X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=6bf42fc8a2e7d33374f73ba04d0df4f8eff57e1a;hb=cd37904452dc95b183ff313ff05720c562902487;hp=114c8d06dc3a3a76fbe22e9ee3aec017e335401c;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp index 114c8d0..6bf42fc 100644 --- a/rarefactcommand.cpp +++ b/rarefactcommand.cpp @@ -22,48 +22,116 @@ //********************************************************************************************************************** -RareFactCommand::RareFactCommand(){ +RareFactCommand::RareFactCommand(string option){ try { globaldata = GlobalData::getInstance(); - string fileNameRoot; - fileNameRoot = getRootName(globaldata->inputFileName); - convert(globaldata->getFreq(), freq); - convert(globaldata->getIters(), nIters); - validCalculator = new ValidCalculators(); + abort = false; + allLines = 1; + lines.clear(); + labels.clear(); + Estimators.clear(); - int i; - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("rarefaction", globaldata->Estimators[i]) == true) { - if (globaldata->Estimators[i] == "sobs") { - rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction"))); - }else if (globaldata->Estimators[i] == "chao") { - rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao"))); - }else if (globaldata->Estimators[i] == "ace") { - convert(globaldata->getAbund(), abund); - if(abund < 5) - abund = 10; - rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace"))); - }else if (globaldata->Estimators[i] == "jack") { - rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack"))); - }else if (globaldata->Estimators[i] == "shannon") { - rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon"))); - }else if (globaldata->Estimators[i] == "npshannon") { - rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon"))); - }else if (globaldata->Estimators[i] == "simpson") { - rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson"))); - }else if (globaldata->Estimators[i] == "bootstrap") { - rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap"))); - }else if (globaldata->Estimators[i] == "coverage") { - rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage"))); - }else if (globaldata->Estimators[i] == "nseqs") { - rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs"))); + //allow user to run help + if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"iters","freq","line","label","calc","abund"}; + 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() == "")) { cout << "You must read a list, sabund or rabund before you can use the rarefaction.single command." << endl; abort = true; } + + //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; } + } + + label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; } + else { + if(label != "all") { splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + + //make sure user did not use both the line and label parameters + if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; 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; + } + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "sobs"; } + else { + if (calc == "default") { calc = "sobs"; } + } + 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, "iters", false); if (temp == "not found") { temp = "1000"; } + convert(temp, nIters); + + if (abort == false) { + + string fileNameRoot = getRootName(globaldata->inputFileName); + int i; + validCalculator = new ValidCalculators(); + + + for (i=0; iisValidCalculator("rarefaction", Estimators[i]) == true) { + if (Estimators[i] == "sobs") { + rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction"))); + }else if (Estimators[i] == "chao") { + rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao"))); + }else if (Estimators[i] == "ace") { + if(abund < 5) + abund = 10; + rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace"))); + }else if (Estimators[i] == "jack") { + rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack"))); + }else if (Estimators[i] == "shannon") { + rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon"))); + }else if (Estimators[i] == "npshannon") { + rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon"))); + }else if (Estimators[i] == "simpson") { + rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson"))); + }else if (Estimators[i] == "bootstrap") { + rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap"))); + }else if (Estimators[i] == "coverage") { + rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage"))); + }else if (Estimators[i] == "nseqs") { + rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs"))); + } + } } } + } - //reset calc for next command - globaldata->setCalc(""); - } catch(exception& e) { cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; @@ -75,6 +143,30 @@ RareFactCommand::RareFactCommand(){ } } +//********************************************************************************************************************** + +void RareFactCommand::help(){ + try { + cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n"; + cout << "The rarefaction.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n"; + cout << "The rarefaction.single command parameters are label, line, iters, freq, calc and abund. No parameters are required, but you may not use " << "\n"; + cout << "both the line and label parameters at the same time. The rarefaction.single command should be in the following format: " << "\n"; + cout << "rarefaction.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n"; + cout << "Example rarefaction.single(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson)." << "\n"; + cout << "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness." << "\n"; + validCalculator->printCalc("rarefaction", cout); + cout << "The label and line parameters are used to analyze specific lines in your input." << "\n"; + cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n"; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the RareFactCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} //********************************************************************************************************************** @@ -83,12 +175,16 @@ RareFactCommand::~RareFactCommand(){ delete input; delete rCurve; delete read; + delete validCalculator; } //********************************************************************************************************************** int RareFactCommand::execute(){ try { + + if (abort == true) { return 0; } + int count = 1; //if the users entered no valid calculators don't execute command @@ -103,13 +199,13 @@ int RareFactCommand::execute(){ //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; + set userLines = lines; //as long as you are not at the end of the file or done wih the lines you want - while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ + if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){ rCurve = new Rarefact(order, rDisplays); rCurve->getCurve(freq, nIters);