X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=34a072b30a0b563fd22ddef60099224bdc6bf9f0;hb=a4f05f09c250323132a4b9427f41a3ededaec634;hp=6042bbecebf848b7a37d158293dc7650d2587c51;hpb=5c076cc7d3842d8050694918948e023334c9839e;p=mothur.git

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 6042bbe..34a072b 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -27,8 +27,7 @@ vector<string> RemoveGroupsCommand::getValidParameters(){
 //**********************************************************************************************************************
 RemoveGroupsCommand::RemoveGroupsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["taxonomy"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> RemoveGroupsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//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
@@ -222,7 +221,7 @@ void RemoveGroupsCommand::help(){
 int RemoveGroupsCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		groupMap = new GroupMap(groupfile);
 		groupMap->readMap();
@@ -259,6 +258,33 @@ int RemoveGroupsCommand::execute(){
 			m->mothurOut("Output File names: "); m->mothurOutEndLine();
 			for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
 			m->mothurOutEndLine();
+			
+			//set fasta file as new current fastafile
+			string current = "";
+			itTypes = outputTypes.find("fasta");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+			}
+			
+			itTypes = outputTypes.find("name");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+			}
+			
+			itTypes = outputTypes.find("group");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+			}
+			
+			itTypes = outputTypes.find("list");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+			}
+			
+			itTypes = outputTypes.find("taxonomy");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+			}
 		}
 		
 		return 0;		
@@ -588,6 +614,8 @@ int RemoveGroupsCommand::fillNames(){
 				names.insert(seqs[i]);
 			}
 		}
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "RemoveGroupsCommand", "fillNames");