X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=a32b202d827d8df18c5696c3fc9ace85f3ddbf22;hb=cd37904452dc95b183ff313ff05720c562902487;hp=0a742ea562852e8097485bea5a67200f6d8524c8;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index 0a742ea..a32b202 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -35,65 +35,138 @@ //********************************************************************************************************************** -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; + lines.clear(); + 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[] = {"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 summary.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 summary.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; + } + + 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); +// format = globaldata->getFormat(); + mult = false; } } - //reset calc for next command - globaldata->setCalc(""); } catch(exception& e) { @@ -105,17 +178,48 @@ SummarySharedCommand::SummarySharedCommand(){ exit(1); } } + +//********************************************************************************************************************** + +void SummarySharedCommand::help(){ + try { + cout << "The summary.shared command can only be executed after a successful read.otu command." << "\n"; + cout << "The summary.shared command parameters are label, line and calc. No parameters are required, but you may not use " << "\n"; + cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n"; + cout << "summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups)." << "\n"; + cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n"; + validCalculator->printCalc("sharedsummary", cout); + cout << "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan" << "\n"; + cout << "The default value for groups is all the groups in your groupfile." << "\n"; + 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. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n"; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the SummarySharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + //********************************************************************************************************************** SummarySharedCommand::~SummarySharedCommand(){ delete input; delete read; + delete validCalculator; } //********************************************************************************************************************** int SummarySharedCommand::execute(){ try { + + if (abort == true) { return 0; } + int count = 1; //if the users entered no valid calculators don't execute command @@ -164,17 +268,22 @@ int SummarySharedCommand::execute(){ 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 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((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){ + if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ cout << lookup[0]->getLabel() << '\t' << count << endl; process(lookup); @@ -223,7 +332,7 @@ int SummarySharedCommand::execute(){ 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();