X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setlogfilecommand.cpp;h=329fd1fdbeb28ba673c883eeb6ea36fe059c64fc;hp=0a3dfc974f1d6ca45352b712efea37a2df02daf0;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index 0a3dfc9..329fd1f 100644
--- a/setlogfilecommand.cpp
+++ b/setlogfilecommand.cpp
@@ -13,10 +13,10 @@
 //**********************************************************************************************************************
 vector<string> SetLogFileCommand::setParameters(){	
 	try {
-		CommandParameter pappend("append", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pappend);
-		CommandParameter pname("name", "String", "", "", "", "", "",false,true); parameters.push_back(pname);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pappend("append", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pappend);
+		CommandParameter pname("name", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pname);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -51,11 +51,10 @@ SetLogFileCommand::SetLogFileCommand(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 {
-			//valid paramters for this command
-			string Array[] =  {"name","append","outputdir","inputdir"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string, string> parameters = parser.getParameters();
@@ -86,9 +85,14 @@ int SetLogFileCommand::execute(){
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		commandFactory = CommandFactory::getInstance();
-		
-		commandFactory->setLogfileName(name, append);
+        commandFactory = CommandFactory::getInstance();
+        
+        string directory = m->hasPath(name);
+        if (directory == "") {
+            commandFactory->setLogfileName(name, append);
+        }else if (m->dirCheck(directory)) {
+            commandFactory->setLogfileName(name, append);
+        }
 		
 		return 0;
 	}