X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=10b998e73d78a3af0d41c3106743c52e6235359b;hb=9ada98592a54c82d08f3d46c9b1d8c3e472a922d;hp=8c7f07c8bb7f73025764e77fa71d3f44585a1e55;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp index 8c7f07c..10b998e 100644 --- a/getsabundcommand.cpp +++ b/getsabundcommand.cpp @@ -11,22 +11,84 @@ //********************************************************************************************************************** -GetSAbundCommand::GetSAbundCommand(){ +GetSAbundCommand::GetSAbundCommand(string option){ try { globaldata = GlobalData::getInstance(); - filename = getRootName(globaldata->inputFileName) + "sabund"; + abort = false; + allLines = 1; + labels.clear(); - openOutputFile(filename, out); + //allow user to run help + if(option == "help") { help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"label","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::iterator 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 += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + } + + //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; } + + //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; } + 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 + getRootName(getSimpleName(globaldata->inputFileName)) + "sabund"; + openOutputFile(filename, out); + } + } + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the GetSAbundCommand class function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** + +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 is label. No parameters are required.\n"); + 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"); + mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n"); + mothurOut("Example get.sabund().\n"); + mothurOut("The default value for label is all labels in your inputfile.\n"); + mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n"); + mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n"); + } + catch(exception& e) { + errorOut(e, "GetSAbundCommand", "help"); exit(1); - } - + } } //********************************************************************************************************************** @@ -38,26 +100,25 @@ GetSAbundCommand::~GetSAbundCommand(){ int GetSAbundCommand::execute(){ try { - int count = 1; + 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); order = globaldata->gorder; - lastOrder = order; + 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 = globaldata->labels; - set userLines = globaldata->lines; - + set userLabels = labels; - while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ - cout << order->getLabel() << '\t' << count << endl; + if(allLines == 1 || labels.count(order->getLabel()) == 1){ + mothurOut(order->getLabel()); mothurOutEndLine(); sabund = new SAbundVector(); *sabund = (order->getSAbundVector()); sabund->print(out); @@ -65,62 +126,69 @@ int GetSAbundCommand::execute(){ processedLabels.insert(order->getLabel()); userLabels.erase(order->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) { - cout << lastOrder->getLabel() << '\t' << count << endl; + if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = order->getLabel(); + + delete order; + order = (input->getOrderVector(lastLabel)); + + mothurOut(order->getLabel()); mothurOutEndLine(); sabund = new SAbundVector(); - *sabund = (lastOrder->getSAbundVector()); + *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; - processedLabels.insert(lastOrder->getLabel()); - userLabels.erase(lastOrder->getLabel()); + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); + + //restore real lastlabel to save below + order->setLabel(saveLabel); } - if (count != 1) { delete lastOrder; } - lastOrder = order; - + + lastLabel = order->getLabel(); + + delete order; order = (input->getOrderVector()); - count++; } //output error messages about any remaining user labels set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - cout << "Your file does not include the label "<< *it; - if (processedLabels.count(lastOrder->getLabel()) != 1) { - cout << ". I will use " << lastOrder->getLabel() << "." << endl; + mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastOrder->getLabel() << "." << endl; + mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); } } - //run last line if you need to + //run last label if you need to if (needToRun == true) { - cout << lastOrder->getLabel() << '\t' << count << endl; + if (order != NULL) { delete order; } + order = (input->getOrderVector(lastLabel)); + + mothurOut(order->getLabel()); mothurOutEndLine(); sabund = new SAbundVector(); - *sabund = (lastOrder->getSAbundVector()); + *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; + delete order; } - delete lastOrder; + globaldata->gorder = NULL; out.close(); return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "GetSAbundCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the GetSAbundCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //**********************************************************************************************************************