X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=86b35a5191d268452d86a2994dd1bcafd06a3001;hb=ee27b6e01a979fdf832668eb87412b029f77e4d7;hp=217045a4a1fc5dc0c83986f3b3a0345b755e1f6c;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index 217045a..86b35a5 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" + //********************************************************************************************************************** @@ -30,6 +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++) { @@ -40,22 +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] == "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"))); } } } @@ -82,6 +117,7 @@ CollectSharedCommand::~CollectSharedCommand(){ delete input; delete cCurve; delete read; + delete util; } //********************************************************************************************************************** @@ -93,24 +129,20 @@ 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 + 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); @@ -123,22 +155,18 @@ 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; - } - } - + 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) { @@ -151,5 +179,5 @@ int CollectSharedCommand::execute(){ } } +/***********************************************************/ -//**********************************************************************************************************************