X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrelabundcommand.cpp;h=8c8d8e1539b8be7e76656be1304ee1f1f01f9a02;hb=e339f9008daa7d37c9a9034829565620a6abe783;hp=74ec992a001e16a91d131a376944165aca1b4622;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 74ec992..8c8d8e1 100644
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -69,6 +69,7 @@ GetRelAbundCommand::GetRelAbundCommand(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();
@@ -110,7 +111,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
 				sharedfile = m->getSharedFile(); 
 				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setSharedFile(sharedfile); }
 			
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -130,7 +131,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
 			else { 
 				pickedGroups = true;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			scale = validParameter.validFile(parameters, "scale", false);				if (scale == "not found") { scale = "totalgroup"; }
@@ -169,11 +170,12 @@ int GetRelAbundCommand::execute(){
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
-			if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
 	
 			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){			
 
 				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+				if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 				getRelAbundance(lookup, out);
 				
 				processedLabels.insert(lookup[0]->getLabel());
@@ -186,7 +188,7 @@ int GetRelAbundCommand::execute(){
 				for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  
 				lookup = input->getSharedRAbundVectors(lastLabel);
 				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-				
+				if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 				getRelAbundance(lookup, out);
 				
 				processedLabels.insert(lookup[0]->getLabel());
@@ -200,13 +202,13 @@ int GetRelAbundCommand::execute(){
 			//prevent memory leak
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 			
-			if (m->control_pressed) {  outputTypes.clear();  m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) {  outputTypes.clear();  m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
 
 			//get next line to process
 			lookup = input->getSharedRAbundVectors();				
 		}
 		
-		if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str());  return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
@@ -227,18 +229,18 @@ int GetRelAbundCommand::execute(){
 			lookup = input->getSharedRAbundVectors(lastLabel);
 			
 			m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-			
+			if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 			getRelAbundance(lookup, out);
 			
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 		}
 	
 		//reset groups parameter
-		m->Groups.clear();  
+		m->clearGroups();  
 		delete input; 
 		out.close();
 		
-		if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
+		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();