X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.cpp;h=51fabf88828eb10617595b10cf8bf6a95396212f;hb=72ebb6fa35b45b149812d47c2b1cb8acaca64659;hp=e7fda2e5dedcd8052b3c610931964377e356a7af;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;p=mothur.git diff --git a/summarycommand.cpp b/summarycommand.cpp index e7fda2e..51fabf8 100644 --- a/summarycommand.cpp +++ b/summarycommand.cpp @@ -31,91 +31,164 @@ //********************************************************************************************************************** -SummaryCommand::SummaryCommand(){ +SummaryCommand::SummaryCommand(string option){ try { globaldata = GlobalData::getInstance(); - validCalculator = new ValidCalculators(); - int i; + abort = false; + allLines = 1; + labels.clear(); + Estimators.clear(); - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) { - if(globaldata->Estimators[i] == "sobs"){ - sumCalculators.push_back(new Sobs()); - }else if(globaldata->Estimators[i] == "chao"){ - sumCalculators.push_back(new Chao1()); - }else if(globaldata->Estimators[i] == "coverage"){ - sumCalculators.push_back(new Coverage()); - }else if(globaldata->Estimators[i] == "geometric"){ - sumCalculators.push_back(new Geom()); - }else if(globaldata->Estimators[i] == "logseries"){ - sumCalculators.push_back(new LogSD()); - }else if(globaldata->Estimators[i] == "qstat"){ - sumCalculators.push_back(new QStat()); - }else if(globaldata->Estimators[i] == "bergerparker"){ - sumCalculators.push_back(new BergerParker()); - }else if(globaldata->Estimators[i] == "bstick"){ - sumCalculators.push_back(new BStick()); - }else if(globaldata->Estimators[i] == "ace"){ - convert(globaldata->getAbund(), abund); - if(abund < 5) - abund = 10; - sumCalculators.push_back(new Ace(abund)); - }else if(globaldata->Estimators[i] == "jack"){ - sumCalculators.push_back(new Jackknife()); - }else if(globaldata->Estimators[i] == "shannon"){ - sumCalculators.push_back(new Shannon()); - }else if(globaldata->Estimators[i] == "npshannon"){ - sumCalculators.push_back(new NPShannon()); - }else if(globaldata->Estimators[i] == "simpson"){ - sumCalculators.push_back(new Simpson()); - }else if(globaldata->Estimators[i] == "bootstrap"){ - sumCalculators.push_back(new Bootstrap()); - }else if (globaldata->Estimators[i] == "nseqs") { - sumCalculators.push_back(new NSeqs()); - }else if (globaldata->Estimators[i] == "goodscoverage") { - sumCalculators.push_back(new GoodsCoverage()); - }else if (globaldata->Estimators[i] == "efron") { - convert(globaldata->getSize(), size); - sumCalculators.push_back(new Efron(size)); - }else if (globaldata->Estimators[i] == "boneh") { - convert(globaldata->getSize(), size); - sumCalculators.push_back(new Boneh(size)); - }else if (globaldata->Estimators[i] == "solow") { - convert(globaldata->getSize(), size); - sumCalculators.push_back(new Solow(size)); - }else if (globaldata->Estimators[i] == "shen") { - convert(globaldata->getSize(), size); - sumCalculators.push_back(new Shen(size)); + //allow user to run help + if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"label","calc","abund","size"}; + 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; } + } + + //make sure the user has already run the read.otu command + if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the summary.single 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; + } + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; } + else { + if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; } + } + splitAtDash(calc, Estimators); + + string temp; + temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } + convert(temp, abund); + + temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; } + convert(temp, size); + + if (abort == false) { + + validCalculator = new ValidCalculators(); + int i; + + for (i=0; iisValidCalculator("summary", Estimators[i]) == true) { + if(Estimators[i] == "sobs"){ + sumCalculators.push_back(new Sobs()); + }else if(Estimators[i] == "chao"){ + sumCalculators.push_back(new Chao1()); + }else if(Estimators[i] == "coverage"){ + sumCalculators.push_back(new Coverage()); + }else if(Estimators[i] == "geometric"){ + sumCalculators.push_back(new Geom()); + }else if(Estimators[i] == "logseries"){ + sumCalculators.push_back(new LogSD()); + }else if(Estimators[i] == "qstat"){ + sumCalculators.push_back(new QStat()); + }else if(Estimators[i] == "bergerparker"){ + sumCalculators.push_back(new BergerParker()); + }else if(Estimators[i] == "bstick"){ + sumCalculators.push_back(new BStick()); + }else if(Estimators[i] == "ace"){ + if(abund < 5) + abund = 10; + sumCalculators.push_back(new Ace(abund)); + }else if(Estimators[i] == "jack"){ + sumCalculators.push_back(new Jackknife()); + }else if(Estimators[i] == "shannon"){ + sumCalculators.push_back(new Shannon()); + }else if(Estimators[i] == "npshannon"){ + sumCalculators.push_back(new NPShannon()); + }else if(Estimators[i] == "simpson"){ + sumCalculators.push_back(new Simpson()); + }else if(Estimators[i] == "bootstrap"){ + sumCalculators.push_back(new Bootstrap()); + }else if (Estimators[i] == "nseqs") { + sumCalculators.push_back(new NSeqs()); + }else if (Estimators[i] == "goodscoverage") { + sumCalculators.push_back(new GoodsCoverage()); + }else if (Estimators[i] == "efron") { + sumCalculators.push_back(new Efron(size)); + }else if (Estimators[i] == "boneh") { + sumCalculators.push_back(new Boneh(size)); + }else if (Estimators[i] == "solow") { + sumCalculators.push_back(new Solow(size)); + }else if (Estimators[i] == "shen") { + sumCalculators.push_back(new Shen(size, abund)); + } + } } } } - - //reset calc for next command - globaldata->setCalc(""); + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "SummaryCommand", "SummaryCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** + +void SummaryCommand::help(){ + try { + mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n"); + mothurOut("The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n"); + mothurOut("The summary.single command parameters are label, calc, abund. No parameters are required.\n"); + mothurOut("The summary.single command should be in the following format: \n"); + mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n"); + mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n"); + validCalculator->printCalc("summary", cout); + mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n"); + mothurOut("The label parameter is used to analyze specific labels in your input.\n"); + mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n"); + } + catch(exception& e) { + errorOut(e, "SummaryCommand", "help"); exit(1); - } + } } + //********************************************************************************************************************** SummaryCommand::~SummaryCommand(){ - delete sabund; - delete input; - delete read; + if (abort == false) { + delete input; globaldata->ginput = NULL; + delete read; + delete validCalculator; + globaldata->sabund = NULL; + } } //********************************************************************************************************************** int SummaryCommand::execute(){ try { - int count = 1; + + if (abort == true) { return 0; } //if the users entered no valid calculators don't execute command if (sumCalculators.size() == 0) { return 0; } @@ -128,7 +201,7 @@ int SummaryCommand::execute(){ read->read(&*globaldata); sabund = globaldata->sabund; - SAbundVector* lastSAbund = sabund; + string lastLabel = sabund->getLabel(); input = globaldata->ginput; for(int i=0;i processedLabels; - set userLabels = globaldata->labels; - - while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) { + set userLabels = labels; + + while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){ + if(allLines == 1 || labels.count(sabund->getLabel()) == 1){ - cout << sabund->getLabel() << '\t' << count << endl; + mothurOut(sabund->getLabel()); mothurOutEndLine(); processedLabels.insert(sabund->getLabel()); userLabels.erase(sabund->getLabel()); - - + outputFileHandle << sabund->getLabel(); for(int i=0;i data = sumCalculators[i]->getValues(sabund); @@ -163,64 +235,71 @@ int SummaryCommand::execute(){ outputFileHandle << endl; } - if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) { - - cout << lastSAbund->getLabel() << '\t' << count << endl; - processedLabels.insert(lastSAbund->getLabel()); - userLabels.erase(lastSAbund->getLabel()); + if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = sabund->getLabel(); + + delete sabund; + sabund = input->getSAbundVector(lastLabel); - outputFileHandle << lastSAbund->getLabel(); + mothurOut(sabund->getLabel()); mothurOutEndLine(); + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); + + outputFileHandle << sabund->getLabel(); for(int i=0;i data = sumCalculators[i]->getValues(lastSAbund); + vector data = sumCalculators[i]->getValues(sabund); outputFileHandle << '\t'; sumCalculators[i]->print(outputFileHandle); } outputFileHandle << endl; + + //restore real lastlabel to save below + sabund->setLabel(saveLabel); } - if (count != 1) { delete lastSAbund; } - lastSAbund = sabund; - + lastLabel = sabund->getLabel(); + + delete sabund; sabund = input->getSAbundVector(); - 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(lastSAbund->getLabel()) != 1) { - cout << ". I will use " << lastSAbund->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 " << lastSAbund->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 << lastSAbund->getLabel() << '\t' << count << endl; - outputFileHandle << lastSAbund->getLabel(); + if (sabund != NULL) { delete sabund; } + sabund = input->getSAbundVector(lastLabel); + + mothurOut(sabund->getLabel()); mothurOutEndLine(); + outputFileHandle << sabund->getLabel(); for(int i=0;i data = sumCalculators[i]->getValues(lastSAbund); + vector data = sumCalculators[i]->getValues(sabund); outputFileHandle << '\t'; sumCalculators[i]->print(outputFileHandle); } outputFileHandle << endl; + delete sabund; } - delete lastSAbund; + outputFileHandle.close(); + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "SummaryCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //**********************************************************************************************************************