X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=39fb17e47a4e2f72692f5d5be15f19866fca2bef;hb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;hp=4eef3b041aaf724e87efb980c6115c9cc78036ce;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 4eef3b0..39fb17e 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -23,21 +23,23 @@ 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();
+
 }
 
 /*******************************************************/
@@ -74,7 +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
@@ -85,8 +86,6 @@ bool ErrorCheck::checkInput(string input) {
 				
 				//is it a valid parameter
 				if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
-
-
 				
 				if (parameter == "phylip" )		{ phylipfile = value; }
 				if (parameter == "column" )		{ columnfile = value; }
@@ -96,9 +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; }
@@ -109,10 +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 == "sorted" )			{ sorted = 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
@@ -133,6 +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; }
@@ -146,7 +162,22 @@ bool ErrorCheck::checkInput(string input) {
 				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;	}
+				
 			}
 		}
 		
@@ -179,7 +210,7 @@ bool ErrorCheck::checkInput(string input) {
 			validateReadFiles();
 		}
 		
-		//are you trying to cluster before you have read something			
+		//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; 
@@ -198,14 +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; }
@@ -219,10 +250,19 @@ 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") || (commandName == "tree.shared") || (commandName == "bootstrap.shared")){ 
+		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 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 (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();
 			}
 		}
 		
@@ -232,17 +272,33 @@ bool ErrorCheck::checkInput(string input) {
 			}
 		}
 		
+		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 == "bin.seqs")) { 
-			if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
+			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();
 		} 
 
@@ -308,6 +364,12 @@ 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;
 		}
@@ -339,8 +401,8 @@ void ErrorCheck::validateReadDist() {
 			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; }
+		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 == "") {
@@ -389,7 +451,7 @@ void ErrorCheck::validateParseFiles() {
 				ableToOpen = openInputFile(groupfile, filehandle);
 				filehandle.close();
 				if (ableToOpen == 1) { //unable to open
-					errorFree = false;;
+					errorFree = false;
 				}
 			}
 		}
@@ -488,6 +550,77 @@ 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
@@ -497,7 +630,7 @@ void ErrorCheck::validateBinFiles() {
 		int ableToOpen;
 		
 		if (fastafile == "") {
-				cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false; 
+				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);
@@ -524,9 +657,17 @@ void ErrorCheck::validateBinFiles() {
 			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";
@@ -553,6 +694,10 @@ void ErrorCheck::clear() {
 	groupfile		=	""; 
 	orderfile		=	"";
 	sharedfile		=	"";
+	fastafile       =   "";
+	nexusfile       =   "";
+	clustalfile     =   "";
+	candidatefile	=	"";
 	line			=	"";
 	label			=	"";
 	method			=   "furthest";