X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=d0179be91a5b2eac505632797a8ebb3f74232282;hb=cd37904452dc95b183ff313ff05720c562902487;hp=4a25cb3208f2695fc50308a8ff7df83deda163a8;hpb=599af78a6ea4916919d460a131e2d0dffa28d35e;p=mothur.git diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index 4a25cb3..d0179be 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -13,29 +13,103 @@ //********************************************************************************************************************** -RareFactSharedCommand::RareFactSharedCommand(){ +RareFactSharedCommand::RareFactSharedCommand(string option){ try { globaldata = GlobalData::getInstance(); - string fileNameRoot; - fileNameRoot = getRootName(globaldata->inputFileName); - format = globaldata->getFormat(); - validCalculator = new ValidCalculators(); - util = new SharedUtil(); + abort = false; + allLines = 1; + lines.clear(); + 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[] = {"iters","line","label","calc","groups"}; + 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() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared command." << endl; abort = true; } + else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared 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; + } - 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", ""))); - } + 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); + + 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) { @@ -51,18 +125,46 @@ RareFactSharedCommand::RareFactSharedCommand(){ //********************************************************************************************************************** +void RareFactSharedCommand::help(){ + try { + cout << "The rarefaction.shared command can only be executed after a successful read.otu command." << "\n"; + cout << "The rarefaction.shared command parameters are label, line, iters, groups and calc. No parameters are required, but you may not use " << "\n"; + cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n"; + cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, groups=yourGroups)." << "\n"; + cout << "Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, calc=sharedobserved)." << "\n"; + cout << "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"; + cout << "The default value for groups is all the groups in your groupfile." << "\n"; + validCalculator->printCalc("sharedrarefaction", cout); + cout << "The label and line parameters are used to analyze specific lines in your input." << "\n"; + cout << "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"; + 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 RareFactSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the RareFactSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + +//********************************************************************************************************************** + RareFactSharedCommand::~RareFactSharedCommand(){ - delete order; delete input; delete rCurve; delete read; - delete util; + 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 @@ -72,35 +174,81 @@ int RareFactSharedCommand::execute(){ read->read(&*globaldata); input = globaldata->ginput; - order = input->getSharedOrderVector(); - - //set users groups - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact"); + lookup = input->getSharedRAbundVectors(); + vector lastLookup = lookup; - while(order != NULL){ + if (lookup.size() < 2) { + cout << "I cannot run the command without at least 2 valid groups."; + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + return 0; + } - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ - //create collectors curve - rCurve = new Rarefact(order, rDisplays); - convert(globaldata->getFreq(), freq); - convert(globaldata->getIters(), nIters); - rCurve->getSharedCurve(freq, nIters); + //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); + rCurve->getSharedCurve(freq, nIters); delete rCurve; - cout << order->getLabel() << '\t' << count << endl; + cout << lookup[0]->getLabel() << '\t' << count << endl; + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + userLines.erase(count); } + if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) { + cout << lastLookup[0]->getLabel() << '\t' << count << endl; + rCurve = new Rarefact(lastLookup, rDisplays); + rCurve->getSharedCurve(freq, nIters); + delete rCurve; + + processedLabels.insert(lastLookup[0]->getLabel()); + userLabels.erase(lastLookup[0]->getLabel()); + } + + //prevent memory leak + if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } } + lastLookup = lookup; + //get next line to process - delete order; - order = input->getSharedOrderVector(); + 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++) { + cout << "Your file does not include the label "<< *it; + if (processedLabels.count(lastLookup[0]->getLabel()) != 1) { + cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl; + needToRun = true; + }else { + cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl; + } + } + + //run last line if you need to + if (needToRun == true) { + cout << lastLookup[0]->getLabel() << '\t' << count << endl; + rCurve = new Rarefact(lastLookup, rDisplays); + rCurve->getSharedCurve(freq, nIters); + delete rCurve; + } + + for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } + for(int i=0;iGroups.clear(); globaldata->setGroups(""); + globaldata->Groups.clear(); return 0; }