X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=ef0485c61886e6f14ae3135f908bf8317855130f;hb=f37a59b81c339f574d97042ff6e364146feb457a;hp=fafc290b0cdf8dd9bce4c7cb626797c6bf1ba4af;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;p=mothur.git diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index fafc290..ef0485c 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -35,88 +35,168 @@ //********************************************************************************************************************** -SummarySharedCommand::SummarySharedCommand(){ +SummarySharedCommand::SummarySharedCommand(string option){ try { globaldata = GlobalData::getInstance(); - outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary"); - openOutputFile(outputFileName, outputFileHandle); - format = globaldata->getFormat(); - validCalculator = new ValidCalculators(); - mult = false; + abort = false; + allLines = 1; + labels.clear(); + Estimators.clear(); - int i; - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) { - if (globaldata->Estimators[i] == "sharedsobs") { - sumCalculators.push_back(new SharedSobsCS()); - }else if (globaldata->Estimators[i] == "sharedchao") { - sumCalculators.push_back(new SharedChao1()); - }else if (globaldata->Estimators[i] == "sharedace") { - sumCalculators.push_back(new SharedAce()); - }else if (globaldata->Estimators[i] == "jabund") { - sumCalculators.push_back(new JAbund()); - }else if (globaldata->Estimators[i] == "sorabund") { - sumCalculators.push_back(new SorAbund()); - }else if (globaldata->Estimators[i] == "jclass") { - sumCalculators.push_back(new Jclass()); - }else if (globaldata->Estimators[i] == "sorclass") { - sumCalculators.push_back(new SorClass()); - }else if (globaldata->Estimators[i] == "jest") { - sumCalculators.push_back(new Jest()); - }else if (globaldata->Estimators[i] == "sorest") { - sumCalculators.push_back(new SorEst()); - }else if (globaldata->Estimators[i] == "thetayc") { - sumCalculators.push_back(new ThetaYC()); - }else if (globaldata->Estimators[i] == "thetan") { - sumCalculators.push_back(new ThetaN()); - }else if (globaldata->Estimators[i] == "kstest") { - sumCalculators.push_back(new KSTest()); - }else if (globaldata->Estimators[i] == "sharednseqs") { - sumCalculators.push_back(new SharedNSeqs()); - }else if (globaldata->Estimators[i] == "ochiai") { - sumCalculators.push_back(new Ochiai()); - }else if (globaldata->Estimators[i] == "anderberg") { - sumCalculators.push_back(new Anderberg()); - }else if (globaldata->Estimators[i] == "kulczynski") { - sumCalculators.push_back(new Kulczynski()); - }else if (globaldata->Estimators[i] == "kulczynskicody") { - sumCalculators.push_back(new KulczynskiCody()); - }else if (globaldata->Estimators[i] == "lennon") { - sumCalculators.push_back(new Lennon()); - }else if (globaldata->Estimators[i] == "morisitahorn") { - sumCalculators.push_back(new MorHorn()); - }else if (globaldata->Estimators[i] == "braycurtis") { - sumCalculators.push_back(new BrayCurtis()); - }else if (globaldata->Estimators[i] == "whittaker") { - sumCalculators.push_back(new Whittaker()); + //allow user to run help + if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"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() == "") { + mothurOut("You must read a list and a group, or a shared before you can use the summary.shared 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 = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } + else { + if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } + } + splitAtDash(calc, Estimators); + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + splitAtDash(groups, Groups); + globaldata->Groups = Groups; + } + + if (abort == false) { + + validCalculator = new ValidCalculators(); + int i; + + for (i=0; iisValidCalculator("sharedsummary", Estimators[i]) == true) { + if (Estimators[i] == "sharedsobs") { + sumCalculators.push_back(new SharedSobsCS()); + }else if (Estimators[i] == "sharedchao") { + sumCalculators.push_back(new SharedChao1()); + }else if (Estimators[i] == "sharedace") { + sumCalculators.push_back(new SharedAce()); + }else if (Estimators[i] == "jabund") { + sumCalculators.push_back(new JAbund()); + }else if (Estimators[i] == "sorabund") { + sumCalculators.push_back(new SorAbund()); + }else if (Estimators[i] == "jclass") { + sumCalculators.push_back(new Jclass()); + }else if (Estimators[i] == "sorclass") { + sumCalculators.push_back(new SorClass()); + }else if (Estimators[i] == "jest") { + sumCalculators.push_back(new Jest()); + }else if (Estimators[i] == "sorest") { + sumCalculators.push_back(new SorEst()); + }else if (Estimators[i] == "thetayc") { + sumCalculators.push_back(new ThetaYC()); + }else if (Estimators[i] == "thetan") { + sumCalculators.push_back(new ThetaN()); + }else if (Estimators[i] == "kstest") { + sumCalculators.push_back(new KSTest()); + }else if (Estimators[i] == "sharednseqs") { + sumCalculators.push_back(new SharedNSeqs()); + }else if (Estimators[i] == "ochiai") { + sumCalculators.push_back(new Ochiai()); + }else if (Estimators[i] == "anderberg") { + sumCalculators.push_back(new Anderberg()); + }else if (Estimators[i] == "kulczynski") { + sumCalculators.push_back(new Kulczynski()); + }else if (Estimators[i] == "kulczynskicody") { + sumCalculators.push_back(new KulczynskiCody()); + }else if (Estimators[i] == "lennon") { + sumCalculators.push_back(new Lennon()); + }else if (Estimators[i] == "morisitahorn") { + sumCalculators.push_back(new MorHorn()); + }else if (Estimators[i] == "braycurtis") { + sumCalculators.push_back(new BrayCurtis()); + }else if (Estimators[i] == "whittaker") { + sumCalculators.push_back(new Whittaker()); + } + } } + + outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary"); + openOutputFile(outputFileName, outputFileHandle); + mult = false; } } - //reset calc for next command - globaldata->setCalc(""); - } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "SummarySharedCommand", "SummarySharedCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SummarySharedCommand class function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + +//********************************************************************************************************************** + +void SummarySharedCommand::help(){ + try { + mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n"); + mothurOut("The summary.shared command parameters are label and calc. No parameters are required.\n"); + mothurOut("The summary.shared command should be in the following format: \n"); + mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n"); + mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n"); + validCalculator->printCalc("sharedsummary", cout); + mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n"); + mothurOut("The default value for groups is all the groups in your groupfile.\n"); + mothurOut("The label parameter is used to analyze specific labels 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. label), '=' and parameters (i.e.yourLabel).\n\n"); + } + catch(exception& e) { + errorOut(e, "SummarySharedCommand", "help"); exit(1); - } + } } + //********************************************************************************************************************** SummarySharedCommand::~SummarySharedCommand(){ - delete input; - delete read; + if (abort == false) { + delete read; + delete validCalculator; + } } //********************************************************************************************************************** int SummarySharedCommand::execute(){ try { - int count = 1; + + if (abort == true) { return 0; } //if the users entered no valid calculators don't execute command if (sumCalculators.size() == 0) { return 0; } @@ -133,7 +213,7 @@ int SummarySharedCommand::execute(){ input = globaldata->ginput; lookup = input->getSharedRAbundVectors(); - vector lastLookup = lookup; + string lastLabel = lookup[0]->getLabel(); //output estimator names as column headers outputFileHandle << "label" <<'\t' << "comparison" << '\t'; @@ -157,86 +237,97 @@ int SummarySharedCommand::execute(){ } 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]; } //close files and clean up outputFileHandle.close(); remove(outputFileName.c_str()); if (mult == true) { outAll.close(); remove(outAllFileName.c_str()); } return 0; + //if you only have 2 groups you don't need a .sharedmultiple file + }else if ((lookup.size() == 2) && (mult == true)) { + mult = false; + outAll.close(); + remove(outAllFileName.c_str()); } //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 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) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) { + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){ - cout << lookup[0]->getLabel() << '\t' << count << endl; + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); process(lookup); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) { - cout << lastLookup[0]->getLabel() << '\t' << count << endl; - process(lastLookup); + 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(); + process(lookup); - processedLabels.insert(lastLookup[0]->getLabel()); - userLabels.erase(lastLookup[0]->getLabel()); + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); } - //prevent memory leak - if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } } - lastLookup = lookup; + + lastLabel = lookup[0]->getLabel(); //get next line to process + //prevent memory leak + 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++) { - cout << "Your file does not include the label "<< *it; - if (processedLabels.count(lastLookup[0]->getLabel()) != 1) { - cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl; + mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl; + mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); } } - //run last line if you need to + //run last label if you need to if (needToRun == true) { - cout << lastLookup[0]->getLabel() << '\t' << count << endl; - process(lastLookup); + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input->getSharedRAbundVectors(lastLabel); + + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + process(lookup); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } - for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); + globaldata->Groups.clear(); //close files outputFileHandle.close(); if (mult == true) { outAll.close(); } + + for(int i=0;iginput = NULL; return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "SummarySharedCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************/ @@ -296,13 +387,9 @@ void SummarySharedCommand::process(vector thisLookup) { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "SummarySharedCommand", "process"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SummarySharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } -/***********************************************************/ \ No newline at end of file +/***********************************************************/