X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=4a3a338944958aa8e9342661847898c20e598f3d;hb=fb01d5df390a98313ca095a812fc240dc079d084;hp=ec35dd601e75abd3ea7b65e32aabcaa1c13b1c90;hpb=2657127a3e1f3b5463f2b3a3b49bc19843f5c9d2;p=mothur.git diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index ec35dd6..4a3a338 100644 --- a/collectsharedcommand.cpp +++ b/collectsharedcommand.cpp @@ -20,7 +20,7 @@ #include "sharedthetayc.h" #include "sharedthetan.h" #include "sharedkstest.h" -#include "sharedbdiversity.h" +#include "whittaker.h" #include "sharednseqs.h" #include "sharedochiai.h" #include "sharedanderbergs.h" @@ -29,6 +29,8 @@ #include "sharedlennon.h" #include "sharedmorisitahorn.h" #include "sharedbraycurtis.h" +#include "sharedjackknife.h" +#include "sharedwhittaker.h" @@ -41,6 +43,7 @@ CollectSharedCommand::CollectSharedCommand(){ fileNameRoot = getRootName(globaldata->inputFileName); format = globaldata->getFormat(); validCalculator = new ValidCalculators(); + util = new SharedUtil(); int i; for (i=0; iEstimators.size(); i++) { @@ -51,42 +54,43 @@ CollectSharedCommand::CollectSharedCommand(){ cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs"))); }else if (globaldata->Estimators[i] == "sharedace") { cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace"))); - }else if (globaldata->Estimators[i] == "sharedjabund") { - cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund"))); - }else if (globaldata->Estimators[i] == "sharedsorensonabund") { - cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund"))); - }else if (globaldata->Estimators[i] == "sharedjclass") { - cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass"))); - }else if (globaldata->Estimators[i] == "sharedsorclass") { - cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass"))); - }else if (globaldata->Estimators[i] == "sharedjest") { - cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest"))); - }else if (globaldata->Estimators[i] == "sharedsorest") { - cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest"))); - }else if (globaldata->Estimators[i] == "sharedthetayc") { - cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc"))); - }else if (globaldata->Estimators[i] == "sharedthetan") { - cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan"))); - }else if (globaldata->Estimators[i] == "sharedkstest") { - cDisplays.push_back(new CollectDisplay(new SharedKSTest(), new SharedOneColumnFile(fileNameRoot+"shared.kstest"))); - }else if (globaldata->Estimators[i] == "sharedbdiversity") { - cDisplays.push_back(new CollectDisplay(new SharedBDiversity(), new SharedOneColumnFile(fileNameRoot+"shared.bdiversity"))); + }else if (globaldata->Estimators[i] == "jabund") { + cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund"))); + }else if (globaldata->Estimators[i] == "sorabund") { + cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund"))); + }else if (globaldata->Estimators[i] == "jclass") { + cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass"))); + }else if (globaldata->Estimators[i] == "sorclass") { + cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass"))); + }else if (globaldata->Estimators[i] == "jest") { + cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest"))); + }else if (globaldata->Estimators[i] == "sorest") { + cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest"))); + }else if (globaldata->Estimators[i] == "thetayc") { + cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc"))); + }else if (globaldata->Estimators[i] == "thetan") { + cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan"))); + }else if (globaldata->Estimators[i] == "kstest") { + cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest"))); + }else if (globaldata->Estimators[i] == "whittaker") { + cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker"))); }else if (globaldata->Estimators[i] == "sharednseqs") { cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs"))); - }else if (globaldata->Estimators[i] == "sharedochiai") { - cDisplays.push_back(new CollectDisplay(new SharedOchiai(), new SharedOneColumnFile(fileNameRoot+"shared.ochiai"))); - }else if (globaldata->Estimators[i] == "sharedanderberg") { - cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg"))); - }else if (globaldata->Estimators[i] == "sharedkulczynski") { - cDisplays.push_back(new CollectDisplay(new SharedKulczynski(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynski"))); - }else if (globaldata->Estimators[i] == "sharedkulczynskicody") { - cDisplays.push_back(new CollectDisplay(new SharedKulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynskicody"))); - }else if (globaldata->Estimators[i] == "sharedlennon") { - cDisplays.push_back(new CollectDisplay(new SharedLennon(), new SharedOneColumnFile(fileNameRoot+"shared.lennon"))); - }else if (globaldata->Estimators[i] == "sharedmorisitahorn") { - cDisplays.push_back(new CollectDisplay(new SharedMorHorn(), new SharedOneColumnFile(fileNameRoot+"shared.morisitahorn"))); - }else if (globaldata->Estimators[i] == "sharedbraycurtis") { - cDisplays.push_back(new CollectDisplay(new SharedBrayCurtis(), new SharedOneColumnFile(fileNameRoot+"shared.braycurtis"))); + + }else if (globaldata->Estimators[i] == "ochiai") { + cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai"))); + }else if (globaldata->Estimators[i] == "anderberg") { + cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg"))); + }else if (globaldata->Estimators[i] == "skulczynski") { + cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski"))); + }else if (globaldata->Estimators[i] == "kulczynskicody") { + cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody"))); + }else if (globaldata->Estimators[i] == "lennon") { + cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon"))); + }else if (globaldata->Estimators[i] == "morisitahorn") { + cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn"))); + }else if (globaldata->Estimators[i] == "braycurtis") { + cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis"))); } } } @@ -113,6 +117,7 @@ CollectSharedCommand::~CollectSharedCommand(){ delete input; delete cCurve; delete read; + delete util; } //********************************************************************************************************************** @@ -124,29 +129,24 @@ int CollectSharedCommand::execute(){ //if the users entered no valid calculators don't execute command if (cDisplays.size() == 0) { return 0; } - if (format == "sharedfile") { - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); + 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->read(&*globaldata); + input = globaldata->ginput; + order = input->getSharedOrderVector(); - input = globaldata->ginput; - SharedList = globaldata->gSharedList; - order = SharedList->getSharedOrderVector(); - } set orderList; //set users groups - setGroups(); + util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect"); + util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex); while(order != NULL){ + orderList.insert(order->getLabel()); + if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ + //create collectors curve cCurve = new Collect(order, cDisplays); convert(globaldata->getFreq(), freq); @@ -158,24 +158,15 @@ int CollectSharedCommand::execute(){ } //get next line to process - if (format == "sharedfile") { - order = input->getSharedOrderVector(); - }else { - //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; - } - } - + delete order; + order = input->getSharedOrderVector(); count++; } set::iterator i; for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i) if(orderList.count(*i) == 0) cout << "'" << *i << "'" << " is not a valid label.\n"; + for(int i=0;iGroups.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 CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} /***********************************************************/