X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=9e2c6681afbad503c02f7116bf797ccd99d5e488;hb=9ca2caadbeac83bb84b3330d9204b1b659d62941;hp=b9fd08debd294870af590f5be48fdc4a7c7ba890;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index b9fd08d..9e2c668 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -8,8 +8,10 @@ */ #include "summarysharedcommand.h" +#include "sharedsobscollectsummary.h" #include "sharedchao1.h" #include "sharedace.h" +#include "sharednseqs.h" #include "sharedjabund.h" #include "sharedsorabund.h" #include "sharedjclass.h" @@ -19,36 +21,51 @@ #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] == "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()); + }else if (globaldata->Estimators[i] == "sharednseqs") { + sumCalculators.push_back(new SharedNSeqs()); + } } } + + //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"; @@ -70,24 +87,37 @@ SummarySharedCommand::~SummarySharedCommand(){ int SummarySharedCommand::execute(){ try { - outputFileName = ((getRootName(globaldata->inputFileName)) + "sharedSummary"); - openOutputFile(outputFileName, outputFileHandle); - - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); + int count = 1; - outputFileHandle << '\t' << '\t' << '\t' << '\t'; //pads file for labels and groupnames + //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; - list = globaldata->glist; - input = globaldata->ginput; - order = list->getSharedOrderVector(); - getGroupComb(); - - int count = 1; while(order != NULL){ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ @@ -101,7 +131,15 @@ int SummarySharedCommand::execute(){ int n = 1; for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare for (int l = n; l < lookup.size(); l++) { - outputFileHandle << order->getLabel() << '\t' << groupComb[n-1] << '\t'; //print out label and group + outputFileHandle << order->getLabel() << '\t'; + + //sort groups to be alphanumeric + if (lookup[k]->getGroup() > lookup[l]->getGroup()) { + outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups + }else{ + outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups + } + for(int i=0;igetValues(lookup[k], lookup[l]); //saves the calculator outputs outputFileHandle << '\t'; @@ -113,15 +151,24 @@ int SummarySharedCommand::execute(){ } } - list = input->getListVector(); //get new list vector to process - if (list != NULL) { - order = list->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) { @@ -140,10 +187,10 @@ 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); } @@ -162,7 +209,6 @@ try { break; } } - } } catch(exception& e) { @@ -176,28 +222,50 @@ try { } -/**************************************************************************************/ -void SummarySharedCommand::getGroupComb() { +//********************************************************************************************************************** +void SummarySharedCommand::setGroups() { try { - string group; - - int n = 1; - for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) { - for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) { - group = globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[l]; - groupComb.push_back(group); + //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]); } - n++; } + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + 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 getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + cout << "An unknown error has occurred in the SummarySharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; exit(1); - } + } } - +/***********************************************************/