X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=717fec2fea1fc1ba23564fc683149e38d177496e;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=89cf4e2732af38c6fff844490effde5f8676e76c;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index 89cf4e2..717fec2 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -12,126 +12,329 @@ #include "sharednseqs.h" //********************************************************************************************************************** - -RareFactSharedCommand::RareFactSharedCommand(){ +vector RareFactSharedCommand::setParameters(){ try { - globaldata = GlobalData::getInstance(); - string fileNameRoot; - fileNameRoot = getRootName(globaldata->inputFileName); - format = globaldata->getFormat(); - validCalculator = new ValidCalculators(); - util = new SharedUtil(); - - 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", ""))); - } - - } - } + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq); + CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); + CommandParameter pcalc("calc", "Multiple", "sharednseqs-sharedobserved", "sharedobserved", "", "", "",true,false); parameters.push_back(pcalc); + CommandParameter pjumble("jumble", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pjumble); + CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); - //reset calc for next command - globaldata->setCalc(""); - + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; } 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"; + m->errorOut(e, "RareFactSharedCommand", "setParameters"); 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"; +} +//********************************************************************************************************************** +string RareFactSharedCommand::getHelpString(){ + try { + string helpString = ""; + ValidCalculators validCalculator; + helpString += "The collect.shared command parameters are shared, label, freq, calc and groups. shared is required if there is no current sharedfile. \n"; + helpString += "The rarefaction.shared command parameters are shared, label, iters, groups, jumble and calc. shared is required if there is no current sharedfile. \n"; + helpString += "The rarefaction command should be in the following format: \n"; + helpString += "rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n"; + helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n"; + helpString += "Example rarefaction.shared(label=unique-0.01-0.03, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n"; + helpString += "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"; + helpString += "The default value for groups is all the groups in your groupfile, and jumble is true.\n"; + helpString += validCalculator.printCalc("sharedrarefaction"); + helpString += "The label parameter is used to analyze specific labels in your input.\n"; + helpString += "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"; + helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "getHelpString"); exit(1); - } - + } } //********************************************************************************************************************** - -RareFactSharedCommand::~RareFactSharedCommand(){ - delete order; - delete input; - delete rCurve; - delete read; - delete util; +RareFactSharedCommand::RareFactSharedCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["sharedrarefaction"] = tempOutNames; + outputTypes["sharedr_nseqs"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); + exit(1); + } } +//********************************************************************************************************************** +RareFactSharedCommand::RareFactSharedCommand(string option) { + try { + abort = false; calledHelp = false; + allLines = 1; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + map::iterator it; + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["sharedrarefaction"] = tempOutNames; + outputTypes["sharedr_nseqs"] = tempOutNames; + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("shared"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["shared"] = inputDir + it->second; } + } + } + + //get shared file + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setSharedFile(sharedfile); } + + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sharedfile); } + + + //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") { m->splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "sharedobserved"; } + else { + if (calc == "default") { calc = "sharedobserved"; } + } + m->splitAtDash(calc, Estimators); + if (m->inUsersGroups("citation", Estimators)) { + ValidCalculators validCalc; validCalc.printCitations(Estimators); + //remove citation from list of calcs + for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } } + } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + m->splitAtDash(groups, Groups); + } + m->Groups = Groups; + + string temp; + temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; } + convert(temp, freq); + + 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 (m->isTrue(temp)) { jumble = true; } + else { jumble = false; } + m->jumble = jumble; + + } + + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); + exit(1); + } +} //********************************************************************************************************************** int RareFactSharedCommand::execute(){ try { - int count = 1; + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + + ValidCalculators validCalculator; + + for (int i=0; iinputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - order = input->getSharedOrderVector(); - }else { - //you are using a list and a groupfile - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); + + input = new InputData(sharedfile, "sharedfile"); + lookup = input->getSharedRAbundVectors(); + string lastLabel = lookup[0]->getLabel(); - input = globaldata->ginput; - SharedList = globaldata->gSharedList; - order = SharedList->getSharedOrderVector(); + if (m->control_pressed) { + m->Groups.clear(); + delete input; + for(int i=0;imothurOut("I cannot run the command without at least 2 valid groups."); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + return 0; } - //set users groups - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact"); - - while(order != NULL){ - - 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; + + //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))) { + if (m->control_pressed) { + m->Groups.clear(); + delete input; + for(int i=0;igetLabel()) == 1){ + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + rCurve = new Rarefact(lookup, rDisplays); + rCurve->getSharedCurve(freq, nIters); delete rCurve; - cout << order->getLabel() << '\t' << count << endl; + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + } + + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + rCurve = new Rarefact(lookup, rDisplays); + rCurve->getSharedCurve(freq, nIters); + delete rCurve; + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); } + + + lastLabel = lookup[0]->getLabel(); //get next line to process - if (format == "sharedfile") { - order = input->getSharedOrderVector(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(); + } + + if (m->control_pressed) { + m->Groups.clear(); + delete input; + for(int i=0;i::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; }else { - //you are using a list and a groupfile - SharedList = input->getSharedListVector(); //get new list vector to process - if (SharedList != NULL) { - order = SharedList->getSharedOrderVector(); //gets new order vector with group info. - }else { - break; - } + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } - - count++; } - + + if (m->control_pressed) { + m->Groups.clear(); + delete input; + for(int i=0;igetSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->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(); + delete input; + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } - //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); 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"; + m->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); - } }