#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();
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; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
commandFactory = CommandFactory::getInstance();