X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=3b03f3694967d6d480ba0dc00153454c7e8b074f;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=a38aeb30dea60a2fe67984fa05dc83b6fb9130e1;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index a38aeb3..3b03f36 100644
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -24,7 +24,7 @@ vector<string> GetRAbundCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetRAbundCommand::GetRAbundCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["rabund"] = tempOutNames;
 	}
@@ -61,12 +61,12 @@ vector<string> GetRAbundCommand::getRequiredFiles(){
 GetRAbundCommand::GetRAbundCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		allLines = 1;
 		labels.clear();
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -157,7 +157,7 @@ GetRAbundCommand::~GetRAbundCommand(){}
 int GetRAbundCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//read first line
 		read = new ReadOTUFile(globaldata->inputFileName);	
@@ -262,6 +262,13 @@ int GetRAbundCommand::execute(){
 		
 		globaldata->gListVector = NULL;
 		
+		//set rabund file as new current rabundfile
+		string current = "";
+		itTypes = outputTypes.find("rabund");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+		}
+		
 		return 0;		
 	}