X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=ff1e2fe0709cf7e4d6549cc11a227ff9dc355e3f;hb=ae9c5b48da9047548f86fc84897926d9f5102312;hp=214bd172e80208f246bede7978ad69329f6e23db;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git diff --git a/setdircommand.cpp b/setdircommand.cpp index 214bd17..ff1e2fe 100644 --- a/setdircommand.cpp +++ b/setdircommand.cpp @@ -10,36 +10,44 @@ #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(){ +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", "getRequiredParameters"); + m->errorOut(e, "SetDirectoryCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector SetDirectoryCommand::getRequiredFiles(){ +string SetDirectoryCommand::getHelpString(){ try { - vector myArray; - return myArray; + 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", "getRequiredFiles"); + m->errorOut(e, "SetDirectoryCommand", "getHelpString"); exit(1); } } @@ -47,15 +55,14 @@ vector SetDirectoryCommand::getRequiredFiles(){ 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 if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"output","input","tempdefault","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -87,48 +94,22 @@ 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 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 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"); - } - 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 if (output == "default") { - GlobalData* globaldata = GlobalData::getInstance(); - string exepath = globaldata->argv; + string exepath = m->argv; output = exepath.substr(0, (exepath.find_last_of('m'))); - m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine(); + m->mothurOut("outputDir=" + output); m->mothurOutEndLine(); commandFactory->setOutputDirectory(output); }else { //add / to name if needed @@ -149,7 +130,7 @@ 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); } } @@ -157,11 +138,10 @@ int SetDirectoryCommand::execute(){ //redirect input if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); } else if (input == "default") { - GlobalData* globaldata = GlobalData::getInstance(); - string exepath = globaldata->argv; + string exepath = m->argv; input = exepath.substr(0, (exepath.find_last_of('m'))); - m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine(); + m->mothurOut("inputDir=" + input); m->mothurOutEndLine(); commandFactory->setInputDirectory(input); }else { //add / to name if needed @@ -182,7 +162,7 @@ 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); } } @@ -191,7 +171,7 @@ int SetDirectoryCommand::execute(){ if (tempdefault == "clear") { #ifdef MOTHUR_FILES string temp = MOTHUR_FILES; - m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine(); + m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine(); m->setDefaultPath(temp); #else string temp = ""; @@ -200,11 +180,10 @@ int SetDirectoryCommand::execute(){ #endif }else if (tempdefault == "") { //do nothing }else if (tempdefault == "default") { - GlobalData* globaldata = GlobalData::getInstance(); - string exepath = globaldata->argv; + string exepath = m->argv; tempdefault = exepath.substr(0, (exepath.find_last_of('m'))); - m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine(); + m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine(); m->setDefaultPath(tempdefault); }else { //add / to name if needed @@ -215,7 +194,7 @@ int SetDirectoryCommand::execute(){ if (lastChar != "\\") { tempdefault += "\\"; } #endif - m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine(); + m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine(); m->setDefaultPath(tempdefault); }