#include <corelib/ncbistl.hpp>#include <corelib/ncbitype.h>#include <corelib/ncbi_limits.h>#include "njn_matrix.hpp"
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Functions | |
| void | flatten (size_t dimension_, const Int4 *const *scoreMatrix_, const double *const *prob_, size_t *dim_, Int4 **score_, double **p_, size_t dimension2_=0) |
| double | lambda (size_t dimMatrix_, const Int4 *const *scoreMatrix_, const double *q_) |
| double | mu (size_t dimension_, const Int4 *score_, const double *prob_) |
| double | lambda (size_t dimension_, const Int4 *score_, const double *prob_) |
| double | muAssoc (size_t dimension_, const Int4 *score_, const double *prob_, double lambda_=0.0) |
| double | muPowerAssoc (size_t dimension_, const Int4 *score_, const double *prob_, double lambda_=0.0, Int4 power_=1) |
| double | thetaMin (size_t dimension_, const Int4 *score_, const double *prob_, double lambda_=0.0) |
| double | rMin (size_t dimension_, const Int4 *score_, const double *prob_, double lambda_=0.0, double thetaMin_=0.0) |
| double | r (size_t dimension_, const Int4 *score_, const double *prob_, double theta_) |
| Int4 | delta (size_t dimension_, const Int4 *score_) |
| double | thetaMinusDelta (double lambda_, size_t dimension_, const Int4 *score_) |
| void | descendingLadderEpoch (size_t dimension_, const Int4 *score_, const double *prob_, double *eSumAlpha_=0, double *eOneMinusExpSumAlpha_=0, bool isStrict_=false, double lambda0_=0.0, double mu0_=0.0, double muAssoc0_=0.0, double thetaMin0_=0.0, double rMin0_=0.0, double time_=0.0, bool *terminated_=0) |
| void | descendingLadderEpochRepeat (size_t dimension_, const Int4 *score_, const double *prob_, double *eSumAlpha_=0, double *eOneMinusExpSumAlpha_=0, bool isStrict_=false, double lambda_=0.0, size_t endW_=0, double *pAlphaW_=0, double *eOneMinusExpSumAlphaW_=0, double lambda0_=0.0, double mu0_=0.0, double muAssoc0_=0.0, double thetaMin0_=0.0, double rMin0_=0.0, double time_=0.0, bool *terminated_=0) |
| bool | isProbDist (size_t dimension_, const double *prob_) |
| bool | isScoreIncreasing (size_t dimension_, const Int4 *score_) |
| bool | isLogarithmic (size_t dimension_, const Int4 *score_, const double *prob_) |
Variables | |
| const double | REL_TOL = 1.0e-6 |
Function Documentation
◆ delta()
Referenced by _mm_cvtps_epi32(), _mm_round_ps(), CInt_fuzz::Add(), CMutableAtomicCounter::Add(), CAtomicCounter::Add(), ResidueProfiles::addOneRow(), CSeqGraphicJob::AddTaskCompleted(), variation_ref::CVariationUtil::AdjustDelinsToInterval(), CExpandGaps::AppendLiteral(), AssemblyGapsToDelta(), CBlobSplitterImpl::AttachToSkeleton(), Blast_CompositionPvalue(), Blur(), BvectorBulkSetTest(), CLadder::CalcDelta(), CStickyTooltipHandler::CheckForNewTip(), CGlWidgetPane::CheckOverlayTimer(), rapidjson::internal::CheckWithinHalfULP(), CChain::CollectTrustedmRNAsProts(), compile_branch(), python::ConvertCVariant2PCObject(), variation::CreateDeltaForOffset(), CDeltaHelper::CreateSSR(), bm::rsc_sparse_vector< Val, SV >::decode(), DeltaBioseqPack(), rapidjson::internal::DigitGen(), CRenderingContext::Draw3DQuad_HorzLines(), CRenderingContext::DrawPseudoBar(), CPhyloTreePane::TreeNavHistory::EqualPanes(), CAlignCollapser::FilterAlignments(), BlockFormater::formatOneRow(), fta_check_con_for_wgs(), fta_create_wgs_seqid(), bm::gap_split(), GapsToDelta(), NSnp::GetAlleles(), CAlnMap::GetAlnPosFromSeqPos(), CAlnVec::GetColumnVector(), CCharHistogram::GetDelimiterProbablities(), variation::GetDeltaLength(), variation::GetFuzz(), BlockModel::getGapToCTerminal(), BlockModel::getGapToNTerminal(), CCharHistogram::GetGroupOccuranceAverage(), CSeq_featHandler::GetLabel(), LocalMaxStatMatrix::getR(), CAlnMap::GetResidueIndexMap(), CWGSScaffoldIterator::GetSeq_inst(), CAlnMap::GetSeqPosFromAlnPos(), CAlnMap::GetSeqPosFromSeqPos(), variation::GetSignedOffset(), CGuiObjectInfoVariant::GetToolTip(), CValidError_graph::GetUngappedSeqLen(), CMultAlign::GetVariationAlignList(), CTreeNodeVboBase::GetVertexBuffer2D(), CAlnVec::GetWholeAlnSeqString(), GlbAlign(), BlockModel::intersect(), BlockModel::intersectOneBlock(), IsDeltaSeqGap(), LclAlign(), LoadSequencesToScope(), impl::CDriverContext::MakeCDBConnection(), MakeMaskingBioseq(), mbedtls_aes_rk_offset(), mbedtls_timing_get_timer_ncbicxx_2_28_8(), mbedtls_xtea_crypt_ecb_ncbicxx_2_28_8(), mdb_node_shrink(), mdb_update_key(), bm::min_delta_apply(), bm::min_delta_u32(), BlockModel::minusOneBlock(), MutationOperationsTest(), CStickyTooltipHandler::Notify(), CTooltip::On(), CTableFixedWidthPanel::OnCTableImportListctrlColDragging(), CSeqMarkHandler::OnMotion(), CFloatingFrame::OnMovingEvent(), CCustomTree::OnWheel(), CPhyTreeFormatter::CBioNodeFinder::operator()(), CPhyTreeFormatter::CExpander::operator()(), CPhyTreeFormatter::CSingleBlastNameExaminer::operator()(), CPhyTreeFormatter::CQueryNodeChecker::operator()(), CPhyTreeNodeGroupper::operator()(), CPhyTreeLabelTracker::operator()(), CPhyTreeNodeAnalyzer::operator()(), CQueryTreePrintFunc::operator()(), CAssignQueryTreeGetArgs::operator()(), CDoQueryTreeGetArgs::operator()(), CWhereQueryTreeGetArgs::operator()(), CQueryHighlightFunction::operator()(), CTreePrintFunc< TTreeNode, TConverter >::operator()(), visitor_detach_subtree::operator()(), CPhyRebuildIndexVisitor::operator()(), visitor_taxid_query::operator()(), visitor_string_query::operator()(), CPhyloTreeSelectionRoot::operator()(), visitor_copy_subtree::operator()(), visitor_paste_subtree::operator()(), CVisitorAccumulateProperty::operator()(), visitor_stringmatch_query::operator()(), CCalcCircularTree::operator()(), CDrawCircularTreeVbo::operator()(), CCalcBoundary::operator()(), CInitPSNodes::operator()(), CCalcRadialTree::operator()(), CDrawRadialTreeVbo::operator()(), CCalcRectangularTree::operator()(), CDrawSplineTreeVbo::operator()(), CDrawPseudoSplineTreeVbo::operator()(), CCalcSlantedTree::operator()(), CDrawSlantedTreeVbo::operator()(), SUidCollector::operator()(), CQueryTreeFieldResolveFunc::operator()(), CScannerEvaluateFunc::operator()(), CQueryTreeCleanPoolFunc::operator()(), CMQueryNodePreprocessor::operator()(), CQueryExecPreProcessFunc::operator()(), CSGQueryNodePreprocessor::operator()(), CQueryExecEvalFunc::operator()(), CQueryTreeResetFunc::operator()(), CBioTree< BioTreeBaseNode< CBioTreeEmptyNodeData, CBioTreeFeatureList > >::CFindUidFunc::operator()(), CBioTree< BioTreeBaseNode< CBioTreeEmptyNodeData, CBioTreeFeatureList > >::CAssignTreeFunc::operator()(), IPhyloTreeVisitor::operator()(), CPhyloTreeDataSource::visitor_read_properties::operator()(), IPhyloTreeRender::ComputePixelHeight::operator()(), Block::operator+(), BlockModel::operator+(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::const_iterator::operator+(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::iterator::operator+(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::const_iterator::operator+=(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::iterator::operator+=(), Block::operator-(), BlockModel::operator-(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::const_iterator::operator-(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::iterator::operator-(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::const_iterator::operator-=(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::iterator::operator-=(), SSNP_Info::ParseSeq_feat(), pcregrep(), variation_ref::CVariationUtil::PrecursorToProt(), CPdf::PrintLineBuffer(), CStatisticsCounters::PrintServerWide(), CQueue::PrintStatistics(), CBam2GraphApp::ProcessFile(), CBDB_Cache::Purge(), NTweakExon::rel_at(), CAlignMarkHandler::Render(), CPhyloNodeData::RenderRotated(), variation::RepackageAssertedSequence(), variation_ref::RepackageAssertedSequence(), SRelLoc::Resolve(), CRgbaColor::RgbToHsv(), CAsnCacheTestApplication::Run(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), s_GenerateCollapsedNode(), s_GetLiteralLength(), s_IsConOrScaffold(), s_IsGoodCharForRadix(), s_ResetQueryNode(), CCigar::Score(), bm::decoder_base::seek(), SeqToDelta(), SeqToDeltaSP(), CAlnMultiRenderer::SetColumnVisible(), CChain::SetConfirmedEnds(), CPdfObject::SetLineDashStyle(), CTimeReporterEntry::SetTimeDelta(), CTextPosition::ShiftCol(), CTextPosition::ShiftRow(), CTextBlock::ShiftRow(), Split_Qscore_SeqGraph_By_DeltaSeq(), CCachedSequence::SplitSeqData(), SRelLoc::SRelLoc(), rapidjson::internal::StrtodFullPrecision(), CBlastTabular::sx_MineSegment(), thetaMinusDelta(), CValidError_bioseq::ValidateCompleteGenome(), VariBandAlign(), VisitorAllRangeTest(), CFlatSeqLoc::x_Add(), IPhyloTreeRender::x_AddCollapsedGeomNode(), IPhyloTreeRender::x_AddCollapsedTextureNode(), CFeatureItem::x_AddQualsVariation(), impl::CDriverContext::x_AdjustCounts(), variation::CVariationUtil::x_AdjustDelinsToInterval(), variation::CHgvsParser::x_AsHgvsInstExpression(), CBioseq_Info::x_CalcBioseqLength(), CHistogramGlyph::x_ComputeDeviation(), x_ConsistencyCheck(), variation_ref::CHgvsParser::x_conversion(), variation::CHgvsParser::x_conversion(), CHgvsProtIrepReader::x_CreateDelinsSubvarref(), CHgvsNaIrepReader::x_CreateSSRVarref(), CHgvsProtIrepReader::x_CreateSSRVarref(), CDiff::x_DiffBisect(), CSplitter::x_DoDragSeparator(), CSplitter::x_DoResize(), COrfSearchJob::x_DoSearch(), CSeqMap::x_DoUpdateSeq_inst(), variation_ref::CHgvsParser::x_duplication(), variation::CHgvsParser::x_duplication(), CSyncQueue< Type, Container, Traits >::x_Erase(), variation::CHgvsParser::x_expr3(), compile_time_bits::const_bitset< static_cast< size_t >(eTestNames::max_test_names), eTestNames >::const_iterator::x_find_next_bit(), IPhyloTreeRender::x_FindBestSize(), CFlatGatherer::x_GatherFeaturesOnRange(), CBoundaryShapeTri::x_GetArc(), IPhyloTreeRender::x_GetEdgeDist(), CValidError_graph::x_GetLitLength(), CBoundaryShapeRoundedRect::x_GetRoudedCornerEdges(), CBoundaryShapeRoundedRect::x_GetRoudedCornerTris(), python::x_GetUTCOffset(), CSplitter::x_GrowCell(), variation_ref::CHgvsParser::x_identity(), variation::CVariationUtil::x_InferNAfromAA(), CAgpConverter::x_InitializeAndCheckCopyOfTemplate(), variation_ref::CHgvsParser::x_InstToString(), CDockManager::x_MoveDragFrame(), CSplitter::x_MoveSeparator(), CDockManager::x_MoveToFloatingFrame(), variation::CHgvsParser::x_no_change(), variation_ref::CHgvsParser::x_nuc_inv(), variation::CHgvsParser::x_nuc_inv(), variation_ref::CHgvsParser::x_nuc_subst(), variation::CHgvsParser::x_nuc_subst(), CPhyloTreeRectCalculator::x_OnStep(), CPhyloTreePriorityNode::x_OnStep(), CPhyloTreeMaxIdCalculator::x_OnStep(), CPhyloTreeSorter::x_OnStep(), CPhyloTreeMaxDirectChildDist::x_OnStep(), CPhyloTreeMaxChildDist::x_OnStep(), CPhyloTreeDistFromRoot::x_OnStep(), CPhyloTreeMidpointDist::x_OnStep(), CPhyloTreeLabelRange::x_OnStep(), CPhyloTreeSorterSubtreeDist::x_OnStep(), CPhyloTreeSorterLabel::x_OnStep(), CPhyloTreeSorterLabelRange::x_OnStep(), IPhyloTreeVisitor::x_OnStep(), CPhyloTreeCalculator::x_OnStep(), IPhyloTreeFilter::x_OnStep(), CGC_Assembly_Parser::x_ParseGCSequence(), variation_ref::CHgvsParser::x_prot_ext(), variation::CHgvsParser::x_prot_ext(), variation_ref::CHgvsParser::x_prot_missense(), variation::CHgvsParser::x_prot_missense(), variation_ref::CVariationUtil::x_ProtToPrecursor(), IPhyloTreeRender::x_RenderNodeHighlight(), IPhyloTreeRender::x_RenderNodeVbo(), IPhyloTreeRender::x_RenderScaleMarker(), CFeaturePanel::x_RenderTitleBar(), CAlnMixMerger::x_SecondRowFits(), variation_ref::CHgvsParser::x_seq_ref(), variation::CHgvsParser::x_seq_ref(), CWGSSeqIterator::x_SetDelta(), CSplign::x_SetPattern(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CSplitter::x_ShrinkCell(), variation_ref::CHgvsParser::x_ssr(), variation::CHgvsParser::x_ssr(), variation_ref::CHgvsParser::x_translocation(), CAlignMarkHandler::x_UpdateMarks(), CAlignMarkHandler::x_UpdateSelection(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CAgpConverter::x_VerifyComponents(), CGl3dWindow::x_Zoom(), and XGappedSeqLocsToDeltaSeqs().
◆ descendingLadderEpoch()
| void LocalMaxStatUtil::descendingLadderEpoch | ( | size_t | dimension_, |
| const Int4 * | score_, | ||
| const double * | prob_, | ||
| double * | eSumAlpha_ = 0, |
||
| double * | eOneMinusExpSumAlpha_ = 0, |
||
| bool | isStrict_ = false, |
||
| double | lambda0_ = 0.0, |
||
| double | mu0_ = 0.0, |
||
| double | muAssoc0_ = 0.0, |
||
| double | thetaMin0_ = 0.0, |
||
| double | rMin0_ = 0.0, |
||
| double | time_ = 0.0, |
||
| bool * | terminated_ = 0 |
||
| ) |
Definition at line 500 of file njn_localmaxstatutil.cpp.
References descendingLadderEpochRepeat().
Referenced by LocalMaxStat::dynProgCalc().
◆ descendingLadderEpochRepeat()
| void LocalMaxStatUtil::descendingLadderEpochRepeat | ( | size_t | dimension_, |
| const Int4 * | score_, | ||
| const double * | prob_, | ||
| double * | eSumAlpha_ = 0, |
||
| double * | eOneMinusExpSumAlpha_ = 0, |
||
| bool | isStrict_ = false, |
||
| double | lambda_ = 0.0, |
||
| size_t | endW_ = 0, |
||
| double * | pAlphaW_ = 0, |
||
| double * | eOneMinusExpSumAlphaW_ = 0, |
||
| double | lambda0_ = 0.0, |
||
| double | mu0_ = 0.0, |
||
| double | muAssoc0_ = 0.0, |
||
| double | thetaMin0_ = 0.0, |
||
| double | rMin0_ = 0.0, |
||
| double | time_ = 0.0, |
||
| bool * | terminated_ = 0 |
||
| ) |
Definition at line 366 of file njn_localmaxstatutil.cpp.
References _ASSERT, DynProgProbLim::getProb(), DynProgProbLim::getProbLost(), DynProgProbLim::getValueUpper(), lambda(), log, mu(), muAssoc(), n_bury(), n_setParameters(), n_step(), prob(), REL_TOL, rMin(), DynProgProbLim::setValueFct(), thetaMin(), DynProgProbLim::update(), and rapidjson::value.
Referenced by descendingLadderEpoch().
◆ flatten()
| void flatten | ( | size_t | dimension_, |
| const Int4 *const * | scoreMatrix_, | ||
| const double *const * | prob_, | ||
| size_t * | dim_, | ||
| Int4 ** | score_, | ||
| double ** | p_, | ||
| size_t | dimension2_ = 0 |
||
| ) |
Referenced by LocalMaxStatMatrix::copy().
◆ isLogarithmic()
| bool LocalMaxStatUtil::isLogarithmic | ( | size_t | dimension_, |
| const Int4 * | score_, | ||
| const double * | prob_ | ||
| ) |
Definition at line 542 of file njn_localmaxstatutil.cpp.
References _ASSERT, isProbDist(), and isScoreIncreasing().
Referenced by LocalMaxStatMatrix::getR().
◆ isProbDist()
Definition at line 520 of file njn_localmaxstatutil.cpp.
References i, REL_TOL, and relApprox().
Referenced by isLogarithmic().
◆ isScoreIncreasing()
Definition at line 532 of file njn_localmaxstatutil.cpp.
References i.
Referenced by isLogarithmic().
◆ lambda() [1/2]
◆ lambda() [2/2]
Referenced by _PSICalculateInformationContentFromScoreMatrix(), alp_sim::alp_sim(), Blast_CalcLambdaFullPrecision(), Blast_CompositionPvalue(), Blast_GetMatrixValues(), Blast_HSPListPHIGetBitScores(), BlastKarlinLHtoK(), BlastKarlinLtoH(), BlastScoreBlkNucleotideMatrixRead(), alp_sim::calculate_main_parameters2m(), CBlastAncillaryData::CBlastAncillaryData(), descendingLadderEpochRepeat(), ExtractPssmAncillaryData(), LocalMaxStatMatrix::getR(), impalaScaleMatrix(), muPowerAssoc(), NNIEdgeTest(), OLSint(), alp_sim::output_main_parameters2m_new(), CAlignFormatUtil::PrintKAParameters(), s_BuildCompressedScoreMatrix(), s_HSPListNormalizeScores(), s_IsContained(), testEdge(), alp_sim::the_criterion(), thetaMin(), wf(), wf2(), and wf4().
◆ mu()
Definition at line 231 of file njn_localmaxstatutil.cpp.
References i.
Referenced by descendingLadderEpochRepeat(), and LocalMaxStatMatrix::getR().
◆ muAssoc()
| double LocalMaxStatUtil::muAssoc | ( | size_t | dimension_, |
| const Int4 * | score_, | ||
| const double * | prob_, | ||
| double | lambda_ = 0.0 |
||
| ) |
Definition at line 272 of file njn_localmaxstatutil.cpp.
References muPowerAssoc().
Referenced by descendingLadderEpochRepeat(), and LocalMaxStatMatrix::getR().
◆ muPowerAssoc()
| double LocalMaxStatUtil::muPowerAssoc | ( | size_t | dimension_, |
| const Int4 * | score_, | ||
| const double * | prob_, | ||
| double | lambda_ = 0.0, |
||
| Int4 | power_ = 1 |
||
| ) |
Definition at line 258 of file njn_localmaxstatutil.cpp.
References lambda(), n_meanPowerAssoc(), and n_setParameters().
Referenced by muAssoc().
◆ r()
Referenced by _MM_GET_ROUNDING_MODE(), _mm_mulhi_epi16(), _mm_mulhi_epu16(), _MM_SET_ROUNDING_MODE(), _PSICalculateInformationContentFromFreqRatios(), _PSICalculateInformationContentFromScoreMatrix(), _PSIComputeFreqRatios(), _PSIComputeFreqRatiosFromCDs(), _PSIComputeScoreProbabilities(), _PSISaveCDDiagnostics(), _PSISaveDiagnostics(), _QualityScore(), _sse2neon_mm_get_denormals_zero_mode(), _sse2neon_mm_get_flush_zero_mode(), _sse2neon_mm_set_denormals_zero_mode(), _sse2neon_mm_set_flush_zero_mode(), _sse2neon_vmull_p64(), CInt_fuzz::Add(), CCompareSeq_locs::SIntervalComparisonResultGroup::Add(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::back_insert_iterator::add_remap_stat(), CSymDustMasker::triplets::add_triplet_info(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::back_insert_iterator::add_value(), bm::bv_ref_vector< BV >::add_vectors(), SequenceDisplay::AddBlockBoundaryRows(), CNcbiTable< TValue, TRow, TColumn >::AddColumn(), SWGSFeatChunkInfo::SFeatureSet::AddContent(), PeriodicTableClass::AddElement(), CAlignRangeCollection< CAlignRange< TSeqPos > >::AddInsertion(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::AddInsertion(), AddMember(), CPsgCgiApp::AddParamsTable(), CCDSInfo::AddPStop(), CNcbiTable< TValue, TRow, TColumn >::AddRow(), AddVariant(), CSeq_align::AlignLengthRatio(), CSymResolver::Append(), rapidjson::GenericPointer< ValueType, Allocator >::Append(), bm::avx2_setbit_to256(), base_value(), BDB_FixedByteStringCompare(), BDB_LStringCompare(), CObjectOStreamJson::BeginClassMember(), bm::sparse_vector_scanner< SV, S_FACTOR >::bfind(), bm::sparse_vector_scanner< bm::rsc_sparse_vector >::bfind_eq_str_impl(), bm::sv_sample_index< SV >::bfind_range(), bm::bit_in< TDecoder >::bic_decode_u16_cm_dry(), bm::bit_in< TDecoder >::bic_decode_u16_rg(), bm::bit_in< TDecoder >::bic_decode_u16_rg_bitset(), bm::bit_in< TDecoder >::bic_decode_u16_rg_dry(), bm::bit_out< TEncoder >::bic_encode_u16_cm(), bm::bit_out< TEncoder >::bic_encode_u16_rg(), bm::bit_out< TEncoder >::bic_encode_u32_cm(), BitString(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), WSDLParser::BuildDataTree(), BZ2_bzDecompress(), CalcMD5(), variation::CalcSOTermsForProt(), IPhyloTreeRender::CalculateExtents(), CalculateInformationContent(), CQualityScoringMethod::CalculateScores(), BLASTer::CalculateSelfHitScores(), CdsTrnaOverlapStr(), StructureSet::CenterViewOnAlignedResidues(), StructureSet::CenterViewOnStructure(), CFeatHistogramDS::CFeatHistogramDS(), CFinalRequestContextUpdater::CFinalRequestContextUpdater(), check_book_tit(), CheckCollectionDate(), rapidjson::internal::Schema< SchemaDocumentType >::CheckDoubleMultipleOf(), CProjectsLstFileFilter::CheckProject(), CheckRangeDeserial(), CheckSourceFeatCoverage(), CheckSourceFeatLocAccs(), ChemicalGraph::ChemicalGraph(), CEUtilsUpdater::CitMatch(), CkCdRegion(), CkEndStop(), bm::bvector< Alloc >::clear_range_no_check(), BlockMultipleAlignment::ClearRowInfo(), CAlignCollapser::ClipNotSupportedFlanks(), CTL_CursorCmdExpl::CloseCursor(), cmpTableValues(), CNcbiMatrix< T >::CNcbiMatrix(), CNcbiTable< TValue, TRow, TColumn >::CNcbiTable(), CLocMapper_Default::CollapseRanges(), CGlState::Color3d(), IRender::Color3d(), CGlState::Color3f(), IRender::Color3f(), CGlState::Color4d(), IRender::Color4d(), CGlRenderDebug::Color4f(), CGlState::Color4f(), IRender::Color4f(), CAlignRange< Position >::CombinationWithAbutting(), bm::aggregator< BV >::combine_and_sub(), bm::bvector< Alloc >::combine_operation(), CGlRect< TVPUnit >::CombineWith(), CRangeCollection< TSeqPos >::CombineWith(), CRangeSet< CPairwiseAln::TPos >::CombineWith(), CAlignRange< Position >::CombineWithAbutting(), bm::sv_sample_index< SV >::common_prefix_length(), CBDB_FieldLString::Compare(), compile_time_bits::Compare(), compare_BV(), compile_time_bits::CompareNocase(), dtl::Diff< elem, vector< elem >, Compare< elem > >::compose(), CTextFsm< MatchType >::ComputeFail(), CDiscrepancyContext::ContainingSet(), CRangeCollection< TSeqPos >::Contains(), CRangeSet< CPairwiseAln::TPos >::Contains(), CLocalRange< TOffset >::Contains(), CMSPeak::ContainsFast(), CLadder::ContainsFast(), convert(), Convert2Matrix(), SMakeProjectT::ConvertLibDepends(), SMakeProjectT::ConvertLibDependsMacro(), ConvertPSSMToBLASTMatrix(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::copy_from(), CSRSearch_Impl< index_t >::copyOffsets(), could_be_empty_branch(), bm::bvector< Alloc >::count_range_no_check(), CPanelGrid::CPanelGrid(), CPssmInputGapsInQuery::CPssmInputGapsInQuery(), CRangeCollection< TSeqPos >::CRangeCollection(), CRangeSet< CPairwiseAln::TPos >::CRangeSet(), SNetStorageRPC::Create(), CAlnMap::CreateAlignFromRange(), DTDParser::CreateEmbeddedName(), BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), CreateObjectLocation(), rapidjson::internal::Schema< SchemaDocumentType >::CreatePattern(), Threader::CreateSeqMtf(), CreateSparseAlign(), CDbapiCursorApp::CreateTable(), CVDBMgr::CRequestContextUpdater::CRequestContextUpdater(), CRgbaColor::CRgbaColor(), CBl2Seq::CSearchResultSet2TSeqAlignVector(), CTLibContext::CTLibContext(), CVisRangeGlyph::CVisRangeGlyph(), dbgetmaxprocs(), DbxrefQualToDbtag(), DefVsHTGKeywords(), CTL_CursorCmdExpl::Delete(), CDbapiSampleApp::DeleteLostTables(), UngappedAlignedBlock::DeleteRow(), UnalignedBlock::DeleteRow(), DelParenthesis(), DoesPatternMatchHighlightedResidues(), CDependent_field_rule::DoesStringMatchRuleExpression(), CField_rule::DoesStringMatchRuleExpression(), AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), SMakeProjectT::DoResolveDefs(), SequenceDisplay::DraggedCell(), CRenderingContext::DrawDisk(), DynamicMatrixTest(), ecdsa_sign_det_restartable(), ecdsa_sign_restartable(), ecdsa_signature_to_asn1(), ecdsa_verify_restartable(), CMultAlign::EmitSequenceFromBase(), CMultAlign::EmitSequenceFromRead(), EmptyBVTest(), bm::sparse_vector_serializer< SV >::encode_remap_matrix(), compile_time_bits::Equal(), CPhyloTreePane::TreeNavHistory::EqualPanes(), EvaluateInitialScore(), CBlobStoreBase::Exists(), ExportPNG(), CGnomonAnnotator::ExtendJustThisChain(), ExtractObjectLocation(), f(), fallbackQSort3(), fallbackSort(), CDbapiTestSpeedApp::FetchFile(), CDbapiTestSpeedApp::FetchResults(), CRgbaGradColorTable::FillGradient(), FillSets(), CAlignCollapser::FilterAlignments(), bm::rs_index< BVAlloc >::find(), bm::sparse_vector_scanner< SV, S_FACTOR >::find_first_eq(), find_fixedlength(), CAlignRangeCollection< CAlignRange< TSeqPos > >::find_insertion_point(), find_minlength(), CSourceModParser::FindAllMods(), FindCompartments(), CContigAssembly::FindDiagFromAlignSet(), CAlignRangeCollExtender< TAlnRngColl >::FindOnSecond(), CEditSeqEndsWithAlign::FindRow(), NAdapterSearch::CSimpleUngappedAligner::FindSingleBest(), CInternalStopFinder::FindStartsStops(), IMovableButton::FindUnoccupiedPosition(), CIndexedDb_New::FindVolume(), CTooltipFrame::FitToWindow(), DTDParser::FixEmbeddedNames(), bm::for_each_bit(), bm::for_each_nzblock(), fta_check_non_tpa_tsa_tls_locations(), fta_get_citgen(), fta_get_str_user_field(), fta_get_user_object(), fta_parse_structured_comment(), fta_parse_tpa_tsa_block(), fta_tokenize_dblink(), fta_tokenize_project(), fta_vnp_structured_comment(), GammaEncoderTest(), CSeq_align::GapLengthRange(), bm::sparse_vector< Val, BV >::gather(), gb_refs_common(), gcd(), gene_feat_fit(), CProjBulderApp::GenerateUnixProjects(), CScore_SegPct::Get(), CScore_Entropy::Get(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::get(), CSeqMaskerUsetArray::get_info(), CSeqMaskerUsetHash::get_info(), get_LSH_hashes(), get_LSH_hashes2(), get_LSH_hashes5(), CSparseAlignment::GetAlnSeqString(), Molecule::GetAlphaCoords(), GetAverage(), CScoreBuilder::GetBlastScoreSpliced(), CNcbiTable< TValue, TRow, TColumn >::GetCell(), CBDB_QueryParserEnvironment::GetChar(), CQueryParserEnv::GetChar(), CRangeSet< CPairwiseAln::TPos >::GetCoveredLength(), CBedCoverageGraph::GetData(), CWigGraph::GetData(), CVcfHeatmap::GetData(), CWigGraph::GetDataCoverage(), CwxTableListCtrl::GetDataRowsSelected(), GetDescrComment(), CSeq_align_Mapper_Base::GetDstAlign(), GetEmblInst(), GetEmblInstContig(), GetEmblMolInfo(), CCgiApplication::GetFastCGIWatchFileRestartDelay(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetFirstPosBySecondPos(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstPosBySecondPos(), GetFlatBiomol(), GetGenBankInstContig(), CSGAlignmentDS::GetGraphCost(), CHitMatrixRenderer::GetGraphs(), CAnnotType_Index::GetIndexRange(), CAliasTypeStrings::GetInitializer(), CMySQL_RowResult::GetItem(), CPhyloNodeData::GetLabelRect(), GetMacDragWindowBounds(), CSeqUtils::GetMappingInfoFromLocation(), CwxSeqMarkerSetDlg::GetMarkerRange(), CSeq_id::GetMatchingTextseqIds(), IPhyloTreeRender::GetMinDimensions(), CRCache::getNRes1(), CRCache::getNRes2(), CPileUpGraph::GetNumberOfReads(), StyleManager::GetObjectStyle(), CPreOrderedOffsetIterator::getOffsetValue(), GetProtRefSeqId(), LocalMaxStat::getR(), CRandom::GetRandIndex(), CRandom::GetRandIndexUint8(), CwxPhyloSettingsDlg::GetRandomNode(), CSeqTableReader::GetRange(), Molecule::GetResidueColor(), CPhyloNodeData::GetRotatedTextBox(), CPhyloNodeData::GetRotatedTextPos(), CSeqTableGrid::GetRowLabelValue(), CSGSegmentMapJob::GetSegmentMapLevels(), CSparseAlignment::GetSeqRange(), CSraRun::GetSequenceLength(), SInteractiveParams::GetService(), GetSetOfSpecies(), CDoiLookup::GetSpecialCharacterReplacement(), CSraRun::GetSpotEntry(), CHitMatrixDataSource::GetStdSegRange(), CNetICacheClient::GetSubkeyList(), CPhyloNodeData::GetTextOut(), CMatePairGlyph::GetTooltip(), CSeqTableReader::GetValue(), CEditingActionFeatPseudo::GetValue(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatAnticodon::GetValue(), CEditingActionFeatTranslExcept::GetValue(), CAlignSeqTableModel::GetValueAt(), GetViralHostsFrom_OH(), GetVirtualCoordinates(), CPsgCgiApp::Help(), Sequence::HighlightPattern(), HighlightResidues(), DeBruijn::CDBGraph::HistogramMinimum(), huft_build(), iexp(), bm::sparse_vector< Val, BV >::import_u_nocheck(), Include(), NAdapterSearch::CSimpleUngappedAligner::Init(), IPhyloTreeRender::InitLabel(), initRTTI(), CAlignRangeCollection< CAlignRange< TSeqPos > >::insert(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert(), CSegmentedRangeCollection::insert(), CMultAlign::InsertDashesInReads(), CCpuFeatures::InstructionSet::InstructionSet(), InternalStopCodon(), CAlignRange< Position >::IntersectingWith(), CRangeCollection< TSeqPos >::IntersectingWith(), CRangeSet< CPairwiseAln::TPos >::IntersectingWith(), CAlignRange< Position >::IntersectionWith(), CAlignRange< Position >::IntersectSecondWith(), CRenderingContext::IntersectVisible(), CRenderingContext::IntersectVisible_Y(), CGlRect< TVPUnit >::IntersectWith(), CAlignRange< Position >::IntersectWith(), CRangeCollection< TSeqPos >::IntersectWith(), CRangeSet< CPairwiseAln::TPos >::IntersectWith(), invmod(), CAlignRange< Position >::IsAbutting(), CODBC_Connection::IsAlive(), CSGAlignmentDS::IsGraphCached(), IMovableButton::IsOccupiedPosition(), CDataType::IsPrimitive(), TreeAlgorithm::isRooted(), CDataType::IsStdType(), CCountries::IsSubstringOfStringInList(), CPhyloTreeWidget::IterateSelection(), KleeneLogicTest(), bm::sparse_vector_deserializer< SV >::load_remap(), CBDB_SplitTest::LoadSplitStore(), LookupNCBIStdaaNumberFromCharacter(), LookupNCBIStdaaNumberFromThreaderResidueNumber(), LookupThreaderResidueNumberFromCharacterAbbrev(), bm::sparse_vector_scanner< SV, S_FACTOR >::lower_bound_str(), bm::lower_bound_u32(), bm::lower_bound_u64(), CLocalAdapterThread::Main(), main(), MakeChainPDBSeqId(), CLocMapper_Default::Map(), CAlignMap::MapRangeAtoB(), CAlignFilter::Match(), rapidjson::internal::GenericRegexSearch< RegexType, Allocator >::MatchRange(), mbedtls_ecdsa_read_signature_restartable_ncbicxx_2_28_8(), mbedtls_ecdsa_sign_det_ext_ncbicxx_2_28_8(), mbedtls_ecdsa_sign_det_ncbicxx_2_28_8(), mbedtls_ecdsa_sign_ncbicxx_2_28_8(), mbedtls_ecdsa_verify_ncbicxx_2_28_8(), mbedtls_ecdsa_write_signature_restartable_ncbicxx_2_28_8(), mbedtls_gf128mul_x_ble(), mbedtls_int_div_int(), mbedtls_mpi_gen_prime_ncbicxx_2_28_8(), mbedtls_mpi_mod_int_ncbicxx_2_28_8(), mdb_find_oldest(), mdb_txn_renew0(), gfx::TimSort< RandomAccessIterator, LessFunction >::minRunLength(), SequenceDisplay::MouseDown(), SequenceDisplay::MouseOver(), IMovableButton::MoveButton(), mpi_check_small_factors(), mpi_sub_hlp(), mpi_write_hlp(), OpenGLRenderer::MyGluCylinder(), OpenGLRenderer::MyGluSphere(), mz_zip_filename_compare(), mz_zip_reader_filename_less(), NCBI_LinearSolution(), NCBI_SingularValueDecomposition(), CAlignedFeatureGraph::NeedTooltip(), CInt_fuzz::Negate(), AlignmentManager::NewAlignments(), rapidjson::internal::GenericRegex< Encoding, Allocator >::NewRange(), CSequenceIStreamBlastDB::next(), CDistMethods::NjTree(), Nlmzip_inflate(), Normalize(), normalize_comment(), compile_time_bits::NotEqual(), StructureWindow::OnCDD(), CwxTableListCtrl::OnGetItemAttr(), CPaintAlignment::OnGetRowHeight(), CPaintSequence::OnGetRowHeight(), IMovableButton::onMouseClick(), CWidgetHandle::OnMove(), IMovableButton::OnRightClick(), StructureWindow::OnSelect(), CSeqGraphicWidget::OnSetSeqMarkerDlg(), CSeqGraphicWidget::OnSetSeqMarkerForSelDlg(), CPhyloTreeWidget::OnStopLayout(), CStickyTooltipHandler::OnTimer(), CPhyloTreeWidget::OnUpdateRotateLabels(), CPhyloTreeWidget::OnUpdateStopLayout(), SNetStorageRPC::Open(), SNetStorageByKeyRPC::Open(), CBlobStoreBase::OpenForRead(), operator!=(), compile_time_bits::operator!=(), CAlignRange< Position >::operator!=(), DeBruijn::LargeInt< precision >::operator%(), ncbi::grid::netcache::search::operator&&(), CRangeCollection< TSeqPos >::operator&=(), CRangeSet< CPairwiseAln::TPos >::operator&=(), compile_time_bits::TInsertSorter< _Traits, _AllowDuplicates >::Less::operator()(), compile_time_bits::const_set_map_base< _Traits, void, tag_DuplicatesNo >::hash_compare::operator()(), std::less< std::integral_constant< ncbi::NStr::ECase, case_sensitive > >::operator()(), std::less< compile_time_bits::tagStrNocase >::operator()(), std::equal_to< compile_time_bits::tagStrNocase >::operator()(), feat_loc_compare::operator()(), PRangeLess< Range >::operator()(), PAlignRangeToLess< TAlignRange >::operator()(), PAlignRangeFromLess< TAlignRange >::operator()(), compile_time_bits::const_set_map_base< _Traits, void, tag_DuplicatesNo >::value_compare::operator()(), CDrawCircularTreeVbo::operator()(), IDBServiceMapper::SDereferenceLess::operator()(), SPCRReactionLess::operator()(), CIndelMapper::operator()(), CSymDustMasker::CIupac2Ncbi2na_converter::operator()(), operator*(), ncbi::grid::netcache::search::operator+(), CRangeCollection< TSeqPos >::operator+=(), CRangeSet< CPairwiseAln::TPos >::operator+=(), operator--(), CRangeCollection< TSeqPos >::operator-=(), CRangeSet< CPairwiseAln::TPos >::operator-=(), DeBruijn::LargeInt< precision >::operator/(), operator<(), CMatchFeat::operator<(), std::operator<<(), operator<<(), operator==(), pythonpp::operator==(), compile_time_bits::operator==(), CAlignRange< Position >::operator==(), ncbi::grid::netcache::search::operator|(), BlockMultipleAlignment::OptimizeBlock(), OrderQual(), CSubtreeBoundary::Overlaps(), ParseGenBankVersion(), ParsePcrPrimers(), rapidjson::internal::GenericRegex< Encoding, Allocator >::ParseRange(), rapidjson::internal::BigInteger::ParseUint64(), rapidjson::internal::GenericRegex< Encoding, Allocator >::ParseUnsigned(), CSeqGlyph::PointInRect(), CPhyloNodeData::PointInTextBox(), Precede(), CWigGraph::Prefetch(), CLocalVDBBlast::PreprocessDBs(), CAttribTableDelimitersPanel::PreviewData(), CTabularFormatter_AlignStart::Print(), CTabularFormatter_AlignEnd::Print(), printed_range(), PrintSAM(), PrintTabular(), CPdfTransform::PrintTo(), CPdfTextTransform::PrintTo(), ShowHideManager::PrivateShowResidues(), CReadDispatcher::Process(), CProcessor_ID2::ProcessData(), WSDLParser::ProcessEndpointTypes(), CProcessor_ID1::ProcessObjStream(), CProcessor_ID1_SNP::ProcessObjStream(), CProcessor_SE::ProcessObjStream(), CProcessor_SE_SNP::ProcessObjStream(), CProcessor_St_SE::ProcessObjStream(), CProcessor_ID2::ProcessObjStream(), CProcessor_ID2_Split::ProcessObjStream(), CProcessor_ID2AndSkel::ProcessObjStream(), CTbl2AsnApp::ProcessOneDirectory(), CDUpdater::processPendingToNormal(), CPSGS_OSGAnnot::ProcessReplies(), CPSGS_OSGGetBlob::ProcessReplies(), CPSGS_OSGGetChunks::ProcessReplies(), CPSGS_OSGResolve::ProcessReplies(), CPSGS_OSGGetBlobBySeqId::ProcessReplies(), CProcessor_St_SE_SNPT::ProcessStream(), PsiBlastSetupScoreBlock(), bm::ptrp_test(), CAlignRangeCollection< CAlignRange< TSeqPos > >::push_back(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::push_back(), QSbuf_ParseDefline(), Splines::quadraticRoots(), CDockManager::RaiseFloatingInZOrder(), CWindowManagerService::RaiseFloatingWindowsInZOrder(), CWindowManager::RaiseFloatingWindowsInZOrder(), IStickyTooltipHandlerHost::RaiseOverlappingWindows(), Rand01(), random_minmax(), CModelCompare::RangeNestedInIntron(), RankFindTest(), CGFFReader::Read(), SEmbeddedStreamReaderWriter::Read(), CStreamReader::Read(), CBlobReader::Read(), read_and_convert(), readGFF3(), CBlobStoreBase::ReadTableDescr(), bm::sv_sample_index< SV >::recalc_range(), CAlignModel::RecalculateAlignMap(), FileMessenger::ReceiveCommands(), CTabDelimitedValidator::RegisterAliases(), CSymDustMasker::triplets::rem_triplet_info(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::remap_from_impl(), CNcbiMatrix< T >::RemoveCol(), CNcbiMatrix< T >::RemoveRow(), CLinearSelHandler::Render(), CTextSelHandler::Render(), CPhyloNodeData::Render(), ReorderVector(), ReportAutofix(), CSRSearch::reportResults(), CCompareSeq_locs::SIntervalComparisonResultGroup::Reset(), CNcbiMatrix< T >::Resize(), CNcbiTable< TValue, TRow, TColumn >::Resize(), CChain::RestoreReasonableConfirmedStart(), CDense_seg::Reverse(), CRenderVector::Rotated(), SequenceDisplay::RowsAdded(), rsmp(), CDiscRepApp::Run(), CPubmedFetchApplication::Run(), CMysqlDemoApp::Run(), COcbdDemoApp::Run(), COdbcSpwhoDemoApp::Run(), CCtlLibDemoAPp::RunSample(), CCtlLibSpWhoDemoApp::RunSample(), CDbapiBcpApp::RunSample(), CDbapiTestSpeedApp::RunSample(), CTestSingleAln_All::RunTest(), CSeqTestManager::RunTests(), s_AddCoalescedLocations(), s_AddGraphToMap(), s_AdjustToAnnotatedCDS(), CIgBlast::s_AppendResults(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPMapperPairedInit(), s_BlastScoreBlk_Copy(), s_BlastSumP(), s_BlastSumPCalc(), s_CollectRelPathes(), s_CompressDiscToDenseq(), s_ExtractSeqidsAndRanges(), s_FindSegmentWithLongNs(), s_ForkChildren(), CSeq_id_Resolver::s_Get(), s_Get_LSH_index_hashes(), s_Get_LSH_index_hashes2(), s_Get_LSH_index_hashes5(), s_GetAlignmentSpans_Interval(), CAdapterSearchApplication::s_GetCoverage(), s_GetGapCount(), s_GetGeneWeight(), s_GetPagination(), s_ImportFromHitlist(), s_IsConnected_(), s_MarkDownHSPList(), ncbi::grid::netcache::search::s_Merge(), s_ProcessHSPList(), s_Read_(), s_Recv(), s_RecvMsg(), s_Resolve(), s_SearchForwardedFor(), s_Select(), s_SetClientIP(), s_SetDtab(), s_SetHitID(), s_SetSessionID(), s_Shutdown(), SAlignment_Segment::SAlignment_Row::SameStrand(), SComparison::SComparison(), CSearch_Base< LEGACY, NHITS, derived_t >::SearchInt(), CSRSearch_Impl< index_t >::searchOneMismatch(), StructureSet::SelectByDistance(), StructureObject::SelectByDistance(), CSeqGraphicPane::SelectSeqLoc(), CTL_CursorCmdExpl::SendDataCmd(), CPSGS_OSGAnnot::SendReplies(), FileMessenger::SendReply(), CPSG_Queue::SImpl::SendRequestAndGetReply(), CBrowserUtils::SendToBrowser(), SeqToDelta(), CRgbaColor::Set(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::set(), bm::bvector< Alloc >::set_range_no_check(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::set_value_no_null(), CGlPreviewSetupWidget::SetAspectRatio(), CBoundaryParms::SetBoundaryEdgeColor(), CReportEntry::SetCds(), CGLCanvas::SetClearColor(), CPhyloTreePS::SetElectricalRepulsion(), CTableImportDataSource::SetFirstImportRow(), CPhyloNodeData::SetLabelRect(), CPrintOptions::SetMarginRight(), CBlastNucleotideOptionsHandle::SetMatchReward(), CBlastOptions::SetMatchReward(), CBlastOptionsLocal::SetMatchReward(), CBlastOptionsHandle::SetOffDiagonalRange(), CBlastOptionsLocal::SetOffDiagonalRange(), CGlPreviewSetupWidget::SetPartitions(), CBlastInputSourceConfig::SetRange(), CCDSInfo::SetReadingFrame(), CMultiAlignerOptions::SetRealign(), CRgbaColor::SetRed(), CCluster::SetRefSeq(), SUv_Timer::SetRepeat(), impl::CConnection::SetResultProcessor(), CSRSearch_Impl< index_t >::setResults4Idx(), CDummyGlyph::SetSize(), CCDSInfo::SetStart(), CCDSInfo::SetStop(), CBlobStoreBase::SetTextSizeServerSide(), CCgiEntry::SetValue(), CGlPane::SetViewport(), CGlPane::SetVisibleRect(), CWinMaskConfig::SFormat(), ShowHideManager::ShowAlignedDomains(), ShowHideManager::ShowAlignedOrAnnotatedDomains(), ShowHideManager::ShowDomainsWithHighlights(), StructureSet::ShowRejects(), CDbapiSampleApp::ShowResults(), ShowHideManager::ShowSelectedResidues(), CAlnMultiPane::SLC_VertScrollToMakeVisible(), dtl::Diff< elem, vector< elem >, Compare< elem > >::snake(), SNcbiMatrix2DoubleMatrix::SNcbiMatrix2DoubleMatrix(), CPointerPot::Sort(), SequenceDisplay::SortRowsByLoopLength(), spci(), SPGetGeneRefsNew(), SPParseDefinition(), sReadAA_I(), sReadAA_M(), SRState::SRState(), SUv_Timer::Start(), StressTestAggregatorShiftAND(), CLocalRange< TOffset >::StrictlyBelow(), CRangeCollection< TSeqPos >::Subtract(), CRangeSet< CPairwiseAln::TPos >::Subtract(), SubtractOnFirst(), SubtractOnSecond(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::sum(), CDiscrepancyVisitorImpl< _Name >::Summarize(), TestTaskBuilder< BV >::task_run(), tds72_get_varmax(), tds_bcp_fread(), tds_generic_get(), tds_put_char_param_as_string(), tds_put_string(), tds_sleep_ms(), tds_variant_get(), test(), TestArraysAndBuffers(), TestCompressSparseVector(), TestEqualSparseVectors(), CTreeCollisionModel2D::TestForNode(), TestStrSparseVector(), tinfl_decompress(), CSeqDB_AliasMask::ToString(), CGeneModel::TranscriptLimits(), CLiteAlign::TranscriptSeq(), CDense_seg::TrimEndGaps(), CSplignTrim::TrimHolesToCodons(), ChemicalGraph::UnpackDomainFeatures(), PSSMWrapper::UnpackMatrix(), ChemicalGraph::UnpackSecondaryStructureFeatures(), CTL_CursorCmdExpl::Update(), CTL_CursorCmdExpl::UpdateBlob(), CAlignRangeCollExtender< TAlnRngColl >::UpdateIndex(), SequenceDisplay::UpdateMaxRowWidth(), CPhyloTreePane::UpdatePane(), CTreeCollisionModel2D::UpdateVisibility(), CValidError_graph::ValidateGraphsOnBioseq(), verify_all_one_ranges(), CRenderingContext::WillLabelFit(), CBlastDB_FastaFormatter::Write(), CNCBlobStorage::WriteDbInfo(), CObjectOStreamAsn::WriteMemberId(), variation::CHgvsParser::x_abs_pos(), CAmbigDataBuilder::x_AddAmbig(), CSGAnnotJob::x_AddGraphToMap(), CFastaReader::x_AddMultiwayAlignment(), CFastaReader::x_AddPairwiseAlignments(), CAlignMarkHandler::x_AlnRangeFromSeqRange(), CODBC_BCPInCmd::x_AssignParams(), CBl2Seq::x_BuildAncillaryData(), CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CAlignGlyph::x_CalcIntervals(), CScoringJob::x_CalculateAlignmentScores(), CScoringJob::x_CalculateSequenceScores(), CMergedPairwiseAln::x_CanInsertRng(), CRemoteBlast::x_CheckResults(), CRemoteBlast::x_CheckResultsDC(), CTreeGraphicsModel::x_CircularLabelMinAngle(), CTreeGraphicsModel::x_CircularLabelTrim(), CVisibleRange::x_Clamp(), CRangeCollection< TSeqPos >::x_CombineWith(), CRangeSet< CPairwiseAln::TPos >::x_CombineWith(), IPhyloTreeRender::x_ComputeNodeBoundary(), CBoundaryShapeTri::x_ComputeRoundedCorner(), CRangeCollection< TSeqPos >::x_Contains(), CRangeSet< CPairwiseAln::TPos >::x_Contains(), CIgBlast::x_ConvertResultType(), CSeq_align_Mapper_Base::x_ConvertSegment(), CSeq_align_Mapper::x_ConvertSegmentCvt(), CNcbiTable< TValue, TRow, TColumn >::x_Copy(), CAlnVecMultiDataSource::x_CreateHandles(), CSparseMultiDataSource::x_CreateHandles(), CSGAlignStatJob::x_CreatePileUpGraphs(), CHitMatrixRenderer::x_DestroyGraphs(), CDiagRangeCollection::x_Diff(), CDiagRangeCollection::x_DiffSecond(), CValidError_imp::x_DoBarcodeTests(), CAlignSmearGlyph::x_Draw(), CClonePlacementGlyph::x_Draw(), CLinkedFeatsGroup::x_Draw(), CAlignGlyph::x_DrawAlignRowSequence(), CFeatGlyph::x_DrawFeatureBar(), CFeatGlyph::x_DrawProjectedRuler(), CFeatGlyph::x_DrawRuler(), CWigGraph::x_FetchData(), CSnpJob::x_FetchGraphs(), CPushback_Streambuf::x_FillBuffer(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_FindInsertionPlace(), CAlnVecRow::x_ForEachAlnSeg(), CNcbiTable< TValue, TRow, TColumn >::x_Free(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetDstPacked(), CTL_LangCmd::x_GetDynamicID(), CSVGRenderer::x_GetGradientColors(), CRuler::x_GetMaxNum(), CSeqTextPane::x_GetOffsetForVariations(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), x_GetProfileMatchRanges(), CRandom::x_GetRand32Bits(), CAlignedFeatureGraph::x_GetRecsSortedByLength(), CMultiAlignView::x_GetRowSeqLoc(), CMultiAligner::x_GetScoreOneCol(), CBlastDB_SeqFormatter::x_GetSeq(), CPrimaryItem::x_GetStrForPrimary(), CRandom::x_GetSysRand32Bits(), CAlignedFeatureGraph::x_GetTooltip(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_align_Mapper_Base::x_HaveMixedStrand(), CFlatGatherer::x_HistoryComments(), x_IfToOwnReader(), x_IfToOwnWriter(), CTrans_table::x_InitFsaTable(), CTrans_table::x_InitFsaTransl(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CSparseIterator::x_InitSegment(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Insert(), CRangeCollection< TSeqPos >::x_Intersects(), CRangeSet< CPairwiseAln::TPos >::x_Intersects(), CRangeCollection< TSeqPos >::x_IntersectWith(), CRangeSet< CPairwiseAln::TPos >::x_IntersectWith(), CAppHitFilter::x_IterateSeqAlignList(), CAlignedFeatureGraph::x_Layout(), CSGSeqGraphJob::x_LoadSeqTable(), CGenbankFormatter::x_LocusHtmlPrefix(), CODBC_RowResult::x_MakeItem(), CLinearSelHandler::x_MouseToSeqPos(), CAmbigDataBuilder::x_PackNewAmbig(), CAmbigDataBuilder::x_PackOldAmbig(), CAlignedFeatureGraph::x_PlaceCluster(), CAlignedFeatureGraph::x_PlaceFeature(), CSGFeatureJob::x_ProcessCachedVcfTabix(), CID2SNPProcessor_Impl::x_ProcessReplyGetSeqId(), CAlnVecRow::x_RenderAlignSegments(), CAlnVecRow::x_RenderAveragableScores(), CAlignGlyph::x_RenderAveragableScores(), CTraceGlyph::x_RenderContour(), CAlignedFeatureGraph::x_RenderFeature(), CAlnVecRow::x_RenderInserts(), IPhyloTreeRender::x_RenderNodeHighlight(), CTreeGraphicsModel::x_RenderNodeLabelsPdf(), CAlnVecRow::x_RenderNonAveragableScores(), CAlignGlyph::x_RenderNonAveragableScores(), CTextSelHandler::x_RenderOpSymbol(), CTextSelHandler::x_RenderRange(), IPhyloTreeRender::x_RenderScaleMarker(), IPhyloTreeRender::x_RenderSelection(), CAlnVecRow::x_RenderSequence(), CFeaturePanel::x_RenderTitleBar(), CAlnVecRow::x_RenderUnaligned(), x_ReorderList(), CMakeProfileDBApp::x_Run(), CVcfHeatmap::x_SaveData(), CHitMatrixRenderer::x_SetGraphs(), CAlignGlyph::x_ShowLabel(), CClonePlacementGlyph::x_ShowLabel(), CFeatGlyph::x_ShowLabel(), CVcfGlyph::x_ShowLabel(), CwxTreeCtrl::x_ShowTooltip(), CwxTableListCtrl::x_ShowTooltip(), CRangeCollection< TSeqPos >::x_Subtract(), CRangeSet< CPairwiseAln::TPos >::x_Subtract(), CScoringJob::x_UpdateBuffer(), CGlyphContainer::x_UpdateComments(), CRawSeqToDeltaSeqByLoc::x_UpdateRows(), CBedImportData::xInitializeRgb(), XMLDefVsHTGKeywords(), XMLGetEMBLBlock(), XMLGetInstContig(), XMLRefs(), CRgbaColor::YuvToRgb(), CGlPane::ZoomRect(), zsc(), CFinalRequestContextUpdater::~CFinalRequestContextUpdater(), CVDBMgr::CRequestContextUpdater::~CRequestContextUpdater(), CTL_LangCmd::~CTL_LangCmd(), and FileMessenger::~FileMessenger().
◆ rMin()
| double LocalMaxStatUtil::rMin | ( | size_t | dimension_, |
| const Int4 * | score_, | ||
| const double * | prob_, | ||
| double | lambda_ = 0.0, |
||
| double | thetaMin_ = 0.0 |
||
| ) |
Definition at line 298 of file njn_localmaxstatutil.cpp.
References n_setParameters(), n_totalProbAssoc(), and thetaMin().
Referenced by descendingLadderEpochRepeat(), and LocalMaxStatMatrix::getR().
◆ thetaMin()
| double LocalMaxStatUtil::thetaMin | ( | size_t | dimension_, |
| const Int4 * | score_, | ||
| const double * | prob_, | ||
| double | lambda_ = 0.0 |
||
| ) |
Definition at line 281 of file njn_localmaxstatutil.cpp.
References bisection(), fabs, lambda(), n_bracket(), n_meanAssoc(), n_setParameters(), and REL_TOL.
Referenced by descendingLadderEpochRepeat(), LocalMaxStatMatrix::getR(), and rMin().
◆ thetaMinusDelta()
Definition at line 343 of file njn_localmaxstatutil.cpp.
References delta().
Referenced by LocalMaxStatMatrix::getR().
Variable Documentation
◆ REL_TOL
| const double REL_TOL = 1.0e-6 |
Definition at line 53 of file njn_localmaxstatutil.hpp.
Referenced by descendingLadderEpochRepeat(), isProbDist(), and thetaMin().
