X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setlogfilecommand.cpp;h=41c8e743122399563b8367fda6a9d4a94f9bda86;hp=19f3ed129ab85b9f66dbea06c56637ea2f8daa42;hb=b25ede2ad307ae76f8a610443e0ec3ec69621ce7;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index 19f3ed1..41c8e74 100644
--- a/setlogfilecommand.cpp
+++ b/setlogfilecommand.cpp
@@ -9,19 +9,52 @@
 
 #include "setlogfilecommand.h"
 
+
+//**********************************************************************************************************************
+vector<string> SetLogFileCommand::setParameters(){	
+	try {
+		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);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SetLogFileCommand", "setParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string SetLogFileCommand::getHelpString(){	
+	try {
+		string helpString = "";
+		helpString += "The set.logfile command can be used to provide a specific name for your logfile and/or to append the log generated by mothur to an existing file.\n";
+		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";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SetLogFileCommand", "getHelpString");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 SetLogFileCommand::SetLogFileCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		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();
@@ -44,35 +77,22 @@ SetLogFileCommand::SetLogFileCommand(string option)  {
 		exit(1);
 	}
 }
-//**********************************************************************************************************************
-
-void SetLogFileCommand::help(){
-	try {
-		m->mothurOut("The set.logfile command can be used to provide a specific name for your logfile and/or to append the log generated by mothur to an existing file.\n");
-		m->mothurOut("The set.logfile command parameters are name and append, name is required. Append is set to false by default.\n");
-		m->mothurOut("The set.logfile command should be in the following format: set.logfile(name=yourLogFileName, append=T).\n");
-		m->mothurOut("Example set.logfile(name=/Users/lab/desktop/output.txt, append=T).\n");
-		m->mothurOut("Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n\n");
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SetLogFileCommand", "help");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-
-SetLogFileCommand::~SetLogFileCommand(){}
 
 //**********************************************************************************************************************
 
 int SetLogFileCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
-		
-		commandFactory = CommandFactory::getInstance();
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		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;
 	}