X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=d2333d74c6890f8d1c5563e22e9f27ba633046f2;hb=0024441c1ff9a98467ba53cc7420a37c98f32e86;hp=434d4a44311f57300c42623c0b052cff012d9e10;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1;p=mothur.git diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index 434d4a4..d2333d7 100644 --- a/collectsharedcommand.cpp +++ b/collectsharedcommand.cpp @@ -8,7 +8,7 @@ */ #include "collectsharedcommand.h" -#include "sharedsobs.h" +#include "sharedsobscollectsummary.h" #include "sharedchao1.h" #include "sharedace.h" #include "sharedjabund.h" @@ -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 "whittaker.h" + //********************************************************************************************************************** @@ -28,34 +41,64 @@ CollectSharedCommand::CollectSharedCommand(){ globaldata = GlobalData::getInstance(); string fileNameRoot; fileNameRoot = getRootName(globaldata->inputFileName); - groupmap = globaldata->gGroupmap; + format = globaldata->getFormat(); + convert(globaldata->getFreq(), freq); + 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", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedSobs") { - cDisplays.push_back(new CollectDisplay(new SharedSobs(), new SharedOneColumnFile(fileNameRoot+"shared.sobs", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedAce") { - cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedJabund") { - cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedSorensonAbund") { - cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedJclass") { - cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedSorClass") { - cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedJest") { - cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "sharedSorEst") { - cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "SharedThetaYC") { - cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc", groupmap->namesOfGroups))); - }else if (globaldata->sharedEstimators[i] == "SharedThetaN") { - cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan", 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"; @@ -75,6 +118,7 @@ CollectSharedCommand::~CollectSharedCommand(){ delete input; delete cCurve; delete read; + delete util; } //********************************************************************************************************************** @@ -82,37 +126,90 @@ CollectSharedCommand::~CollectSharedCommand(){ int CollectSharedCommand::execute(){ try { int count = 1; - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); - input = globaldata->ginput; - SharedList = globaldata->gSharedList; - order = SharedList->getSharedOrderVector(); + //if the users entered no valid calculators don't execute command + if (cDisplays.size() == 0) { return 0; } - while(order != NULL){ + read = new ReadOTUFile(globaldata->inputFileName); + read->read(&*globaldata); + + input = globaldata->ginput; + order = input->getSharedOrderVector(); + SharedOrderVector* lastOrder = order; + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = globaldata->labels; + set userLines = globaldata->lines; + + //set users groups + util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect"); + util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex); + + while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + 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); cCurve->getSharedCurve(freq); - delete cCurve; cout << order->getLabel() << '\t' << count << endl; + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); + userLines.erase(count); + + //you have a label the user want that is smaller than this line and the last line has not already been processed + } + + if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) { + //create collectors curve + cCurve = new Collect(lastOrder, cDisplays); + cCurve->getSharedCurve(freq); + delete cCurve; + + cout << lastOrder->getLabel() << '\t' << count << endl; + processedLabels.insert(lastOrder->getLabel()); + userLabels.erase(lastOrder->getLabel()); } - SharedList = input->getSharedListVector(); //get new list vector to process - if (SharedList != NULL) { - order = SharedList->getSharedOrderVector(); //gets new order vector with group info. - count++; + if (count != 1) { delete lastOrder; } + lastOrder = order; + + //get next line to process + order = input->getSharedOrderVector(); + count++; + } + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + cout << "Your file does not include the label "<< *it; + if (processedLabels.count(lastOrder->getLabel()) != 1) { + cout << ". I will use " << lastOrder->getLabel() << "." << endl; + needToRun = true; }else { - break; + cout << ". Please refer to " << lastOrder->getLabel() << "." << endl; } + } + //run last line if you need to + if (needToRun == true) { + cCurve = new Collect(lastOrder, cDisplays); + cCurve->getCurve(freq); + delete cCurve; + + cout << lastOrder->getLabel() << '\t' << count << endl; } - + + delete lastOrder; for(int i=0;iGroups.clear(); globaldata->setGroups(""); + return 0; } catch(exception& e) { @@ -125,5 +222,5 @@ int CollectSharedCommand::execute(){ } } +/***********************************************************/ -//**********************************************************************************************************************