X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=setdircommand.cpp;h=3135b8133c851e5fe58a13ee32e29da05da90216;hb=55ec7cde88d5512e177fe9488d5ee13793853bad;hp=b6626b872d31030d791362ec8ebf68f3f3aaa3e6;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git diff --git a/setdircommand.cpp b/setdircommand.cpp index b6626b8..3135b81 100644 --- a/setdircommand.cpp +++ b/setdircommand.cpp @@ -9,19 +9,59 @@ #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; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { - //valid paramters for this command - string Array[] = {"output","input","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -37,9 +77,12 @@ SetDirectoryCommand::SetDirectoryCommand(string option) { 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 == "")) { - m->mothurOut("You must provide either an input or output for the set.outdir command."); m->mothurOutEndLine(); abort = true; + if ((input == "") && (output == "") && (tempdefault == "")) { + m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true; } } } @@ -50,38 +93,24 @@ SetDirectoryCommand::SetDirectoryCommand(string option) { } //********************************************************************************************************************** -void SetDirectoryCommand::help(){ - try { - m->mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n"); - m->mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n"); - m->mothurOut("The set.dir command parameter is output and is required.\n"); - m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n"); - m->mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n"); - m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory).\n"); - m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "SetDirectoryCommand", "help"); - exit(1); - } -} -//********************************************************************************************************************** - -SetDirectoryCommand::~SetDirectoryCommand(){} - -//********************************************************************************************************************** - int SetDirectoryCommand::execute(){ try { - if (abort == true) { return 0; } + 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 { + 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 { //add / to name if needed string lastChar = output.substr(output.length()-1); #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) @@ -91,7 +120,7 @@ int SetDirectoryCommand::execute(){ #endif //test to make sure directory exists - output = getFullPathName(output); + output = m->getFullPathName(output); string outTemp = output + "temp"; ofstream out; out.open(outTemp.c_str(), ios::trunc); @@ -100,14 +129,20 @@ int SetDirectoryCommand::execute(){ }else{ out.close(); remove(outTemp.c_str()); - m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine(); + m->mothurOut("outputDir=" + output); m->mothurOutEndLine(); commandFactory->setOutputDirectory(output); } } //redirect input if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); } - else { + 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 { //add / to name if needed string lastChar = input.substr(input.length()-1); #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) @@ -117,7 +152,7 @@ int SetDirectoryCommand::execute(){ #endif //test to make sure directory exists - input = getFullPathName(input); + input = m->getFullPathName(input); string inTemp = input + "temp"; ofstream in; in.open(inTemp.c_str(), ios::trunc); @@ -126,15 +161,46 @@ int SetDirectoryCommand::execute(){ }else{ in.close(); remove(inTemp.c_str()); - m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine(); + 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 { + //add / to name if needed + string lastChar = tempdefault.substr(tempdefault.length()-1); + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if (lastChar != "/") { tempdefault += "/"; } + #else + if (lastChar != "\\") { tempdefault += "\\"; } + #endif + + m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine(); + m->setDefaultPath(tempdefault); + } return 0; } catch(exception& e) { - m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand"); + m->errorOut(e, "SetDirectoryCommand", "execute"); exit(1); } }