X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=eca2033ed6b0f675374e4e855933a8142a6435c5;hb=fd00cd216d3a38ccea22eae258e601df64218b05;hp=fcd2b00ea28805a54646524d831dd90d9784100e;hpb=7e0cf6431e287072c40b2c10c9e08199fce29ef4;p=mothur.git diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index fcd2b00..eca2033 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -11,6 +11,7 @@ #include "sharedsobscollectsummary.h" #include "sharedchao1.h" #include "sharedace.h" +#include "sharednseqs.h" #include "sharedjabund.h" #include "sharedsorabund.h" #include "sharedjclass.h" @@ -19,6 +20,15 @@ #include "sharedsorest.h" #include "sharedthetayc.h" #include "sharedthetan.h" +#include "sharedkstest.h" +#include "whittaker.h" +#include "sharedochiai.h" +#include "sharedanderbergs.h" +#include "sharedkulczynski.h" +#include "sharedkulczynskicody.h" +#include "sharedlennon.h" +#include "sharedmorisitahorn.h" +#include "sharedbraycurtis.h" //********************************************************************************************************************** @@ -30,9 +40,7 @@ SummarySharedCommand::SummarySharedCommand(){ openOutputFile(outputFileName, outputFileHandle); format = globaldata->getFormat(); validCalculator = new ValidCalculators(); - - //set users groups - setGroups(); + util = new SharedUtil(); int i; for (i=0; iEstimators.size(); i++) { @@ -43,26 +51,46 @@ SummarySharedCommand::SummarySharedCommand(){ 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] == "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()); } + } } - //reset calc for next command globaldata->setCalc(""); @@ -81,6 +109,7 @@ SummarySharedCommand::SummarySharedCommand(){ SummarySharedCommand::~SummarySharedCommand(){ delete input; delete read; + delete util; } //********************************************************************************************************************** @@ -93,14 +122,14 @@ int SummarySharedCommand::execute(){ if (sumCalculators.size() == 0) { return 0; } if (format == "sharedfile") { - read = new ReadPhilFile(globaldata->inputFileName); + 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 ReadPhilFile(globaldata->inputFileName); + read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); input = globaldata->ginput; @@ -108,19 +137,22 @@ int SummarySharedCommand::execute(){ 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; - + 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()); } @@ -128,7 +160,16 @@ 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' << (lookup[k]->getGroup() + lookup[l]->getGroup()) << '\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'; @@ -170,99 +211,4 @@ 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; - } - } - } - - //get rid of vectors from groups you don't want to analyze - for (int r = 0; r < lookup.size(); r++) { - if (inUsersGroups(lookup[r]->getGroup(), globaldata->Groups) != true) { - lookup.erase(lookup.begin()+r); - } - } - - } - 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::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); - } - -} /***********************************************************/