X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=7e1b4773ddb0505861fd90a2c0064b37ce5e9c59;hb=e911fa88572a16ef40e0b51fb132ab6e02370797;hp=0928d2e6b439b9775e62b5abd8c91b4254216e67;hpb=37519fc35c0eb1523e84227517694c4015847c6d;p=mothur.git diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index 0928d2e..7e1b477 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -13,53 +13,157 @@ //********************************************************************************************************************** -RareFactSharedCommand::RareFactSharedCommand(){ +RareFactSharedCommand::RareFactSharedCommand(string option){ try { globaldata = GlobalData::getInstance(); - string fileNameRoot; - fileNameRoot = getRootName(globaldata->inputFileName); - format = globaldata->getFormat(); - validCalculator = new ValidCalculators(); + + abort = false; + allLines = 1; + lines.clear(); + labels.clear(); + Estimators.clear(); + Groups.clear(); - int i; - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) { - if (globaldata->Estimators[i] == "sharedobserved") { - rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", ""))); - }else if (globaldata->Estimators[i] == "sharednseqs") { - rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.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","line","label","calc","groups", "jumble"}; + 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->getSharedFile() == "") { + if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; } + else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); 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 != "")) { 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; + } + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "sharedobserved"; } + else { + if (calc == "default") { calc = "sharedobserved"; } } + splitAtDash(calc, Estimators); + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + splitAtDash(groups, Groups); + } + globaldata->Groups = Groups; + + string temp; + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } + convert(temp, nIters); + + temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; } + if (isTrue(temp)) { jumble = true; } + else { jumble = false; } + globaldata->jumble = jumble; + + if (abort == false) { + + string fileNameRoot = getRootName(globaldata->inputFileName); +// format = globaldata->getFormat(); + + + validCalculator = new ValidCalculators(); + + for (int i=0; iisValidCalculator("sharedrarefaction", Estimators[i]) == true) { + if (Estimators[i] == "sharedobserved") { + rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", ""))); + }else if (Estimators[i] == "sharednseqs") { + rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", ""))); + } + } + } + } + } - - //reset calc for next command - globaldata->setCalc(""); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + +//********************************************************************************************************************** + +void RareFactSharedCommand::help(){ + try { + mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n"); + mothurOut("The rarefaction.shared command parameters are label, line, iters, groups, jumble and calc. No parameters are required, but you may not use \n"); + mothurOut("both the line and label parameters at the same time. The rarefaction command should be in the following format: \n"); + mothurOut("rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n"); + mothurOut("Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n"); + mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n"); + mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n"); + validCalculator->printCalc("sharedrarefaction", cout); + mothurOut("The label and line parameters are used to analyze specific lines in your input.\n"); + mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n"); + mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n"); + } + catch(exception& e) { + errorOut(e, "RareFactSharedCommand", "help"); exit(1); - } - + } } //********************************************************************************************************************** RareFactSharedCommand::~RareFactSharedCommand(){ - delete input; - delete rCurve; - delete read; + if (abort == false) { + delete input; globaldata->ginput = NULL; + delete read; + delete validCalculator; + } } //********************************************************************************************************************** int RareFactSharedCommand::execute(){ try { + + if (abort == true) { return 0; } + int count = 1; //if the users entered no valid calculators don't execute command @@ -70,51 +174,92 @@ int RareFactSharedCommand::execute(){ input = globaldata->ginput; lookup = input->getSharedRAbundVectors(); - + string lastLabel = lookup[0]->getLabel(); + if (lookup.size() < 2) { - cout << "I cannot run the command without at least 2 valid groups."; + mothurOut("I cannot run the command without at least 2 valid groups."); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; } - - while(lookup[0] != NULL){ - - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){ - //create collectors curve + //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; + + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + + if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ + rCurve = new Rarefact(lookup, rDisplays); - convert(globaldata->getFreq(), freq); - convert(globaldata->getIters(), nIters); rCurve->getSharedCurve(freq, nIters); - delete rCurve; - cout << lookup[0]->getLabel() << '\t' << count << endl; + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + userLines.erase(count); } - //prevent memory leak - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(lastLabel); + + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + rCurve = new Rarefact(lookup, rDisplays); + rCurve->getSharedCurve(freq, nIters); + delete rCurve; + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + } + + lastLabel = lookup[0]->getLabel(); + //get next line to process + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(); count++; } - + + //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); + if (processedLabels.count(lastLabel) != 1) { + mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + needToRun = true; + }else { + mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + } + } + + //run last line if you need to + if (needToRun == true) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input->getSharedRAbundVectors(lastLabel); + + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + rCurve = new Rarefact(lookup, rDisplays); + rCurve->getSharedCurve(freq, nIters); + delete rCurve; + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + for(int i=0;iGroups.clear(); globaldata->setGroups(""); + globaldata->Groups.clear(); return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "RareFactSharedCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } }