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/*
* setoutdircommand.cpp
* Mothur
*
* Created by westcott on 1/21/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "setdircommand.h"
//**********************************************************************************************************************
vector<string> SetDirectoryCommand::setParameters(){
try {
CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault);
CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug);
CommandParameter pmodnames("modifynames", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmodnames);
CommandParameter pinput("input", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pinput);
CommandParameter poutput("output", "String", "", "", "", "", "","",false,false,true); parameters.push_back(poutput);
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, "SetDirectoryCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string SetDirectoryCommand::getHelpString(){
try {
string helpString = "";
helpString += "The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n";
helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
helpString += "The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n";
helpString += "The set.dir command can also be used to run mothur in debug mode.\n";
helpString += "The set.dir command can also be used to set the modifynames parameter. Default=t, meaning if your sequence names contain ':' change them to '_' to avoid issues while making trees. modifynames=F will leave sequence names as they are.\n";
helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n";
helpString += "To run mothur in debug mode set debug=true. Default debug=false.\n";
helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";
helpString += "To return the input to the current working directory you may enter: input=clear.\n";
helpString += "To set the output to the directory where mothur.exe is located you may enter: output=default.\n";
helpString += "To set the input to the directory where mothur.exe is located you may enter: input=default.\n";
helpString += "To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n";
helpString += "To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n";
helpString += "The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n";
helpString += "Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n";
helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SetDirectoryCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
SetDirectoryCommand::SetDirectoryCommand(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; }
}
output = validParameter.validFile(parameters, "output", false);
if (output == "not found") { output = ""; }
input = validParameter.validFile(parameters, "input", false);
if (input == "not found") { input = ""; }
tempdefault = validParameter.validFile(parameters, "tempdefault", false);
if (tempdefault == "not found") { tempdefault = ""; }
bool debug = false;
bool nodebug = false;
debugOnly = false;
string temp = validParameter.validFile(parameters, "debug", false);
if (temp == "not found") { debug = false; nodebug=true; }
else { debug = m->isTrue(temp); }
m->debug = debug;
bool nomod = false;
temp = validParameter.validFile(parameters, "modifynames", false);
if (temp == "not found") { modifyNames = true; nomod=true; }
else { modifyNames = m->isTrue(temp); }
m->modifyNames = modifyNames;
if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); }
if ((input == "") && (output == "") && (tempdefault == "") && nodebug && nomod) {
m->mothurOut("You must provide either an input, output, tempdefault, debug or modifynames for the set.outdir command."); m->mothurOutEndLine(); abort = true;
}else if((input == "") && (output == "") && (tempdefault == "")) { debugOnly = true; }
}
}
catch(exception& e) {
m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
exit(1);
}
}
//**********************************************************************************************************************
int SetDirectoryCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (debugOnly) { }
else {
commandFactory = CommandFactory::getInstance();
m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
//redirect output
if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
else if (output == "default") {
string exepath = m->argv;
output = exepath.substr(0, (exepath.find_last_of('m')));
m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
commandFactory->setOutputDirectory(output);
}else {
if (m->dirCheck(output)) {
m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
commandFactory->setOutputDirectory(output);
}
}
//redirect input
if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); }
else if (input == "default") {
string exepath = m->argv;
input = exepath.substr(0, (exepath.find_last_of('m')));
m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
commandFactory->setInputDirectory(input);
}else {
if (m->dirCheck(input)) {
m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
commandFactory->setInputDirectory(input);
}
}
//set default
if (tempdefault == "clear") {
#ifdef MOTHUR_FILES
string temp = MOTHUR_FILES;
m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
m->setDefaultPath(temp);
#else
string temp = "";
m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();
m->setDefaultPath(temp);
#endif
}else if (tempdefault == "") { //do nothing
}else if (tempdefault == "default") {
string exepath = m->argv;
tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
m->setDefaultPath(tempdefault);
}else {
if (m->dirCheck(tempdefault)) {
m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
m->setDefaultPath(tempdefault);
}
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SetDirectoryCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************/
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