Revert to previous commit

[mothur.git] / setlogfilecommand.cpp

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
new file mode 100644 (file)
index 0000000..576a37c
--- /dev/null
+++ b/setlogfilecommand.cpp
@@ -0,0 +1,99 @@
+/*
+ *  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);
+       }
+}
+//**********************************************************************************************************************/