moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / setlogfilecommand.cpp

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
deleted file mode 100644 (file)
index 576a37c..0000000
--- a/setlogfilecommand.cpp
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- *  setlogfilecommand.cpp
- *  Mothur
- *
- *  Created by westcott on 4/27/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#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); 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; calledHelp = false;   
-               
-               //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();
-                       
-                       OptionParser parser(option);
-                       map<string, string> parameters = parser.getParameters();
-                       
-                       ValidParameters validParameter;
-                       //check to make sure all parameters are valid for command
-                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
-                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
-                       }
-               
-                       name = validParameter.validFile(parameters, "name", false);                     
-                       if (name == "not found") {  m->mothurOut("name is a required parameter for the set.logfile command."); abort = true; } 
-                       
-                       string temp = validParameter.validFile(parameters, "append", false);            if (temp == "not found") {  temp = "F";  }
-                       append = m->isTrue(temp);
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SetLogFileCommand", "SetLogFileCommand");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
-int SetLogFileCommand::execute(){
-       try {
-               
-               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
-               
-               commandFactory = CommandFactory::getInstance();
-               
-               commandFactory->setLogfileName(name, append);
-               
-               return 0;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SetLogFileCommand", "execute");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************/