X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setlogfilecommand.cpp;h=128c5671ed55712d2293e0b3c3959da17a7e9f05;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=00e702c7b86d3d7bd16dfa5a162250f49402dae1;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index 00e702c..128c567 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);		}
@@ -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();