X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=7d3daef96cccf6d7b1604728fd1eaff9f2b78048;hb=f37a59b81c339f574d97042ff6e364146feb457a;hp=b3e8d8fbfa817900f6f1802310d9c18680bc1c15;hpb=eb1c88346fb246e95a6b38935b103f95e38b82ca;p=mothur.git diff --git a/collectcommand.cpp b/collectcommand.cpp index b3e8d8f..7d3daef 100644 --- a/collectcommand.cpp +++ b/collectcommand.cpp @@ -22,122 +22,258 @@ #include "logsd.h" #include "bergerparker.h" #include "bstick.h" +#include "goodscoverage.h" +#include "efron.h" +#include "boneh.h" +#include "solow.h" +#include "shen.h" +#include "coverage.h" //********************************************************************************************************************** - - -CollectCommand::CollectCommand(){ +CollectCommand::CollectCommand(string option){ try { globaldata = GlobalData::getInstance(); - string fileNameRoot; - fileNameRoot = getRootName(globaldata->inputFileName); - int i; - validCalculator = new ValidCalculators(); - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) { - if (globaldata->Estimators[i] == "sobs") { - cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs"))); - }else if (globaldata->Estimators[i] == "chao") { - cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao"))); - }else if (globaldata->Estimators[i] == "nseqs") { - cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs"))); - }else if (globaldata->Estimators[i] == "ace") { - convert(globaldata->getAbund(), abund); - cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace"))); - }else if (globaldata->Estimators[i] == "jack") { - cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack"))); - }else if (globaldata->Estimators[i] == "shannon") { - cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon"))); - }else if (globaldata->Estimators[i] == "npshannon") { - cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon"))); - }else if (globaldata->Estimators[i] == "simpson") { - cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson"))); - }else if (globaldata->Estimators[i] == "bootstrap") { - cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap"))); - }else if (globaldata->Estimators[i] == "geom") { - cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geom"))); - }else if (globaldata->Estimators[i] == "qstat") { - cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat"))); - }else if (globaldata->Estimators[i] == "logsd") { - cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logsd"))); - }else if (globaldata->Estimators[i] == "bergerparker") { - cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker"))); - }else if (globaldata->Estimators[i] == "bstick") { - cDisplays.push_back(new CollectDisplay(new BStick(), new OneColumnFile(fileNameRoot+"bstick"))); + abort = false; + allLines = 1; + labels.clear(); + Estimators.clear(); + + //allow user to run help + if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"freq","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 collect.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, "freq", false); if (temp == "not found") { temp = "100"; } + convert(temp, freq); + + 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) { + string fileNameRoot = getRootName(globaldata->inputFileName); + int i; + validCalculator = new ValidCalculators(); + + for (i=0; iisValidCalculator("single", Estimators[i]) == true) { + if (Estimators[i] == "sobs") { + cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs"))); + }else if (Estimators[i] == "chao") { + cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao"))); + }else if (Estimators[i] == "nseqs") { + cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs"))); + }else if (Estimators[i] == "coverage") { + cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage"))); + }else if (Estimators[i] == "ace") { + cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace"))); + }else if (Estimators[i] == "jack") { + cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack"))); + }else if (Estimators[i] == "shannon") { + cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon"))); + }else if (Estimators[i] == "npshannon") { + cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon"))); + }else if (Estimators[i] == "simpson") { + cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson"))); + }else if (Estimators[i] == "bootstrap") { + cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap"))); + }else if (Estimators[i] == "geometric") { + cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric"))); + }else if (Estimators[i] == "qstat") { + cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat"))); + }else if (Estimators[i] == "logseries") { + cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries"))); + }else if (Estimators[i] == "bergerparker") { + cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker"))); + }else if (Estimators[i] == "bstick") { + cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick"))); + }else if (Estimators[i] == "goodscoverage") { + cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage"))); + }else if (Estimators[i] == "efron") { + cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron"))); + }else if (Estimators[i] == "boneh") { + cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh"))); + }else if (Estimators[i] == "solow") { + cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow"))); + }else if (Estimators[i] == "shen") { + cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen"))); + } + } } } } - //reset calc for next command - globaldata->setCalc(""); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "CollectCommand", "CollectCommand"); exit(1); + } +} +//********************************************************************************************************************** + +void CollectCommand::help(){ + try { + mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n"); + mothurOut("The collect.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 collect.single command parameters are label, freq, calc and abund. No parameters are required. \n"); + mothurOut("The collect.single command should be in the following format: \n"); + mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n"); + mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n"); + mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n"); + validCalculator->printCalc("single", cout); + mothurOut("The label parameter is used to analyze specific labels in your input.\n"); + mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n"); } - catch(...) { - cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + catch(exception& e) { + errorOut(e, "CollectCommand", "help"); exit(1); - } - + } } //********************************************************************************************************************** CollectCommand::~CollectCommand(){ - delete order; - delete input; - delete cCurve; - delete read; + if (abort == false) { + //delete order; + delete input; globaldata->ginput = NULL; + delete read; + delete validCalculator; + globaldata->gorder = NULL; + } } //********************************************************************************************************************** int CollectCommand::execute(){ try { - int count = 1; + + if (abort == true) { return 0; } //if the users entered no valid calculators don't execute command if (cDisplays.size() == 0) { return 0; } - read = new ReadPhilFile(globaldata->inputFileName); + read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); order = globaldata->gorder; + string lastLabel = order->getLabel(); input = globaldata->ginput; - set orderList; - while(order != NULL){ + //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; - orderList.insert(order->getLabel()); - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ + while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if(allLines == 1 || labels.count(order->getLabel()) == 1){ + cCurve = new Collect(order, cDisplays); - convert(globaldata->getFreq(), freq); cCurve->getCurve(freq); + delete cCurve; + + mothurOut(order->getLabel()); mothurOutEndLine(); + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); + + } + //you have a label the user want that is smaller than this label and the last label has not already been processed + if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + + delete order; + order = (input->getOrderVector(lastLabel)); + + cCurve = new Collect(order, cDisplays); + cCurve->getCurve(freq); delete cCurve; - cout << order->getLabel() << '\t' << count << endl; + mothurOut(order->getLabel()); mothurOutEndLine(); + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); } + + lastLabel = order->getLabel(); + + delete order; order = (input->getOrderVector()); - count++; } - set::iterator i; - for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i) - if(orderList.count(*i) == 0) - cout << "'" << *i << "'" << " is not a valid label.\n"; - for(int i=0;i::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + needToRun = true; + }else { + mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + } + } + + //run last label if you need to + if (needToRun == true) { + if (order != NULL) { delete order; } + order = (input->getOrderVector(lastLabel)); + + mothurOut(order->getLabel()); mothurOutEndLine(); + + cCurve = new Collect(order, cDisplays); + cCurve->getCurve(freq); + delete cCurve; + delete order; + } + + + for(int i=0;i