the last parameter and value
@@ -111,7 +118,8 @@ bool ErrorCheck::checkInput(string input) {
 				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 == "phylip" )		{ phylipfile = value; }
 				if (parameter == "column" )		{ columnfile = value; }				
@@ -134,13 +142,16 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "line" )			{ line = value; }
 				if (parameter == "label" )			{ label = value; }
 				if (parameter == "random" )			{ randomtree = value;	}
-
+				if (parameter == "abund" )          { abund = value; }
+				if (parameter == "sorted" )			{ sorted = value;	}
+				if (parameter == "scale" )			{ scale = 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();
@@ -148,13 +159,17 @@ 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") {
@@ -163,12 +178,16 @@ bool ErrorCheck::checkInput(string input) {
 		}
 		
 		//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 == "")  {
@@ -183,6 +202,12 @@ bool ErrorCheck::checkInput(string input) {
 		}
 		
 		//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; }
@@ -192,13 +217,34 @@ bool ErrorCheck::checkInput(string input) {
 			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 == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.shared") || (commandName == "bootstrap.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 or bootstrap.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 or bootstrap.shared 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;
 }
 
@@ -220,7 +266,7 @@ 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();
@@ -284,6 +330,13 @@ void ErrorCheck::validateReadDist() {
 		ifstream filehandle;
 		int ableToOpen;
 		
+		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 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; }
 		
@@ -409,7 +462,7 @@ 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; 
 		}
 		
@@ -433,6 +486,58 @@ void ErrorCheck::validateReadPhil() {
 }
 /*******************************************************/
 
+/******************************************************/
+//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() {