X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setlogfilecommand.cpp;h=329fd1fdbeb28ba673c883eeb6ea36fe059c64fc;hp=88c792c8b4b485bb8019a45fcac8c09f420511d6;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=d4429ccc354708f3c9a13c809ba9b57c22908d2b

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index 88c792c..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);		}
@@ -51,6 +51,7 @@ 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 {
 			vector<string> myArray = setParameters();
@@ -84,9 +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;
 	}