X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=a76db24282e2c00032ec747de2d1d5decf20e095;hb=264c8a3c759d9a999c485236e98dac98d4f0db5f;hp=407e57bfcaca82628aa60923e9bcb687a6a25416;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git diff --git a/setdircommand.cpp b/setdircommand.cpp index 407e57b..a76db24 100644 --- a/setdircommand.cpp +++ b/setdircommand.cpp @@ -9,18 +9,52 @@ #include "setdircommand.h" +//********************************************************************************************************************** +vector SetDirectoryCommand::getValidParameters(){ + try { + string Array[] = {"output","input","tempdefault","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SetDirectoryCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector SetDirectoryCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SetDirectoryCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector SetDirectoryCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SetDirectoryCommand", "getRequiredFiles"); + 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"}; + string Array[] = {"output","input","tempdefault","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -37,9 +71,12 @@ 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; } } } @@ -54,10 +91,15 @@ 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("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"); + m->mothurOut("The set.dir command parameters are input, output and tempdefault and one 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("To return the input to the current working directory you may enter: input=clear.\n"); + m->mothurOut("To set the output to the directory where mothur.exe is located you may enter: output=default.\n"); + m->mothurOut("To set the input to the directory where mothur.exe is located you may enter: input=default.\n"); + m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n"); + m->mothurOut("To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n"); + m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\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"); } @@ -75,14 +117,20 @@ SetDirectoryCommand::~SetDirectoryCommand(){} int SetDirectoryCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } commandFactory = CommandFactory::getInstance(); - //redirect output if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); } - else { + else if (output == "default") { + GlobalData* globaldata = GlobalData::getInstance(); + string exepath = globaldata->argv; + output = exepath.substr(0, (exepath.find_last_of('m'))); + + m->mothurOut("Changing output directory to " + 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) @@ -92,7 +140,7 @@ 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); @@ -108,7 +156,14 @@ int SetDirectoryCommand::execute(){ //redirect input if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); } - else { + else if (input == "default") { + GlobalData* globaldata = GlobalData::getInstance(); + string exepath = globaldata->argv; + input = exepath.substr(0, (exepath.find_last_of('m'))); + + m->mothurOut("Changing input directory to " + 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) @@ -118,7 +173,7 @@ 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); @@ -131,11 +186,43 @@ int SetDirectoryCommand::execute(){ commandFactory->setInputDirectory(input); } } + + //set default + if (tempdefault == "clear") { + #ifdef MOTHUR_FILES + string temp = MOTHUR_FILES; + m->mothurOut("Resetting default directory to " + 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") { + GlobalData* globaldata = GlobalData::getInstance(); + string exepath = globaldata->argv; + tempdefault = exepath.substr(0, (exepath.find_last_of('m'))); + + m->mothurOut("Changing default directory to " + 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("Changing default directory to " + tempdefault); m->mothurOutEndLine(); + m->setDefaultPath(tempdefault); + } return 0; } catch(exception& e) { - m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand"); + m->errorOut(e, "SetDirectoryCommand", "execute"); exit(1); } }