X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=06dbce79b1685a93c13c38f0b3906e6b8f7e9fe3;hb=599af78a6ea4916919d460a131e2d0dffa28d35e;hp=a6479da20d4e5b52a09cdb06d76676f26ed583e4;hpb=44c1323a88b2a697c7047df1b3bb8c59eadd15b1;p=mothur.git diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index a6479da..06dbce7 100644 --- a/collectsharedcommand.cpp +++ b/collectsharedcommand.cpp @@ -19,6 +19,19 @@ #include "sharedsorest.h" #include "sharedthetayc.h" #include "sharedthetan.h" +#include "sharedkstest.h" +#include "whittaker.h" +#include "sharednseqs.h" +#include "sharedochiai.h" +#include "sharedanderbergs.h" +#include "sharedkulczynski.h" +#include "sharedkulczynskicody.h" +#include "sharedlennon.h" +#include "sharedmorisitahorn.h" +#include "sharedbraycurtis.h" +#include "sharedjackknife.h" +#include "sharedwhittaker.h" + //********************************************************************************************************************** @@ -28,34 +41,63 @@ CollectSharedCommand::CollectSharedCommand(){ globaldata = GlobalData::getInstance(); string fileNameRoot; fileNameRoot = getRootName(globaldata->inputFileName); - //groupmap = globaldata->gGroupmap; + format = globaldata->getFormat(); + validCalculator = new ValidCalculators(); + util = new SharedUtil(); int i; - for (i=0; isharedEstimators.size(); i++) { - if (globaldata->sharedEstimators[i] == "sharedChao") { - cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao"))); - }else if (globaldata->sharedEstimators[i] == "sharedSobs") { - cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs"))); - }else if (globaldata->sharedEstimators[i] == "sharedAce") { - cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace"))); - }else if (globaldata->sharedEstimators[i] == "sharedJabund") { - cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund"))); - }else if (globaldata->sharedEstimators[i] == "sharedSorensonAbund") { - cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund"))); - }else if (globaldata->sharedEstimators[i] == "sharedJclass") { - cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass"))); - }else if (globaldata->sharedEstimators[i] == "sharedSorClass") { - cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass"))); - }else if (globaldata->sharedEstimators[i] == "sharedJest") { - cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest"))); - }else if (globaldata->sharedEstimators[i] == "sharedSorEst") { - cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest"))); - }else if (globaldata->sharedEstimators[i] == "SharedThetaYC") { - cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc"))); - }else if (globaldata->sharedEstimators[i] == "SharedThetaN") { - cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan"))); + for (i=0; iEstimators.size(); i++) { + if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) { + if (globaldata->Estimators[i] == "sharedchao") { + cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao"))); + }else if (globaldata->Estimators[i] == "sharedsobs") { + 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] == "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] == "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"))); + } } } + + //reset calc for next command + globaldata->setCalc(""); + } catch(exception& e) { cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; @@ -75,6 +117,7 @@ CollectSharedCommand::~CollectSharedCommand(){ delete input; delete cCurve; delete read; + delete util; } //********************************************************************************************************************** @@ -82,15 +125,24 @@ CollectSharedCommand::~CollectSharedCommand(){ int CollectSharedCommand::execute(){ try { int count = 1; - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); + //if the users entered no valid calculators don't execute command + if (cDisplays.size() == 0) { return 0; } + + read = new ReadOTUFile(globaldata->inputFileName); + read->read(&*globaldata); + input = globaldata->ginput; - SharedList = globaldata->gSharedList; - order = SharedList->getSharedOrderVector(); + order = input->getSharedOrderVector(); - while(order != NULL){ + set orderList; + //set users groups + 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); @@ -102,17 +154,20 @@ int CollectSharedCommand::execute(){ cout << order->getLabel() << '\t' << count << endl; } - SharedList = input->getSharedListVector(); //get new list vector to process - if (SharedList != NULL) { - order = SharedList->getSharedOrderVector(); //gets new order vector with group info. - count++; - }else { - break; - } - + //get next line to process + 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.clear(); globaldata->setGroups(""); + return 0; } catch(exception& e) { @@ -125,5 +180,5 @@ int CollectSharedCommand::execute(){ } } +/***********************************************************/ -//**********************************************************************************************************************