X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=e989233c7b86c3efae39d5a7f1b5b0541a365bd5;hb=9ca2caadbeac83bb84b3330d9204b1b659d62941;hp=63a267d043d143d85435ba5c3259389df6f387af;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index 63a267d..e989233 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 +19,7 @@ #include "sharedsorest.h" #include "sharedthetayc.h" #include "sharedthetan.h" +#include "sharednseqs.h" //********************************************************************************************************************** @@ -27,32 +29,44 @@ CollectSharedCommand::CollectSharedCommand(){ globaldata = GlobalData::getInstance(); string fileNameRoot; fileNameRoot = getRootName(globaldata->inputFileName); - groupmap = globaldata->gGroupmap; + format = globaldata->getFormat(); + validCalculator = new ValidCalculators(); 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] == "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] == "sharednseqs") { + cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs"))); + } + } } + + //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"; @@ -79,15 +93,32 @@ CollectSharedCommand::~CollectSharedCommand(){ int CollectSharedCommand::execute(){ try { int count = 1; - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); - input = globaldata->ginput; - list = globaldata->glist; - order = list->getSharedOrderVector(); + //if the users entered no valid calculators don't execute command + if (cDisplays.size() == 0) { return 0; } - while(order != NULL){ + if (format == "sharedfile") { + read = new ReadPhilFile(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; + SharedList = globaldata->gSharedList; + order = SharedList->getSharedOrderVector(); + } + set orderList; + //set users groups + setGroups(); + + 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); @@ -99,17 +130,30 @@ 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++; + //get next line to process + if (format == "sharedfile") { + order = input->getSharedOrderVector(); }else { - break; + //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; + } } - + + 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) { @@ -124,3 +168,50 @@ int CollectSharedCommand::execute(){ //********************************************************************************************************************** +void CollectSharedCommand::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 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); + } + +} +/***********************************************************/ +