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/*
* 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,true); parameters.push_back(pname);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
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";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SetLogFileCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
SetLogFileCommand::SetLogFileCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
name = validParameter.validPath(parameters, "name");
if (name == "not found") { m->mothurOut("name is a required parameter for the set.logfile command."); abort = true; }
string temp = validParameter.valid(parameters, "append"); if (temp == "not found") { temp = "F"; }
append = util.isTrue(temp);
if (outputdir == ""){ outputdir = util.hasPath(name); }
}
}
catch(exception& e) {
m->errorOut(e, "SetLogFileCommand", "SetLogFileCommand");
exit(1);
}
}
//**********************************************************************************************************************
int SetLogFileCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
string directory = util.hasPath(name);
if (directory == "") {
m->setLogFileName(outputdir+name, append);
}else if (util.dirCheckWritable(directory)) {
m->setLogFileName(name, append);
}
m->mothurOut("\nSetting logfile name to " + m->getLogFileName() + "\n\n");
return 0;
}
catch(exception& e) {
m->errorOut(e, "SetLogFileCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************/
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