X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=5f587a9b83a1a140409fc0cbdfa4bba0169ea518;hb=cfb66eb46a9678a751a8f21f3ea740dffd525f5e;hp=067d246d4c50f1427840c3879be04bac2ff7cdf8;hpb=b2dca66a02f8f82aa5528e531eace60fbbd2967b;p=mothur.git

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 067d246..5f587a9 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -17,7 +17,6 @@ ErrorCheck::ErrorCheck() {
 	globaldata = GlobalData::getInstance();
 	validCommand = new ValidCommands();
 	validParameter = new ValidParameters();
-	validCalculator = new ValidCalculators();
 }
 /*******************************************************/
 
@@ -38,6 +37,7 @@ void ErrorCheck::refresh() {
 	format = globaldata->getFormat();
 	method = globaldata->getMethod();
 	randomtree = globaldata->getRandomTree();
+	sharedfile = globaldata->getSharedFile();
 }
 
 /*******************************************************/
@@ -73,14 +73,15 @@ 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) != true) { return false; }
 				
 				if (parameter == "phylip" )		{ phylipfile = value; }
 				if (parameter == "column" )		{ columnfile = value; }
@@ -92,6 +93,7 @@ bool ErrorCheck::checkInput(string input) {
 				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; }
@@ -101,56 +103,16 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "fileroot" )		{ fileroot = value; }
 				if (parameter == "line" )			{ line = value; }
 				if (parameter == "label" )			{ label = value; }
-				if (parameter == "randomtree" )		{ randomtree = 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;	}
 			}
 			
 			//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) != true) { return false; }
 				
 				if (parameter == "phylip" )		{ phylipfile = value; }
 				if (parameter == "column" )		{ columnfile = value; }				
@@ -160,6 +122,7 @@ bool ErrorCheck::checkInput(string input) {
 				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; }
@@ -171,55 +134,13 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "fileroot" )		{ fileroot = value; }
 				if (parameter == "line" )			{ line = value; }
 				if (parameter == "label" )			{ label = value; }
-				if (parameter == "randomtree" )		{ randomtree = 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; }
 			}
 		}
 		
 		//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; }
-	
 		
 		if (commandName == "read.dist") { 
 			validateReadFiles();
@@ -228,9 +149,13 @@ 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
+			}else if (listfile != "") { //you want to do single commands
 				validateReadFiles();
 				validateReadPhil();
+			}else if ((listfile == "") && (sharedfile == "")) {
+				cout << "You must enter either a listfile or a sharedfile with the read.otu command. " << endl; return false; 
+			}else{//you are reading a shared file
+				validateReadFiles();
 			}
 		}else if (commandName == "read.tree") { 
 			validateTreeFiles(); //checks the treefile and groupfile parameters
@@ -240,17 +165,21 @@ 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)) {
+			 cout << "You must read in a matrix 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 == "0")  {
-				if ((globaldata->getTreeFile() == "") || (globaldata->getGroupFile() == "")) {
-					cout << "You must read a treefile and a groupfile or set the randomtree parameter to 1, before you may execute the parsimony command." << endl; return false;  }
+			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;  }
 			}
 		}
 		
@@ -260,6 +189,12 @@ 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; }
@@ -270,11 +205,12 @@ bool ErrorCheck::checkInput(string input) {
 		}
 		
 		if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){ 
-			if (globaldata->getListFile() == "") { cout << "You must read a list and a group 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 before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+			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; }
+			}
 		}
- 
-		
+
 		return errorFree;
 }
 
@@ -296,7 +232,7 @@ 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();
@@ -330,6 +266,12 @@ 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{ //no file given
 			errorFree = false;
 		}
@@ -354,6 +296,13 @@ 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; }
 		
@@ -515,6 +464,7 @@ void ErrorCheck::clear() {
 	namefile		=	"";
 	groupfile		=	""; 
 	orderfile		=	"";
+	sharedfile		=	"";
 	line			=	"";
 	label			=	"";
 	method			=   "furthest";