X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=4a3a338944958aa8e9342661847898c20e598f3d;hb=fb01d5df390a98313ca095a812fc240dc079d084;hp=63a267d043d143d85435ba5c3259389df6f387af;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index 63a267d..4a3a338 100644 --- a/collectsharedcommand.cpp +++ b/collectsharedcommand.cpp @@ -8,6 +8,7 @@ */ #include "collectsharedcommand.h" +#include "sharedsobscollectsummary.h" #include "sharedchao1.h" #include "sharedace.h" #include "sharedjabund.h" @@ -18,6 +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" + //********************************************************************************************************************** @@ -27,32 +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+"sharedChao", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedAce") { - cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"sharedAce", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedJabund") { - cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"SharedJabund", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedSorensonAbund") { - cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"SharedSorensonAbund", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedJclass") { - cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"SharedJclass", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedSorClass") { - cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"SharedSorClass", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedJest") { - cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"SharedJest", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedSorEst") { - cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"SharedSorEst", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "SharedThetaYC") { - cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"SharedThetaYC", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "SharedThetaN") { - cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"SharedThetaN", groupmap->namesOfGroups))); + 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"; @@ -72,6 +117,7 @@ CollectSharedCommand::~CollectSharedCommand(){ delete input; delete cCurve; delete read; + delete util; } //********************************************************************************************************************** @@ -79,16 +125,28 @@ 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; - list = globaldata->glist; - order = list->getSharedOrderVector(); + order = input->getSharedOrderVector(); + 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); convert(globaldata->getFreq(), freq); @@ -99,17 +157,21 @@ int CollectSharedCommand::execute(){ cout << order->getLabel() << '\t' << count << endl; } - list = input->getListVector(); //get new list vector to process - if (list != NULL) { - order = list->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) { @@ -122,5 +184,5 @@ int CollectSharedCommand::execute(){ } } +/***********************************************************/ -//**********************************************************************************************************************