X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=18470d0df300f3b37249b9e4fc7fb05a8211518f;hb=28b6634fd8f44d28b957b9ace79703c0ac79741c;hp=c451ef7aeb6ead4065f55a18bea99cb1840b530f;hpb=44c1323a88b2a697c7047df1b3bb8c59eadd15b1;p=mothur.git diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index c451ef7..18470d0 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -20,38 +20,49 @@ #include "sharedthetayc.h" #include "sharedthetan.h" + //********************************************************************************************************************** SummarySharedCommand::SummarySharedCommand(){ try { globaldata = GlobalData::getInstance(); + outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary"); + openOutputFile(outputFileName, outputFileHandle); + format = globaldata->getFormat(); + validCalculator = new ValidCalculators(); int i; - for (i=0; isharedSummaryEstimators.size(); i++) { - if (globaldata->sharedSummaryEstimators[i] == "sharedSobs") { - sumCalculators.push_back(new SharedSobsCS()); - }else if (globaldata->sharedSummaryEstimators[i] == "sharedChao") { - sumCalculators.push_back(new SharedChao1()); - }else if (globaldata->sharedSummaryEstimators[i] == "sharedAce") { - sumCalculators.push_back(new SharedAce()); - }else if (globaldata->sharedSummaryEstimators[i] == "sharedJabund") { - sumCalculators.push_back(new SharedJAbund()); - }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorensonAbund") { - sumCalculators.push_back(new SharedSorAbund()); - }else if (globaldata->sharedSummaryEstimators[i] == "sharedJclass") { - sumCalculators.push_back(new SharedJclass()); - }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorClass") { - sumCalculators.push_back(new SharedSorClass()); - }else if (globaldata->sharedSummaryEstimators[i] == "sharedJest") { - sumCalculators.push_back(new SharedJest()); - }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorEst") { - sumCalculators.push_back(new SharedSorEst()); - }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaYC") { - sumCalculators.push_back(new SharedThetaYC()); - }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaN") { - sumCalculators.push_back(new SharedThetaN()); + 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] == "sharedjabund") { + sumCalculators.push_back(new SharedJAbund()); + }else if (globaldata->Estimators[i] == "sharedsorensonabund") { + sumCalculators.push_back(new SharedSorAbund()); + }else if (globaldata->Estimators[i] == "sharedjclass") { + sumCalculators.push_back(new SharedJclass()); + }else if (globaldata->Estimators[i] == "sharedsorclass") { + sumCalculators.push_back(new SharedSorClass()); + }else if (globaldata->Estimators[i] == "sharedjest") { + sumCalculators.push_back(new SharedJest()); + }else if (globaldata->Estimators[i] == "sharedsorest") { + sumCalculators.push_back(new SharedSorEst()); + }else if (globaldata->Estimators[i] == "sharedthetayc") { + sumCalculators.push_back(new SharedThetaYC()); + }else if (globaldata->Estimators[i] == "sharedthetan") { + sumCalculators.push_back(new SharedThetaN()); + } } } + + //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"; @@ -73,23 +84,37 @@ SummarySharedCommand::~SummarySharedCommand(){ int SummarySharedCommand::execute(){ try { - outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary"); - openOutputFile(outputFileName, outputFileHandle); - - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); + int count = 1; + //if the users entered no valid calculators don't execute command + if (sumCalculators.size() == 0) { return 0; } + + if (format == "sharedfile") { + read = new ReadPhilFile(globaldata->inputFileName); + read->read(&*globaldata); + + input = globaldata->ginput; + order = input->getSharedOrderVector(); + }else { + //you are using a list and a groupfile + read = new ReadPhilFile(globaldata->inputFileName); + read->read(&*globaldata); + + input = globaldata->ginput; + SharedList = globaldata->gSharedList; + order = SharedList->getSharedOrderVector(); + } + + //set users groups + setGroups(); + + //output estimator names as column headers outputFileHandle << "label" <<'\t' << "comparison" << '\t'; for(int i=0;igetName(); } outputFileHandle << endl; - SharedList = globaldata->gSharedList; - input = globaldata->ginput; - order = SharedList->getSharedOrderVector(); - - int count = 1; while(order != NULL){ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ @@ -115,15 +140,24 @@ int SummarySharedCommand::execute(){ } } - SharedList = input->getSharedListVector(); //get new list vector to process - if (SharedList != NULL) { - order = SharedList->getSharedOrderVector(); //gets new order vector with group info. - count++; + //get next line to process + if (format == "sharedfile") { + order = input->getSharedOrderVector(); }else { - break; + //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; + } } + count++; } - + + //reset groups parameter + globaldata->Groups.clear(); globaldata->setGroups(""); + return 0; } catch(exception& e) { @@ -142,10 +176,10 @@ void SummarySharedCommand::getSharedVectors(){ try { lookup.clear(); //create and initialize vector of sharedvectors, one for each group - for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) { + for (int i = 0; i < globaldata->Groups.size(); i++) { SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins()); temp->setLabel(order->getLabel()); - temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]); + temp->setGroup(globaldata->Groups[i]); lookup.push_back(temp); } @@ -164,7 +198,6 @@ try { break; } } - } } catch(exception& e) { @@ -179,3 +212,49 @@ try { } //********************************************************************************************************************** +void SummarySharedCommand::setGroups() { + try { + //if the user has not entered specific groups to analyze then do them all + if (globaldata->Groups.size() != 0) { + if (globaldata->Groups[0] != "all") { + //check that groups are valid + for (int i = 0; i < globaldata->Groups.size(); i++) { + if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) { + cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl; + // erase the invalid group from globaldata->Groups + globaldata->Groups.erase(globaldata->Groups.begin()+i); + } + } + + //if the user only entered invalid groups + if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) { + cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; + for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { + globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]); + } + } + }else{//user has enter "all" and wants the default groups + globaldata->Groups.clear(); + for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { + globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]); + } + globaldata->setGroups(""); + } + }else { + for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { + globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]); + } + } + + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the SummarySharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + +} +/***********************************************************/