+++ /dev/null
-/*
- * 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 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<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 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<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 = ""; }
-
- 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);
- }
-}
-//**********************************************************************************************************************/
projects / mothur.git / blobdiff