X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=eea7b25c4ade2bd6a98f5cea0eaabd9b1787ede8;hb=e4827e0945cbda536064e5a345996b2a7dfcbb81;hp=347ed0446c5e7c72cba1fac4dbab452b2992a606;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf;p=mothur.git diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index 347ed04..eea7b25 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -8,9 +8,10 @@ */ #include "summarysharedcommand.h" -#include "sharedsobs.h" +#include "sharedsobscollectsummary.h" #include "sharedchao1.h" #include "sharedace.h" +#include "sharednseqs.h" #include "sharedjabund.h" #include "sharedsorabund.h" #include "sharedjclass.h" @@ -19,39 +20,81 @@ #include "sharedsorest.h" #include "sharedthetayc.h" #include "sharedthetan.h" +#include "sharedkstest.h" +#include "sharedbdiversity.h" +#include "sharedochiai.h" +#include "sharedanderbergs.h" +#include "sharedkulczynski.h" +#include "sharedkulczynskicody.h" +#include "sharedlennon.h" +#include "sharedmorisitahorn.h" +#include "sharedbraycurtis.h" + //********************************************************************************************************************** SummarySharedCommand::SummarySharedCommand(){ try { globaldata = GlobalData::getInstance(); + outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary"); + openOutputFile(outputFileName, outputFileHandle); + format = globaldata->getFormat(); + validCalculator = new ValidCalculators(); + util = new SharedUtil(); int i; - for (i=0; isharedSummaryEstimators.size(); i++) { - if (globaldata->sharedSummaryEstimators[i] == "sharedSobs") { - sumCalculators.push_back(new SharedSobs()); - }else if (globaldata->sharedEstimators[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] == "jabund") { + sumCalculators.push_back(new JAbund()); + }else if (globaldata->Estimators[i] == "sorensonabund") { + 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] == "bdiversity") { + sumCalculators.push_back(new BDiversity()); + } + } } + //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"; @@ -67,36 +110,50 @@ SummarySharedCommand::SummarySharedCommand(){ SummarySharedCommand::~SummarySharedCommand(){ delete input; delete read; + delete util; } //********************************************************************************************************************** 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 ReadOTUFile(globaldata->inputFileName); + 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 = globaldata->ginput; + SharedList = globaldata->gSharedList; + order = SharedList->getSharedOrderVector(); + } + + //set users groups + util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary"); + + //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(); - getGroupComb(); - - int count = 1; while(order != NULL){ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ cout << order->getLabel() << '\t' << count << endl; - getSharedVectors(); //fills group vectors from order vector. + util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector. //fills group vectors from order vector. //randomize group order if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); } @@ -104,7 +161,16 @@ 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' << '\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'; @@ -116,15 +182,24 @@ 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) { @@ -137,70 +212,4 @@ int SummarySharedCommand::execute(){ } } -//********************************************************************************************************************** - -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++) { - SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins()); - temp->setLabel(order->getLabel()); - temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]); - lookup.push_back(temp); - } - - int numSeqs = order->size(); - //sample all the members - for(int i=0;iget(i); - int abundance; - - //set info for sharedvector in chosens group - for (int j = 0; j < lookup.size(); j++) { - if (chosen.group == lookup[j]->getGroup()) { - abundance = lookup[j]->getAbundance(chosen.bin); - lookup[j]->set(chosen.bin, (abundance + 1), chosen.group); - break; - } - } - - } - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SummarySharedCommand class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} - -/**************************************************************************************/ -void SummarySharedCommand::getGroupComb() { - 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); - } - 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"; - 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"; - exit(1); - } - -} - +/***********************************************************/