fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / setlogfilecommand.cpp

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index 00e702c7b86d3d7bd16dfa5a162250f49402dae1..576a37c11a26a656d34a9af69972dc4c3a329233 100644 (file)
--- a/setlogfilecommand.cpp
+++ b/setlogfilecommand.cpp
@@ -35,7 +35,7 @@ string SetLogFileCommand::getHelpString(){
                helpString += "The set.logfile command parameters are name and append, name is required. Append is set to false by default.\n";
                helpString += "The set.logfile command should be in the following format: set.logfile(name=yourLogFileName, append=T).\n";
                helpString += "Example set.logfile(name=/Users/lab/desktop/output.txt, append=T).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -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();