X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=06524921a4db4670bdb4a7253977178f468c9b19;hb=0024441c1ff9a98467ba53cc7420a37c98f32e86;hp=8b80580a26faf27b8504f55039e494952a9f1be9;hpb=cdcf99b7760701e6869ca8e4e6e91c8e8c4ae186;p=mothur.git

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 8b80580..0652492 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -236,7 +236,7 @@ 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 ((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; }
@@ -246,17 +246,34 @@ 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") || (commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.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, 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; 
@@ -289,6 +306,7 @@ bool ErrorCheck::checkInput(string input) {
 				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();
 		} 
 
@@ -354,6 +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;
 		}
@@ -385,8 +409,8 @@ 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 == "") {
@@ -435,7 +459,7 @@ void ErrorCheck::validateParseFiles() {
 				ableToOpen = openInputFile(groupfile, filehandle);
 				filehandle.close();
 				if (ableToOpen == 1) { //unable to open
-					errorFree = false;;
+					errorFree = false;
 				}
 			}
 		}