| /dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/trimmomatic/ |
| H A D | TrimmomaticSupport.cpp | 61 LocalWorkflow::TrimmomaticStepsRegistry::releaseInstance(); in ~TrimmomaticSupport()
65 …LocalWorkflow::TrimmomaticStepsRegistry *registry = LocalWorkflow::TrimmomaticStepsRegistry::getIn… in initTrimmomaticSteps()
66 registry->registerEntry(new LocalWorkflow::AvgQualStepFactory()); in initTrimmomaticSteps()
67 registry->registerEntry(new LocalWorkflow::CropStepFactory()); in initTrimmomaticSteps()
68 registry->registerEntry(new LocalWorkflow::HeadCropStepFactory()); in initTrimmomaticSteps()
70 registry->registerEntry(new LocalWorkflow::LeadingStepFactory()); in initTrimmomaticSteps()
71 registry->registerEntry(new LocalWorkflow::MaxInfoStepFactory()); in initTrimmomaticSteps()
72 registry->registerEntry(new LocalWorkflow::MinLenStepFactory()); in initTrimmomaticSteps()
74 registry->registerEntry(new LocalWorkflow::ToPhred33StepFactory()); in initTrimmomaticSteps()
75 registry->registerEntry(new LocalWorkflow::ToPhred64StepFactory()); in initTrimmomaticSteps()
[all …]
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| /dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/ |
| H A D | ExternalToolSupportPlugin.cpp | 481 LocalWorkflow::MAFFTWorkerFactory::init(); in registerWorkers()
486 LocalWorkflow::TCoffeeWorkerFactory::init(); in registerWorkers()
491 LocalWorkflow::TopHatWorkerFactory::init(); in registerWorkers()
493 LocalWorkflow::MACSWorkerFactory::init(); in registerWorkers()
496 LocalWorkflow::SeqPosWorkerFactory::init(); in registerWorkers()
498 LocalWorkflow::CAP3WorkerFactory::init(); in registerWorkers()
500 LocalWorkflow::BwaMemWorkerFactory::init(); in registerWorkers()
501 LocalWorkflow::BwaWorkerFactory::init(); in registerWorkers()
502 LocalWorkflow::BowtieWorkerFactory::init(); in registerWorkers()
508 LocalWorkflow::SnpEffFactory::init(); in registerWorkers()
[all …]
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| /dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/library/ |
| H A D | IncludedProtoFactoryImpl.cpp | 59 … coreLog.error(LocalWorkflow::ScriptWorker::tr("For input port was set empty data type")); in _getScriptProto()
73 … coreLog.error(LocalWorkflow::ScriptWorker::tr("For output port was set empty data type")); in _getScriptProto()
82 …Descriptor inDesc(IN_PORT_ID, LocalWorkflow::ScriptWorker::tr("Input data"), LocalWorkflow::Script… in _getScriptProto()
83 …Descriptor outDesc(OUT_PORT_ID, LocalWorkflow::ScriptWorker::tr("Output data"), LocalWorkflow::Scr… in _getScriptProto()
94 namePrefix = LocalWorkflow::ScriptWorkerFactory::ACTOR_ID; in _getScriptProto()
101 proto->setPrompter(new LocalWorkflow::ScriptPromter()); in _getScriptProto()
142 …Descriptor outDesc(OUT_PORT_ID, LocalWorkflow::ExternalProcessWorker::tr("Output data"), LocalWork… in _getExternalToolProto()
200 proto->setPrompter(new LocalWorkflow::ExternalProcessWorkerPrompter()); in _getExternalToolProto()
256 proto->setPrompter(new LocalWorkflow::SchemaWorkerPrompter()); in _getSchemaActorProto()
267 …QScopedPointer<LocalWorkflow::ExternalProcessWorkerFactory> factory(new LocalWorkflow::ExternalPro… in _registerExternalToolWorker()
[all …]
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| H A D | CoreLib.cpp | 100 using namespace LocalWorkflow;
344 …CandidatesSplitterRegistry::instance()->registerSplitter(new LocalWorkflow::SeReadsListSplitter()); in init()
345 …CandidatesSplitterRegistry::instance()->registerSplitter(new LocalWorkflow::PeReadsListSplitter()); in init()
459 …CandidatesSplitterRegistry::instance()->unregisterSplitter(LocalWorkflow::SeReadsListSplitter::ID); in cleanup()
460 …CandidatesSplitterRegistry::instance()->unregisterSplitter(LocalWorkflow::PeReadsListSplitter::ID); in cleanup()
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| /dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/spades/ |
| H A D | SpadesTask.cpp | 70 …SpadesTask::OPTION_DATASET_TYPE, LocalWorkflow::SpadesWorker::DATASET_TYPE_STANDARD_ISOLATE).toStr… in prepare()
74 …QString runningMode = settings.getCustomValue(SpadesTask::OPTION_RUNNING_MODE, LocalWorkflow::Spad… in prepare()
75 if (runningMode == LocalWorkflow::SpadesWorker::RUNNING_MODE_ASSEMBLY_ONLY) { in prepare()
77 } else if (runningMode == LocalWorkflow::SpadesWorker::RUNNING_MODE_ERROR_CORRECTION_ONLY) { in prepare()
82 …QString sequencingPlatform = inputDataDialogSettings.value(LocalWorkflow::SpadesWorkerFactory::SEQ… in prepare()
96 …QString k = settings.getCustomValue(SpadesTask::OPTION_K_MER, LocalWorkflow::SpadesWorker::K_MER_A… in prepare()
97 if (k != LocalWorkflow::SpadesWorker::K_MER_AUTO) { in prepare()
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| /dports/biology/ugene/ugene-40.1/src/plugins/ngs_reads_classification/src/ |
| H A D | NgsReadsClassificationUtils.cpp | 65 int NgsReadsClassificationUtils::countClassified(const LocalWorkflow::TaxonomyClassificationResult … in countClassified()
66 LocalWorkflow::TaxonomyClassificationResult::const_iterator it; in countClassified()
69 …if (it.value() != LocalWorkflow::TaxonomyTree::UNCLASSIFIED_ID && it.value() != LocalWorkflow::Tax… in countClassified()
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| H A D | TaxonomySupport.h | 43 namespace LocalWorkflow {
203 Q_DECLARE_METATYPE(U2::LocalWorkflow::TaxID)
204 Q_DECLARE_METATYPE(U2::LocalWorkflow::TaxIDSet)
205 Q_DECLARE_METATYPE(U2::LocalWorkflow::TaxonomyClassificationResult)
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| H A D | NgsReadsClassificationPlugin.cpp | 100 LocalWorkflow::TaxonomyTree::getInstance(); in run()
117 LocalWorkflow::ClassificationFilterWorkerFactory::init(); in NgsReadsClassificationPlugin()
118 LocalWorkflow::ClassificationReportWorkerFactory::init(); in NgsReadsClassificationPlugin()
119 LocalWorkflow::EnsembleClassificationWorkerFactory::init(); in NgsReadsClassificationPlugin()
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| /dports/biology/ugene/ugene-40.1/src/plugins/pcr/src/ |
| H A D | PcrPlugin.cpp | 66 LocalWorkflow::FindPrimerPairsWorkerFactory::init(); in PcrPlugin()
67 LocalWorkflow::PrimersGrouperWorkerFactory::init(); in PcrPlugin()
68 LocalWorkflow::InSilicoPcrWorkerFactory::init(); in PcrPlugin()
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| H A D | PrimersGrouperWorker.cpp | 46 namespace LocalWorkflow { namespace
248 report += createColumn(LocalWorkflow::PrimersGrouperWorker::tr("Group name")); in createReport()
249 report += createColumn(LocalWorkflow::PrimersGrouperWorker::tr("Forward primer name")); in createReport()
250 report += createColumn(LocalWorkflow::PrimersGrouperWorker::tr("Forward primer sequence")); in createReport()
251 report += createColumn(LocalWorkflow::PrimersGrouperWorker::tr("Reverse primer name")); in createReport()
252 report += createColumn(LocalWorkflow::PrimersGrouperWorker::tr("Reverse primer sequence")); in createReport()
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| H A D | FindPrimerPairsWorker.cpp | 46 namespace LocalWorkflow { namespace
215 report += createColumn(LocalWorkflow::FindPrimerPairsWorker::tr("Forward primer name")); in createReport()
216 report += createColumn(LocalWorkflow::FindPrimerPairsWorker::tr("Reverse primer name")); in createReport()
217 report += createColumn(LocalWorkflow::FindPrimerPairsWorker::tr("Forward Tm")); in createReport()
218 report += createColumn(LocalWorkflow::FindPrimerPairsWorker::tr("Reverse Tm")); in createReport()
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| /dports/biology/ugene/ugene-40.1/src/plugins/dna_export/src/ |
| H A D | DNAExportPlugin.cpp | 74 LocalWorkflow::ImportPhredQualityWorkerFactory::init(); in DNAExportPlugin()
75 LocalWorkflow::ExportPhredQualityWorkerFactory::init(); in DNAExportPlugin()
76 LocalWorkflow::GenerateDNAWorkerFactory::init(); in DNAExportPlugin()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Script/src/js/ |
| H A D | ActorWrap.cpp | 106 LocalWorkflow::BaseWorker *worker = obj->actor->castPeer<LocalWorkflow::BaseWorker>(); in isDone()
117 LocalWorkflow::BaseWorker *worker = obj->actor->castPeer<LocalWorkflow::BaseWorker>(); in isReady()
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| H A D | JsScheduler.cpp | 44 …LocalWorkflow::BaseWorker *worker = schema->actorById(actor)->castPeer<LocalWorkflow::BaseWorker>(… in tick()
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| /dports/biology/ugene/ugene-40.1/src/plugins/kraken_support/src/ |
| H A D | KrakenClassifyTask.h | 55 const LocalWorkflow::TaxonomyClassificationResult &getParsedReport() const;
64 LocalWorkflow::TaxonomyClassificationResult parsedReport;
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| H A D | KrakenSupportPlugin.cpp | 50 LocalWorkflow::KrakenBuildWorkerFactory::init(); in KrakenSupportPlugin()
51 LocalWorkflow::KrakenClassifyWorkerFactory::init(); in KrakenSupportPlugin()
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| H A D | KrakenBuildValidator.cpp | 41 …const int minimizerLength = actor->getParameter(LocalWorkflow::KrakenBuildWorkerFactory::MINIMIZER… in validateMinimizerLength()
42 …const int kMerLength = actor->getParameter(LocalWorkflow::KrakenBuildWorkerFactory::K_MER_LENGTH_A… in validateMinimizerLength()
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| H A D | KrakenClassifyTask.cpp | 61 const LocalWorkflow::TaxonomyClassificationResult &KrakenClassifyTask::getParsedReport() const { in getParsedReport()
115 LocalWorkflow::TaxID assID = assStr.toUInt(&ok); in run()
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| /dports/biology/ugene/ugene-40.1/src/plugins/diamond_support/src/ |
| H A D | DiamondSupportPlugin.cpp | 50 LocalWorkflow::DiamondBuildWorkerFactory::init(); in DiamondSupportPlugin()
51 LocalWorkflow::DiamondClassifyWorkerFactory::init(); in DiamondSupportPlugin()
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| H A D | DiamondClassifyTask.h | 74 const LocalWorkflow::TaxonomyClassificationResult &getParsedReport() const;
84 LocalWorkflow::TaxonomyClassificationResult parsedReport;
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| /dports/biology/ugene/ugene-40.1/src/plugins/wevote_support/src/ |
| H A D | WevoteTask.h | 51 const LocalWorkflow::TaxonomyClassificationResult &getClassification() const;
70 LocalWorkflow::TaxonomyClassificationResult classification;
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| /dports/biology/ugene/ugene-40.1/src/plugins/clark_support/src/ |
| H A D | ClarkSupportPlugin.cpp | 53 LocalWorkflow::ClarkBuildWorkerFactory::init(); in ClarkSupportPlugin()
54 LocalWorkflow::ClarkClassifyWorkerFactory::init(); in ClarkSupportPlugin()
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| /dports/biology/ugene/ugene-40.1/src/plugins/ngs_reads_classification/transl/ |
| H A D | russian.ts | 74 <name>U2::LocalWorkflow::ClassificationFilterPrompter</name>
81 <name>U2::LocalWorkflow::ClassificationFilterTask</name>
104 <name>U2::LocalWorkflow::ClassificationFilterWorker</name>
223 <name>U2::LocalWorkflow::ClassificationReportTask</name>
230 <name>U2::LocalWorkflow::ClassificationReportWorker</name>
273 <name>U2::LocalWorkflow::EnsembleClassificationPrompter</name>
280 <name>U2::LocalWorkflow::EnsembleClassificationTask</name>
291 <name>U2::LocalWorkflow::EnsembleClassificationWorker</name>
390 <name>U2::LocalWorkflow::GenomicLibraryDialog</name>
401 <name>U2::LocalWorkflow::TaxonSelectionDialog</name>
[all …]
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| /dports/biology/ugene/ugene-40.1/src/plugins/weight_matrix/src/ |
| H A D | WeightMatrixPlugin.cpp | 76 LocalWorkflow::PWMatrixWorkerFactory::init(); in WeightMatrixPlugin()
77 LocalWorkflow::PFMatrixWorkerFactory::init(); in WeightMatrixPlugin()
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| /dports/biology/ugene/ugene-40.1/src/plugins/annotator/src/ |
| H A D | AnnotatorPlugin.cpp | 68 LocalWorkflow::CollocationWorkerFactory::init(); in AnnotatorPlugin()
69 LocalWorkflow::GeneByGeneReportWorkerFactory::init(); in AnnotatorPlugin()
|