X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=9c89f7f82f1f93cbaadfa1277d2b1002a7fa3f0b;hb=b72799e7908e2a3a0cf4f03e796b077a97ace6ac;hp=570d64e34166cafcf734181a370dd9fc854e64a3;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 570d64e..9c89f7f 100644
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -39,7 +39,7 @@ string GetRAbundCommand::getHelpString(){
 		helpString += "Example get.rabund(sorted=F).\n";
 		helpString += "The default value for label is all labels in your inputfile.\n";
 		helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -69,6 +69,7 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -115,12 +116,12 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { listfile = ""; abort = true; }
 			else if (listfile == "not found") { listfile = ""; }
-			else {  format = "list"; inputfile = listfile; }
+			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 			
 			sabundfile = validParameter.validFile(parameters, "sabund", true);
 			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
 			else if (sabundfile == "not found") { sabundfile = ""; }
-			else {  format = "sabund"; inputfile = sabundfile; }
+			else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 			
 			
 			//check for optional parameter and set defaults
@@ -194,8 +195,6 @@ int GetRAbundCommand::execute(){
 					
 					if(sorted)	{   rabund->print(out);				}
 					else		{	rabund->nonSortedPrint(out);	}
-					
-					delete rabund;
 															
 					processedLabels.insert(rabund->getLabel());
 					userLabels.erase(rabund->getLabel());
@@ -214,8 +213,6 @@ int GetRAbundCommand::execute(){
 					if(sorted)	{   rabund->print(out);				}
 					else		{	rabund->nonSortedPrint(out);	}
 
-					delete rabund;
-
 					processedLabels.insert(rabund->getLabel());
 					userLabels.erase(rabund->getLabel());