X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=ebfa839161fc3d59cd27f9a2f8e2e24743b85e7e;hb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;hp=ba05ea1e11d3e5e603ec84babe81ee172c68a440;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp index ba05ea1..ebfa839 100644 --- a/getsabundcommand.cpp +++ b/getsabundcommand.cpp @@ -10,42 +10,118 @@ #include "getsabundcommand.h" //********************************************************************************************************************** +vector GetSAbundCommand::setParameters(){ + try { + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist); + CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + 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, "GetSAbundCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string GetSAbundCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The get.sabund command parameters is list, rabund and label. list or rabund is required unless a valid current file exists.\n"; + helpString += "The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n"; + helpString += "The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n"; + helpString += "Example get.sabund().\n"; + helpString += "The default value for label is all labels in your inputfile.\n"; + helpString += "The get.sabund command outputs a .sabund file containing the labels you selected.\n"; + helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "GetSAbundCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +GetSAbundCommand::GetSAbundCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["sabund"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); + exit(1); + } +} +//********************************************************************************************************************** GetSAbundCommand::GetSAbundCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - labels.clear(); //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[] = {"label","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); + map::iterator it; ValidParameters validParameter; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - //if the user changes the output directory command factory will send this info to us in the output parameter - string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ - outputDir = ""; - outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + //initialize outputTypes + vector tempOutNames; + outputTypes["sabund"] = tempOutNames; + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("list"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["list"] = inputDir + it->second; } + } + + it = parameters.find("rabund"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["rabund"] = inputDir + it->second; } + } } - - //make sure the user has already run the read.otu command - if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { m->mothurOut("You must read a list or rabund before you can use the get.sabund command."); m->mothurOutEndLine(); abort = true; } - //check for optional parameter and set defaults + + //check for required parameters + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { listfile = ""; abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { format = "list"; inputfile = listfile; } + + rabundfile = validParameter.validFile(parameters, "rabund", true); + if (rabundfile == "not open") { rabundfile = ""; abort = true; } + else if (rabundfile == "not found") { rabundfile = ""; } + else { format = "rabund"; inputfile = rabundfile; } + + + //check for optional parameter and set defaults // ...at some point should added some additional type checking... label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } @@ -54,16 +130,27 @@ GetSAbundCommand::GetSAbundCommand(string option) { else { allLines = 1; } } - //if the user has not specified any labels use the ones from read.otu - if(label == "") { - allLines = globaldata->allLines; - labels = globaldata->labels; - } - - if (abort == false) { - filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund"; - m->openOutputFile(filename, out); + if ((listfile == "") && (rabundfile == "")) { + //is there are current file available for any of these? + //give priority to shared, then list, then rabund, then sabund + //if there is a current shared file, use it + listfile = m->getListFile(); + if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + rabundfile = m->getRabundFile(); + if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a list or rabund file."); m->mothurOutEndLine(); + abort = true; + } + } } + + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); } + + } } @@ -74,91 +161,63 @@ GetSAbundCommand::GetSAbundCommand(string option) { } //********************************************************************************************************************** -void GetSAbundCommand::help(){ - try { - m->mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n"); - m->mothurOut("The get.sabund command parameters is label. No parameters are required.\n"); - m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n"); - m->mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n"); - m->mothurOut("Example get.sabund().\n"); - m->mothurOut("The default value for label is all labels in your inputfile.\n"); - m->mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "GetSAbundCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -GetSAbundCommand::~GetSAbundCommand(){ -} - -//********************************************************************************************************************** - int GetSAbundCommand::execute(){ try { - if (abort == true) { return 0; } - - //using order vector so you don't have to distinguish between the list and rabund files - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); + if (abort == true) { if (calledHelp) { return 0; } return 2; } + filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "sabund"; + m->openOutputFile(filename, out); + + input = new InputData(inputfile, format); + sabund = input->getSAbundVector(); + string lastLabel = sabund->getLabel(); - order = globaldata->gorder; - string lastLabel = order->getLabel(); - input = globaldata->ginput; //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; set userLabels = labels; - if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete sabund; delete input; return 0; } - while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(allLines == 1 || labels.count(order->getLabel()) == 1){ - m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - sabund = new SAbundVector(); - *sabund = (order->getSAbundVector()); + if(allLines == 1 || labels.count(sabund->getLabel()) == 1){ + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + sabund->print(out); delete sabund; - if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete sabund; delete input; return 0; } - processedLabels.insert(order->getLabel()); - userLabels.erase(order->getLabel()); + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); } - if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - string saveLabel = order->getLabel(); + if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = sabund->getLabel(); - delete order; - order = (input->getOrderVector(lastLabel)); + delete sabund; + sabund = (input->getSAbundVector(lastLabel)); - m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - sabund = new SAbundVector(); - *sabund = (order->getSAbundVector()); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); sabund->print(out); delete sabund; - if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete sabund; delete input; return 0; } - processedLabels.insert(order->getLabel()); - userLabels.erase(order->getLabel()); + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); //restore real lastlabel to save below - order->setLabel(saveLabel); + sabund->setLabel(saveLabel); } - lastLabel = order->getLabel(); + lastLabel = sabund->getLabel(); - delete order; - order = (input->getOrderVector()); + delete sabund; + sabund = (input->getSAbundVector()); } //output error messages about any remaining user labels @@ -176,28 +235,32 @@ int GetSAbundCommand::execute(){ //run last label if you need to if (needToRun == true) { - if (order != NULL) { delete order; } - order = (input->getOrderVector(lastLabel)); + if (sabund != NULL) { delete sabund; } + sabund = (input->getSAbundVector(lastLabel)); - m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - sabund = new SAbundVector(); - *sabund = (order->getSAbundVector()); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); sabund->print(out); delete sabund; - if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete input; return 0; } - delete order; } - globaldata->gorder = NULL; - + out.close(); + delete input; m->mothurOutEndLine(); m->mothurOut("Output File Name: "); m->mothurOutEndLine(); - m->mothurOut(filename); m->mothurOutEndLine(); + m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["sabund"].push_back(filename); m->mothurOutEndLine(); + //set sabund file as new current sabundfile + string current = ""; + itTypes = outputTypes.find("sabund"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); } + } + return 0; }