X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=5a33253ff1ec2b67a9e995b940f09349241494f5;hb=d205e70ae86dbee2efc2df02f2717975854de6ba;hp=570d64e34166cafcf734181a370dd9fc854e64a3;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 570d64e..5a33253 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
@@ -183,19 +184,17 @@ int GetRAbundCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) {  outputTypes.clear();  out.close(); remove(filename.c_str()); delete rabund; delete input; return 0; }
+		if (m->control_pressed) {  outputTypes.clear();  out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; }
 		
 		while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
 			if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 					m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 					
-					if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+					if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
 					
 					if(sorted)	{   rabund->print(out);				}
 					else		{	rabund->nonSortedPrint(out);	}
-					
-					delete rabund;
 															
 					processedLabels.insert(rabund->getLabel());
 					userLabels.erase(rabund->getLabel());
@@ -209,13 +208,11 @@ int GetRAbundCommand::execute(){
 					
 					m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 					
-					if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+					if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
 					
 					if(sorted)	{   rabund->print(out);				}
 					else		{	rabund->nonSortedPrint(out);	}
 
-					delete rabund;
-
 					processedLabels.insert(rabund->getLabel());
 					userLabels.erase(rabund->getLabel());
 					
@@ -249,7 +246,7 @@ int GetRAbundCommand::execute(){
 			
 			m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 					
-			if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0; }
 			
 			if(sorted)	{   rabund->print(out);				}
 			else		{	rabund->nonSortedPrint(out);	}