X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=4ae2eaa004f9df9cc75c12b63626ffa7fad71ea7;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=5d99b6917b0130e0bec11742ab8fa862c4613db6;hpb=71b2121662daae3f9044252887d1c16eeddd85bb;p=mothur.git diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp index 5d99b69..4ae2eaa 100644 --- a/getsabundcommand.cpp +++ b/getsabundcommand.cpp @@ -10,189 +10,261 @@ #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(string option){ +//********************************************************************************************************************** +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; - lines.clear(); - labels.clear(); //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[] = {"line","label"}; - 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; } } - //make sure the user has already run the read.otu command - if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund command."); mothurOutEndLine(); abort = true; } + //initialize outputTypes + vector tempOutNames; + outputTypes["sabund"] = tempOutNames; - //check for optional parameter and set defaults - // ...at some point should added some additional type checking... - line = validParameter.validFile(parameters, "line", false); - if (line == "not found") { line = ""; } - else { - if(line != "all") { splitAtDash(line, lines); allLines = 0; } - else { allLines = 1; } + //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; } + } } + + //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; m->setListFile(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; m->setRabundFile(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 = ""; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } - //make sure user did not use both the line and label parameters - if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; } - //if the user has not specified any line or labels use the ones from read.otu - else if((line == "") && (label == "")) { - allLines = globaldata->allLines; - labels = globaldata->labels; - lines = globaldata->lines; - } - - if (abort == false) { - filename = getRootName(globaldata->inputFileName) + "sabund"; - 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); } + + } } catch(exception& e) { - errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -void GetSAbundCommand::help(){ - try { - mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n"); - mothurOut("The get.sabund command parameters are line and label. No parameters are required, and you may not use line and label at the same time.\n"); - mothurOut("The line and label allow you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n"); - mothurOut("The get.sabund command should be in the following format: get.sabund(line=yourLines, label=yourLabels).\n"); - mothurOut("Example get.sabund(line=1-3-5).\n"); - mothurOut("The default value for line and label are all lines in your inputfile.\n"); - mothurOut("The get.sabund command outputs a .sabund file containing the lines you selected.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n"); - } - catch(exception& e) { - errorOut(e, "GetSAbundCommand", "help"); + m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); exit(1); } } - -//********************************************************************************************************************** - -GetSAbundCommand::~GetSAbundCommand(){ -} - //********************************************************************************************************************** int GetSAbundCommand::execute(){ try { - if (abort == true) { return 0; } - - int count = 1; + if (abort == true) { if (calledHelp) { return 0; } return 2; } + filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "sabund"; + m->openOutputFile(filename, out); - //using order vector so you don't have to distinguish between the list and rabund files - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); + 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; - set userLines = lines; + + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; delete input; return 0; } - while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){ - mothurOut(order->getLabel()); 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) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; delete input; return 0; } - processedLabels.insert(order->getLabel()); - userLabels.erase(order->getLabel()); - userLines.erase(count); + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); } - if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - delete order; - order = (input->getOrderVector(lastLabel)); + if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = sabund->getLabel(); + + delete sabund; + sabund = (input->getSAbundVector(lastLabel)); - mothurOut(order->getLabel()); mothurOutEndLine(); - sabund = new SAbundVector(); - *sabund = (order->getSAbundVector()); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); sabund->print(out); - delete sabund; + + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); 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 + sabund->setLabel(saveLabel); } - lastLabel = order->getLabel(); + lastLabel = sabund->getLabel(); - delete order; - order = (input->getOrderVector()); - count++; + delete sabund; + sabund = (input->getSAbundVector()); } //output error messages about any remaining user labels set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } - //run last line if you need to + //run last label if you need to if (needToRun == true) { - delete order; - order = (input->getOrderVector(lastLabel)); + if (sabund != NULL) { delete sabund; } + sabund = (input->getSAbundVector(lastLabel)); - mothurOut(order->getLabel()); mothurOutEndLine(); - sabund = new SAbundVector(); - *sabund = (order->getSAbundVector()); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); sabund->print(out); delete sabund; - delete order; + + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; return 0; } + } - globaldata->gorder = NULL; - + out.close(); + delete input; + + m->mothurOutEndLine(); + m->mothurOut("Output File Name: "); 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; } catch(exception& e) { - errorOut(e, "GetSAbundCommand", "execute"); + m->errorOut(e, "GetSAbundCommand", "execute"); exit(1); } }