X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setdircommand.cpp;fp=setdircommand.cpp;h=55b752dba4f40e76f11a46d2608e75d43c0de506;hp=0000000000000000000000000000000000000000;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a diff --git a/setdircommand.cpp b/setdircommand.cpp new file mode 100644 index 0000000..55b752d --- /dev/null +++ b/setdircommand.cpp @@ -0,0 +1,168 @@ +/* + * setoutdircommand.cpp + * Mothur + * + * Created by westcott on 1/21/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "setdircommand.h" + +//********************************************************************************************************************** +vector SetDirectoryCommand::setParameters(){ + try { + CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault); + CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput); + CommandParameter poutput("output", "String", "", "", "", "", "",false,false); 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 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 parameters are input, output and tempdefault and one is required.\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 myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + //check to make sure all parameters are valid for command + for (map::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 = ""; } + + if ((input == "") && (output == "") && (tempdefault == "")) { + m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true; + } + } + } + catch(exception& e) { + m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int SetDirectoryCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + 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); + } +} +//**********************************************************************************************************************/