X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setdircommand.cpp;h=42e49a1be039ce16f6ea412ca8b9de15fea106f1;hp=b0d12b87bc49f4d3b6e9cae63558ba622b199701;hb=615301e57c25e241356a9c2380648d117709458d;hpb=42d411d3362186465347aeabdd3155bd3259671e diff --git a/setdircommand.cpp b/setdircommand.cpp index b0d12b8..42e49a1 100644 --- a/setdircommand.cpp +++ b/setdircommand.cpp @@ -12,12 +12,13 @@ //********************************************************************************************************************** vector SetDirectoryCommand::setParameters(){ try { - CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault); - CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdebug); - 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); + CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault); + CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug); + CommandParameter pmodnames("modifynames", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmodnames); + CommandParameter pinput("input", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pinput); + CommandParameter poutput("output", "String", "", "", "", "", "","",false,false,true); 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); } @@ -36,6 +37,7 @@ string SetDirectoryCommand::getHelpString(){ 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 can also be used to run mothur in debug mode.\n"; + helpString += "The set.dir command can also be used to set the modifynames parameter. Default=t, meaning if your sequence names contain ':' change them to '_' to avoid issues while making trees. modifynames=F will leave sequence names as they are.\n"; helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n"; helpString += "To run mothur in debug mode set debug=true. Default debug=false.\n"; helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n"; @@ -92,9 +94,18 @@ SetDirectoryCommand::SetDirectoryCommand(string option) { if (temp == "not found") { debug = false; nodebug=true; } else { debug = m->isTrue(temp); } m->debug = debug; + + bool nomod = false; + temp = validParameter.validFile(parameters, "modifynames", false); + if (temp == "not found") { modifyNames = true; nomod=true; } + else { modifyNames = m->isTrue(temp); } + m->modifyNames = modifyNames; + + if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); } + - if ((input == "") && (output == "") && (tempdefault == "") && nodebug) { - m->mothurOut("You must provide either an input, output, tempdefault or debug for the set.outdir command."); m->mothurOutEndLine(); abort = true; + if ((input == "") && (output == "") && (tempdefault == "") && nodebug && nomod) { + m->mothurOut("You must provide either an input, output, tempdefault, debug or modifynames for the set.outdir command."); m->mothurOutEndLine(); abort = true; }else if((input == "") && (output == "") && (tempdefault == "")) { debugOnly = true; } } } @@ -110,67 +121,67 @@ int SetDirectoryCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } - if (debugOnly) { return 0; } - - 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); + if (debugOnly) { } + else { + 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); + + //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(); + + //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(); +#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)) { +#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); + m->setDefaultPath(tempdefault); + }else { + if (m->dirCheck(tempdefault)) { + m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine(); + m->setDefaultPath(tempdefault); + } } } - return 0; } catch(exception& e) {