fixes while testing 1.33.0

[mothur.git] / setlogfilecommand.cpp

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index 88c792c8b4b485bb8019a45fcac8c09f420511d6..329fd1fdbeb28ba673c883eeb6ea36fe059c64fc 100644 (file)
--- 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;
        }