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Functions | |
| template<typename T > | |
| T | bitsToNats (T x_) |
| template<typename T > | |
| T | natsToBits (T x_) |
| template<typename T > | |
| T | hartleysToNats (T x_) |
| template<typename T > | |
| T | natsToHartleys (T x_) |
| template<typename T > | |
| T | hartleysToBits (T x_) |
| template<typename T > | |
| T | bitsToHartleys (T x_) |
| template<typename T > | |
| T | exp2 (T x_) |
| template<typename T > | |
| T | log2 (T x_) |
| template<typename T > | |
| T | exp10 (T x_) |
| template<typename T > | |
| T | log10 (T x_) |
| template<typename T > | |
| T | max (T x_, T y_) |
| template<typename T > | |
| T | max3 (T a_, T b_, T c_) |
| template<typename T > | |
| T | min (T x_, T y_) |
| template<typename T > | |
| T | plus (T x_) |
| template<typename T > | |
| T | minus (T x_) |
| template<typename T > | |
| T | signum (T x_) |
| template<typename T > | |
| T | heaviside (T x_) |
| template<typename T > | |
| T | psqrt (T x_) |
| template<typename T > | |
| T | square (T x_) |
| template<typename T > | |
| T | bound (T x_, T xlo_, T xhi_) |
| template<typename T > | |
| T | probability (T x_) |
| template<typename T > | |
| T | prob (T x_) |
| template<typename T > | |
| bool | isProb (T x_) |
| template<typename T > | |
| T | positive (T x_) |
| template<typename T > | |
| T | negative (T x_) |
Function Documentation
◆ bitsToHartleys()
Definition at line 98 of file njn_function.hpp.
References bitsToNats(), and natsToHartleys().
◆ bitsToNats()
◆ bound()
Definition at line 116 of file njn_function.hpp.
Referenced by CColumnLayout::BuildLayout(), CCompactLayout::BuildLayout(), CLayeredLayout::BuildLayout(), CSimpleLayout::BuildLayout(), CInlineLayout::BuildLayout(), COverlayLayout::BuildLayout(), CLinkedFeatsGroup::GetHTMLActiveAreas(), CBinsTrack::InitHTMLActiveArea(), CGraphTrack::InitHTMLActiveArea(), CVarTrack::InitHTMLActiveArea(), CVcfTrack::InitHTMLActiveArea(), main(), s_Offset(), CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CSGAlignmentJob::x_GetAlignments(), CLayeredLayout::x_LayerByPos(), CLayeredLayout::x_LayerBySize(), CTreeGraphicsModel::x_RenderNodeLabelsPdf(), ILayoutPolicy::x_SeparateObjects(), CColumnLayout::x_SetObjectPos(), CLayeredLayout::x_SetObjectPos(), and CLayoutGroup::x_UpdateBoundingBox().
◆ exp10()
Definition at line 102 of file njn_function.hpp.
References LN_10.
◆ exp2()
Definition at line 100 of file njn_function.hpp.
References LN_2.
Referenced by CDBUDPriorityMapper::GetServerOptions().
◆ hartleysToBits()
Definition at line 97 of file njn_function.hpp.
References hartleysToNats(), and natsToBits().
◆ hartleysToNats()
◆ heaviside()
Definition at line 111 of file njn_function.hpp.
◆ isProb()
Definition at line 125 of file njn_function.hpp.
◆ log10()
Definition at line 103 of file njn_function.hpp.
Referenced by CondensedColumnUnaligned::AddRowChar(), BlastHSPCBSStreamClose(), Blur(), CExprParser::CExprParser(), NSnpBins::ChooseSignificant(), CWriteDB_Impl::Close(), CompressLength(), CScatterPlotGlyph::ComputeAxisRange(), ComputeNormalizedProteinEntropy(), AlignmentDisplay::DumpCondensed(), DumpText(), CTextUtils::GetCharsCount(), SHitColoringParams::GetColorNorm(), CGlTextureFont::GetMaxWidth(), CTextUtils::GetMaxWidth(), mu::Parser::Log10(), main(), SLogScaleData::MapValue(), CSpectrumSet::Peaks2Spectrum(), PrintSAM(), CWriteDB_File::RenameFileIndex(), CWriteDB_Volume::RenameFileIndex(), seqsubmit_split::CSeqSubSplitter::Run(), s_log_value(), CRegularGridGen::SelectBaseStep(), CRegularGridGen::SelectScreenStep(), CHistogramGlyph::SetAxisRange(), CTableImportListCtrl::SetDataSource(), SHitColoringParams::SetPrecision(), CObjectOStreamXml::WriteDouble2(), CFeaturePanel::x_CalcGridStep(), CGlDrawScale::x_CalcMaxLabelSize(), CRuler::x_CalculatePosLabelsStep(), CBinsGlyph::x_Draw(), CGeneMarkerGlyph::x_Draw(), CScatterPlotGlyph::x_Draw(), CHistogramGlyph::x_DrawLogRuler(), CDownloadJob::x_FormatSize(), SLogScaleData::x_InitDenominator(), CGlDrawScale::x_Normalize(), CLDBlockTrack::x_OnIconClicked(), CFeaturePanel::x_RenderFeatureGrid(), CXmlValueItem::x_RenderXml(), and CCrossPanelIR::x_SelectBaseStep().
◆ log2()
Definition at line 101 of file njn_function.hpp.
Referenced by CExonSelectorApplication::ChainExons(), and ProcessSAM().
◆ max()
- Examples
- /home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp, and /home/coremake/doxygen/cxx/include/util/data_histogram.hpp.
Definition at line 105 of file njn_function.hpp.
Referenced by _mm_cvtps_pi16(), _mm_cvtps_pi8(), CSeq_annot_SplitInfo::Add(), CBlobSplitterImpl::Add(), CTMgr_LengthStats::Add(), CTMgr_PositionStats::Add(), SGraphMaker::AddActualValues(), CAlignCollapser::AddAlignment(), CAlignDistGraph::AddAlignment(), CMergeTree::AddEquiv(), CProteinAlignText::AddHoleText(), CRasterizer< A >::AddInterval(), CDensityMap< CntType >::AddRange(), CBamFileRangeSet::AddRanges(), CDensityMap< CntType >::AddRanges(), CBamRefSeqChunkInfo::AddRefSeqRange(), CScoreBuilderBase::AddScore(), CPhyloSelectionSetMgr::AddSet(), CPdf::AddShadedTris(), CGraphStatCollector_Glyph::AddStat(), StyleManager::AddUserStyle(), CSrvStatTerm< T >::AddValue(), CSrvStatTerm< T >::AddValues(), CPaintSequence::AdjustFeatStartStop(), CEditSequence::AdjustFeatureLocations(), CEditSequence::AdjustProtFeatureLocations(), CSeqGraphicPane::AdjustViewPortHeightToImage(), AlignFNog(), SMakeProjectT::AnalyzeMakeIn(), AreAbuttingOnProduct(), CModelCompare::AreSimilar(), CSplignArgUtil::ArgsToSplign(), mu::ParserByteCode::AsciiDump(), compile_time_bits::bitset_traits< _Ty, _Size, u_type >::assemble_mask(), CCompartmentAccessor< THit >::AsSeqAlignSet(), CNCBlobKey::Assign(), BadScore(), BlastHSPCullingOptionsNew(), BOOST_AUTO_TEST_CASE(), IPhyloTreeRender::BufferedRender(), CColumnLayout::BuildLayout(), CCompactLayout::BuildLayout(), CSimpleLayout::BuildLayout(), COverlayLayout::BuildLayout(), BVImportTest(), CPhyloTreePS::CalcForces(), variation::CalcSOTermsForProt(), CChain::CalculateDropLimits(), IPhyloTreeRender::CalculateExtents(), CScatterGraph::CalculateLimits(), CHTML_table::CalculateNumberOfColumns(), CAlnVec::CalculatePercentIdentity(), CChain::CalculateSupportAndWeightFromMembers(), CSeqVector_CI::CanGetRange(), CBlastFormattingMatrix::CBlastFormattingMatrix(), CCalcRectangularTree::CCalcRectangularTree(), CCalcSlantedTree::CCalcSlantedTree(), CChain::CChain(), CCompartmentFinder< THit >::CCompartment::CCompartment(), CCompressionDictionary::CCompressionDictionary(), CExprValue::CExprValue(), CGlDrawScale::CGlDrawScale(), CGraphTrack::CGraphTrack(), CExonSelectorApplication::ChainExons(), CSeqDBAtlas::ChangeOpenedFilseCount(), CSeqTable_sparse_index::ChangeToBit_set(), check_match_limit(), CheckBlobSize(), CSeqUtils::CheckMaxSearchSegments(), CheckSourceFeatCoverage(), CHitGlyph::CHitGlyph(), CAnnotationASN1::CImplementationData::CImplementationData(), CAlignCollapser::CleanSelfTranscript(), CNCStat::ClientBlobRead(), CNCStat::ClientBlobWrite(), CAlignCollapser::ClipESTorSR(), DeBruijn::CDBGraphDigger::SContig::ClipLeft(), CChain::ClipLowCoverageUTR(), CAlignCollapser::ClipNotSupportedFlanks(), DeBruijn::CDBGraphDigger::SContig::ClipRight(), BlockModel::clipToRange(), CNcbiApplogApp::Cmd_Generate(), CGridCommandLineInterfaceApp::Cmd_SubmitJob(), CNumberValidator::CNumberValidator(), NTweakExon::Collapse(), CollapseExonStructure(), SBamIndexRefIndex::CollectEstimatedCoverage(), CChain::CollectTrustedmRNAsProts(), CChainer::CChainerImpl::CombineCompatibleChains(), CombineCorrectionsAndIndels(), CGlRect< TVPUnit >::CombineWith(), CBDB_RawFile::CompactEx(), CSeqportUtil_implementation::Complement(), CReadBlastApp::complete_overlap(), compress2(), IPhyloTreeRender::ComputeScale(), CBoundaryShapeRectBase::ComputeShape(), CBoundaryShapeRectBase::ComputeShapeWithLabels(), CBoundaryShapeTri::ComputeShapeWithLabels(), CSeqportUtil_implementation::Convert(), ConvertDendiagToPairwiseAln(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), DMAlignedOptimalScore::convertScoreToDistance(), ConvertSeqAlignToPairwiseAln(), ConvertStdsegToPairwiseAln(), CountQueryCoverage(), CPager::CPager(), CPmidValidator::CPmidValidator(), CRasterizer< A >::CRasterizer(), CNamedPipeHandle::Create(), CreateAlignRow(), CBlastBioseqMaker::CreateBioseqFromId(), CreateCompartmentAccessor(), CreateConfigurableFile(), CWinMaskFilesDlg::CreateControls(), Threader::CreateCorDef(), variation_ref::CVariationUtil::CreateFlankLocs(), variation::CVariationUtil::CreateFlankLocs(), CGlShader::CreateShader(), CDeltaHelper::CreateSSR(), CPagerView::CreateSubNodes(), CPagerViewButtons::CreateSubNodes(), CFileIO::CreateTemporary(), CSeqTextVariationGraph::CSeqTextVariationGraph(), Splines::cubicRoots(), CVCFVariantList::CVCFVariantList(), CWGSFeatureIterator::CWGSFeatureIterator(), CAttribIntMenuItem::Dec(), CAttribFloatMenuItem::Dec(), CSelListModelImpl< Item >::DeleteItem(), DFS::DFS(), CNCStat::DiskBlobWrite(), CEquivRange::Distance(), CMostAffinityJob< TImpl >::Done(), CSeqMaskerOstatOpt::doSetUnitCount(), CSampleTest::DoTest(), DP_CalculateMaxLoopLength(), CPhyloTreePS::Draw(), CGlDrawScale::Draw(), CDumpSysInfo::DumpSystemInfo(), CMultAlign::EmitSequenceFromRead(), EndAdded(), SBamIndexRefIndex::EstimateDataSizeByAlnStartPos(), CCassandraFullscanRunner::Execute(), CMemoryFile::Extend(), CGnomonAnnotator::ExtendJustThisChain(), CFormattingArgs::ExtractAlgorithmOptions(), CTableImportDataSource::ExtractFixedFields(), CEFetch_Request::FetchIdList(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), FillSetClearIntervals(), FillSets(), FillSetsIntervals(), FillSetsRandom(), FillSetsRandomMethod(), FillSetsRandomOne(), FillSetsRegular(), FillSparseIntervals(), CAlignCollapser::FilterAlignments(), DeBruijn::CDBGraphDigger::FilterNeighbors(), CRgbaGradColorTable::FindClosestColor(), FindCompartments(), CChainer::CChainerImpl::FindContainedAlignments(), FindFGapIntronNog(), FindGeneticCode(), findHighestScoringRowByPssm(), FindIGapIntrons(), CContigAssembly::FindMaxRange(), COMSSASearch::FindMinMaxSearchSettingId(), COMSSASearch::FindMinMaxSpectrumNumber(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CObjectConverter::FindRelationByName(), CObjectConverter::FindRelations(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CSeqTextDataSource::FindSequenceFragment(), CSeqTextDataSource::FindSequenceFragmentList(), CReadBlastApp::fit_blast(), CSubSource::FixDateFormat(), COrgMod::FixHostCapitalization(), CSubSource::FixIsolationSourceCapitalization(), CSubSource::FixSexQualifierValue(), CSubSource::FixTissueTypeCapitalization(), FloatingPointSpinCtrl::FloatingPointSpinCtrl(), CExonSelectorApplication::FormatPaired(), FormatPaired(), FrAlign(), FrAlignFNog1(), fta_check_feat_overlap(), CInstance::GapDistance(), CCassandraFilteredPlan::Generate(), generate_sparse_bvector(), CRegExFSA::GenerateArrayMapData(), CChoiceTypeStrings::GenerateClassCode(), CRegularGridGen::GenerateGrid(), CEnumTypeStrings::GenerateTypeCode(), CScore_StartStopCodon::Get(), CScore_BlastRatio::Get(), CVDBObjectCacheBase::Get(), ctll::parser< Grammar, input, ActionSelector, IgnoreUnknownActions >::get_current_term(), get_LSH_hashes2(), SBaseStats::get_min_max(), ctll::parser< Grammar, input, ActionSelector, IgnoreUnknownActions >::get_previous_term(), get_string_size_longchar(), CAlnVecMultiDataSource::GetAlnFromSeq(), CSparseMultiDataSource::GetAlnFromSeq(), SBamIndexRefIndex::GetAlnOverStarts(), CCSraRefSeqIterator::GetAlnOverStarts(), CSparseAlignment::GetAlnSeqString(), CSeqDBVol::GetAmbigPartialSeq(), CAlignDistGraph::GetAndRemoveNearestPair(), CFeatureParams::GetBarHeight(), CQuerySet::GetBestRank(), CScoreBuilder::GetBlastScoreDenseg(), CLZOCompression::GetBlockSizeMax(), CPhyloNodeData::GetBoundingRect(), CAlignCollapser::GetCollapsedAlgnments(), CColumnScoringMethod::GetColorForScore(), CMatrixScoringMethod::GetColorForScore(), SHitColoringParams::GetColorNorm(), CRgbaGradColorTable::GetColorTexCoord(), CPSGSResolveErrors::GetCombinedErrorCode(), CBDB_BlobDeMux::GetCoordinates(), CMultAlign::GetCounts(), NParamsBuilder::SInteractive::GetDataLimit(), CDensityMap< CntType >::GetDensityMap(), CSeqTextVariationGraph::GetDrawWidth(), CDiffList::GetEditDistance(), variation::CVariationUtil::GetEffectiveTranscriptLength(), AMatrix_base::GetExtremalEntries(), CSeqGlyph::GetFadeFactor(), GetFeatureProtein(), CPaintSequence::GetFeatWholeRange(), GetFloatingPointDialog::GetFloatingPointDialog(), CBlastQuerySourceBioseqSet::GetGeneticCodeId(), CSGAlignmentDS::GetGraphCost(), CAlignFormatUtil::GetGraphiscLink(), CPosToIndex::GetIndexForPosition(), CTL_RowResult::GetItemInternal(), CBioseq_set::GetLabel(), CPhyloNodeData::GetLabelRect(), CNCBlobStorage::GetLatestBlobExpire(), CVCFVariantsBase::GetLeftShiftedStartPos(), GetLength(), CBlastQuerySourceOM::GetLength(), SBamIndexRefIndex::GetLimitRange(), CBulkLocationPanel::GetLocForBioseq(), CVcfVariant::GetLongestAlleleLen(), SAlignmentScoringModel::GetLongestMatchrunLen(), CHistogramGlyph::GetMax(), CAlignShadow::GetMax(), CVariantDescriptors::GetMaxFeatureLength(), CSeqDBVolSet::GetMaxLength(), CIntervalTree::GetMaxRootCoordinate(), CGlTextureFont::GetMaxWidth(), CTextUtils::GetMaxWidth(), CGlBitmapFont::GetMetric(), ColumnResidueProfile::getMostFrequentResidue(), CAgressiveResizeStrategy::GetNewCapacity(), CPowerOfTwoResizeStrategy::GetNewCapacity(), CPhyloNodeData::GetNodeLayoutSize(), CSeqDBNegativeList::GetNumOids(), CAlignRange< Position >::GetPositionMax(), CCSraAlignIterator::GetQualityGraph(), CAlignShadow::GetQueryMax(), CCSraShortReadIterator::GetReadRange(), CHandleRange::GetRight(), CApplyRNAITSDlg::GetRNAITSList_AlignCoordFromDlg(), CApplyRNAITSDlg::GetRNAITSList_SeqCoordFromDlg(), CTableDataSUC::GetRowsCount(), CCodingPropensity::GetScore(), CGnomonEngine::GetScore(), CPhyloTree::GetSelectedBoundary(), CHitMatrixRenderer::GetSelectedHitElemsRect(), CAlignFormatUtil::GetSeqAlignCoverageParams(), CSeqTextDataSourceInterval::GetSeqData(), CAlnVecMultiDataSource::GetSeqFromAln(), CSparseMultiDataSource::GetSeqFromAln(), CSraRun::GetSequenceLength(), CDBLB_ServiceMapper::GetServerOptions(), CRulerPanel::GetSize(), CCassConnection::GetSizeEstimates(), GetSortedFeatList(), CAdvancedAlignCleanup::GetSplignCompartments(), CSraRun::GetSpotEntry(), CSeq_bond::GetStop(), CCgiContext::GetStreamStatus(), CStructCommentFieldPanel::GetStructCommentFields(), CAlignShadow::GetSubjMax(), CPub::GetTitles(), CCassConnection::GetTokenRanges(), CSequenceTrack::GetTooltip(), CGuiObjectInfoVariant::GetToolTip(), CMultAlign::GetVariationAlignList(), gz_comp(), gz_load(), CMostAffinityJob< TImpl >::HasJob(), DeBruijn::HistogramRange(), CSplignTrim::ImproveFromLeft(), CNWFormatter::SSegment::ImproveFromLeft1(), CSplignTrim::ImproveFromRight(), CNWFormatter::SSegment::ImproveFromRight1(), bm::sparse_vector< Val, BV >::inc_no_null(), inflate_table(), CPhyloTreePS::Init(), CSeqScores::Init(), MATR< char >::Init(), CElementaryMatching::CBoolVector::Init(), IPhyloTreeRender::InitCollisionInfo(), CAlignCollapser::InitContig(), CHistogramData::InitDataPoints(), CTableDataListCtrl::InitDataSource(), COpenDlg::InitDialog(), CNCDistributionConf::Initialize(), CNCDistributionConf::InitMirrorConfig(), CNcbiTestApplication::InitTestFramework(), InRange(), CGene::Insert(), CMultAlign::InsertDashesInBase(), CProjBulderApp::InsertDep(), CSelListModelImpl< Item >::InsertItem(), CSelListModelImpl< Item >::InsertItems(), IntegerSpinCtrl::IntegerSpinCtrl(), interlocked_dec_max(), interlocked_inc_max(), internal_dfa_exec(), CAlignRange< Position >::IntersectSecondWith(), CGlRect< TVPUnit >::IntersectWith(), CAlignRange< Position >::IntersectWith(), CCddInputData::CHit::IntersectWith(), CSeqDB_BitSet::IntersectWith(), IntervalsCheck(), CGene::IsAlternative(), COrgMod::IsStrainValid(), CSubSource::IsValidSexQualifierValue(), CSplignTrim::JoinExons(), CButtonPanel::Layout(), CMinPanelContainer::Layout(), CMapItem::Layout(), CMatrixScoringMethod::Load(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCompressionDictionary::LoadFromStream(), CNetScheduleJobSerializer::LoadJobInput(), CBamRefSeqInfo::LoadPileupChunk(), COpenObjectsPanel::LoadSettings(), CMainFrame::LoadSettings(), CWidgetDisplayStyle::LoadSettings(), CTableImportDataSource::LoadTable(), CPrefetchThreadOld::Main(), CChainer::CChainerImpl::MakeChains(), MakeCompartment(), CBamIndex::MakeEstimatedCoverageAnnot(), Map(), CMemoryFileMap::Map(), CMappingRange::Map_Range(), match(), CReadBlastApp::match_na(), mu::Parser::Max(), mu::ParserInt::Max(), SAutoMinMaxLimits< T, is_signed >::max(), SAutoMinMaxLimits< T, false >::max(), ncbi::boost_fp_impl::tt_detail::fpt_limits< FPT >::max_value(), CHMM_State::MaxLen(), CNCBlobStorage::MeasureDB(), CInstance::MergeIn(), CFeatureGenerator::SImplementation::MergeSeq_locs(), SAutoMinMaxLimits< T, is_signed >::min(), CDepthCollection::MinDepthForRange(), CTextSelectItem::MouseLeftDown(), CPaintSequence::MouseToFeature(), MutationOperationsTest(), CBDB_Env::MutexSetMax(), CNSPreciseTime::Never(), CNSTPreciseTime::Never(), CBDB_BlobDeMux::NewPlane(), CDistMethods::NjTree(), Nlm_ClearDestString(), Nlm_StepBound(), Nlm_StringNCat(), Nlm_StringNCmp(), Nlm_StringNCpy(), Nlm_StringNCpy_0(), Nlm_StringNICmp(), Nlm_StrNICmp(), Nlm_StrNIPCmp(), ON_EVENT(), CPSGS_AnnotProcessor::OnAnnotBlobProp(), CAlnStatGlyph::OnLeftDblClick(), CAttribTableDelimitersPanel::OnListctrlColLeftClick(), CWidgetHandle::OnMove(), CGradientPanel::OnPaint(), CQueryParsePanel::OnSearchctrlTextEnter(), CSeqGraphicPane::OnSearchTip(), CTextItemPanel::OnTimer(), CBDB_Cache::Open(), CObject::operator new(), CdsNumOrder::operator()(), SRangesBySize::operator()(), SRangesByPctIdent::operator()(), CInitPSNodes::operator()(), CCalcSlantedTree::operator()(), CReadBlastApp::overlaps(), CReadBlastApp::overlaps_prot_na(), PackSeqPntCheckCpp(), CLogLatencies::Parse(), CSeq_id_Textseq_Info::ParseAcc(), CFastaReader::ParseDataLine(), pcre_printint(), CChain::PeaksAndLimits(), CChangePhyloExpandCollapseCmd::PerformEdit(), PiiOk(), DeBruijn::CDBGraph::PlusFraction(), CGnomonAnnotator::Predict(), CGroupMapWidget::CGroupItem::PreferredHeight(), CMapItem::PreferredHeight(), CGraphContainer::PreferredSize(), CGridCommandLineInterfaceApp::PrepareRemoteAppJobInput(), IImageGrabber::PreviewImages(), CAlignDistGraph::Print(), CTabularFormatter_AlignEnd::Print(), CTabularFormatter_NearestGap::Print(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), CPsgPerfApplication::PrintResult(), CCommandArgDescriptions::PrintUsage(), CResolveRequest::Process(), SBamIndexRefIndex::ProcessBin(), CProjectTreeBuilder::ProcessDir(), ProductToSource(), CNCBlobAccessor::Purge(), CBDB_Cache::Purge(), QSbuf_ParseScores(), random_minmax(), RangeRandomFillTest(), CChunkFile::RawRead(), CSeqIdChunkFile::RawRead(), SBamIndexRefIndex::Read(), CGlimmerReader::Read(), CBDB_PropertyDictionary< PropKey, PropValue >::Read(), CFileIO::Read(), CCompressionIStream::Read(), CCompressionIOStream::Read(), read_repeat_counts(), CFastaReader::ReadAlignedSet(), SQueueParameters::ReadClientRegistryTimeoutReader(), SQueueParameters::ReadClientRegistryTimeoutWorkerNode(), ReadIntoUtf8(), SQueueParameters::ReadQueue(), CAgpRow::ReadSeqPos(), CTableImportDataSource::RecomputeFields(), CTableImportDataSource::RecomputeHeaders(), CHMM_State::RegionStop(), CObjectConverter::Register(), CBioTreeFeatureDictionary::Register(), SPSGS_AnnotRequest::RegisterBioseqInfo(), SPSGS_AnnotRequest::RegisterProcessedName(), CPhyloTreeDataSource::Relabel(), NDirectNetStorageImpl::CObj::Relocate(), CAlignDistGraph::RemoveEquivs(), SequenceViewerWidget_SequenceArea::RemoveRubberband(), CRuler::Render(), CLinearSelHandler::Render(), CPhyloNodeData::RenderRotated(), IBoundaryShape::RenderVbo(), CChainer::CChainerImpl::ReplicatePStops(), CSparseKmerCounts::Reset(), CBinaryKmerCounts::Reset(), CGnomonEngine::ResetRange(), CSeqportUtil_implementation::Reverse(), CSeqportUtil_implementation::ReverseComplement(), CRgbaColor::RgbToHsv(), CDeltaBlastApp::Run(), SGridWorkerNodeImpl::Run(), CCompartmentAccessor< THit >::Run(), CXcompareAnnotsApplication::Run(), CTestTranscript_Orfs::RunTest(), s_AbsMax(), s_AddPrimers(), s_AddProjItemToDll(), s_AddToLog(), s_AlignDist(), s_BlastEvenGapLinkHSPs(), s_BuiltInSM(), s_CalcCoverageCount(), s_CodingPropensity(), s_CompareProtProdToTrans(), s_ConvertValue(), s_CreateThreadPool(), s_DetermineComponentType(), s_Distance(), s_DoNWalign(), s_EquivalentScores(), s_ExonToDenseg(), s_FindBestSubRange(), s_FindQueueThread(), s_GenerateCollapsedNode(), s_Get_LSH_index_hashes2(), s_GetAlignmentMismatches(), s_GetEvalue(), s_GetFontDescender(), s_GetLatLong(), s_GetMinMax(), CHitFilter< THit >::s_GetOverlap(), s_GetPrimerInfo(), CGlPane::s_GetShift(), s_GetStrForStructuredComment(), s_GetUncoveredLength(), s_HighPairFrequencies(), s_IsValidSexQualifierPhrase(), s_MakeDomainString(), s_MakeStep(), s_MaskQuerySeq(), s_ReadSpecificParams(), s_Reserve(), s_ReserveMore(), s_RunOfStars(), s_SeqDBMaskSequence(), s_SetSplitQuerySeqInterval(), s_ShouldFetchOneByOne(), s_SubsequentIntron(), s_SysAllocLongWay(), s_Test_Extremes(), s_Test_Interval(), SAlignExtended::SAlignExtended(), CWGSDb_Impl::SAmbiguityInfo::SAmbiguityInfo(), CSymDustMasker::save_masked_regions(), CMainFrame::SaveSettings(), ScanForCpGs(), COverlapScorer::ScoreAlignments(), CSeqTextPane::ScrollToPosition(), CCSraAlignIterator::Select(), CCompactSAMApplication::SelectBestLocations(), CExonSelectorApplication::SelectBestLocations(), CGnomonEngine::SelectBestReadingFrame(), CScriptPanel::SelectMacros(), CWGSFeatureIterator::SelectRowRange(), SeqIntCheckCpp(), CAutoDefExonListClause::SeqLocIntersect(), SeqPntCheckCpp(), SerializationTest(), CIgBlastTabularInfo::SetAirrFormatData(), FloatingPointTextCtrl::SetAllowedRange(), IntegerTextCtrl::SetAllowedRange(), CHistogramGlyph::SetAxisMaxFixed(), CHistogramGlyph::SetAxisRange(), CLZOCompression::SetBlockSize(), CBDB_RawFile::SetBtreeMinKeysPerPage(), CBDB_Env::SetCacheSize(), CAlnMultiRenderer::SetColumnWidth(), CMapControl::SetColumnWidth(), CTableImportDataSource::SetCommentChar(), CChain::SetConfirmedEnds(), CChain::SetConfirmedStartStopForCompleteProteins(), CChain::SetConsistentCoverage(), CNCBlobAccessor::SetCurBlobExpire(), CPhyloTreeWidget::SetDataSource(), CTableImportListCtrl::SetDataSource(), CPhyloTreeWidget::SetDataSourceNoUpdate(), NDirectNetStorageImpl::CNetCache::SetExpiration(), CChainer::CChainerImpl::SetFlagsForChains(), CIdHandler::SetId(), CIgBlastTabularInfo::SetIgAnnotation(), CIgBlastTabularInfo::SetIgCDR3FWR4Annotation(), CNcbiApplogApp::SetInfo(), CSelListModelImpl< Item >::SetItems(), SBamIndexRefIndex::SetLengthFromHeader(), CGffFeatureRecord::SetLocation(), CDensityMap< score_type >::SetMax(), CReader::SetMaximumConnections(), CMapControl::SetMaxItemHeight(), IEditingAction::SetMaxRecords(), SAnnotSelector::SetMaxSearchSegments(), SAnnotSelector::SetMaxSearchTime(), SAnnotSelector::SetMaxSize(), CBDB_FieldSimpleInt< Uint2 >::SetMaxVal(), CBDB_FieldSimpleFloat< float >::SetMaxVal(), CNCMMCentral::SetMemLimits(), CNCBlobAccessor::SetNewBlobExpire(), CUser_field::SetNumFromSize(), CPhyloTreeWidget::SetPortLimits(), CDBUDRandomMapper::SetPreference(), CGlPane::SetScaleRefPoint(), CSeq_annot_SplitInfo::SetSeq_annot(), COligoSpecificityTemplate::SetTargetSize(), ProgressMeter::SetValue(), SHitColoringParams::SetValueRange(), SetWBHardSizeLimit(), CwxAlnStatOptionsDlg::SetZoomLevel(), SimpleGapFillSets(), CAlignCompare::SAlignment::Slice(), CSelListModelImpl< Item >::SLM_SelectTo(), dtl::Diff< elem, vector< elem >, Compare< elem > >::snake(), SortMixLoc(), SourceToProduct(), NParamsBuilder::SParallelProcessing< SInteractiveParams >::SParallelProcessing(), CSplitter::Split(), CCassandraFullscanPlan::SplitTokenRangesForLimits(), CSeq_annot_Info::StartSortedIterator(), CIntervalTree::Stat(), SPSG_Request::StatePrefix(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CTempStringEx::substr(), SwapTest(), CHitFilter< THit >::sx_GetEndsInRange(), sx_Round(), TestDataNotFound(), TestSparseVector_Stress(), CPaintSequence::TranslateCDS(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), CRawScoreVector< Key, Score >::TrimCount(), CWordPairIndexer::TrimPunctuation(), uncompress2(), CPhyloTreePS::Update(), CGeneGroup::Update(), CGlyphContainer::Update(), CPileUpGraph::UpdateAlignStats(), CPhyloTreePS::UpdateAndSynch(), IPhyloTreeRender::CExtentDimension::UpdateExtent(), CAlignRangeCollExtender< TAlnRngColl >::UpdateIndex(), CPrintSetupDlg::UpdateMargins(), CPSGS_CassProcessorBase::UpdateOverallStatus(), CCompositeTextItem::UpdatePositions(), CExon::UpdatePrevExon(), CTreeCollisionModel2D::UpdateScaled(), CCompositeDesktopItem::UpdateSize(), CRootDesktopItem::UpdateSize(), CTreeCollisionModel2D::UpdateVisibility(), CDense_seg::Validate(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseq::ValidateTwintrons(), CChain::ValidPolyA(), CMultAlign::Variations(), VisitXmlNodes(), CBDB_PropertyDictionary< PropKey, PropValue >::Write(), CBDB_BlobDictionary< Key >::Write(), CFileIO::Write(), CNamedPipeHandle::Write(), CCompressionOStream::Write(), CCompressionIOStream::Write(), CPipeHandle::Write(), CNCBlobStorage::WriteBlobStat(), CSrvSocketTask::WriteData(), CAlignmentTrack::x_AddAlignmentLayout(), CPhrap_Contig::x_AddAlignRanges(), CSGAnnotJob::x_AddGraphToMap(), CTooltipFrame::x_AddLineToWidget(), CNCStat::x_AddStats(), CGlPane::x_AdjustVisibleRect(), CSplicedAligner32::x_Align(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateDomain(), CUtf8::x_Append(), CSeqDBOIDList::x_ApplyNegativeList(), CPhyloTreePS::x_ApplyNeighborCellForces(), CPhyloTreePS::x_ApplyRepulsiveForces(), CPhyloTreePS::x_ApplyRepulsiveForcesHashed(), CUtf8::x_AsBasicString(), CGvfWriteRecord::x_AssignAttributeEndRange(), CGvfWriteRecord::x_AssignAttributeStartRange(), CGBDocument::x_AssignViewIndex(), CPhyloPdfGrabber::x_BeginCaptures(), CTooltipFrame::x_BreakIntoLines(), CMultiAligner::x_BuildAlignmentIterative(), CDumpASNIndex::x_BuildIndexAndSeqIdInfo(), CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CPhyTreeCalc::x_CalcAlnSegInfo(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CAlignGlyph::x_CalcIntervals(), CGlDrawScale::x_CalcMaxLabelSize(), CAlignDistGraph::x_CalculateAllDistances(), CMatrixScoringMethod::x_CalculateConsensusRange(), CMapControl::x_CalculateLayout(), CMatrixScoringMethod::x_CalculateNonConsensusRange(), CSeqTextPane::x_CalculateOffsetList(), CAlignDistGraph::x_CalculateOneDistance(), CRuler::x_CalculatePosLabelsStep(), CMapItem::x_CalculateRealTextWidth(), CBandAligner::x_CheckMemoryLimit(), CNCActiveSyncControl::x_CheckSlotOurSync(), CNCActiveSyncControl::x_CheckSlotTheirSync(), CBDB_Cache::x_CheckTimeStampExpired(), CTreeGraphicsModel::x_CircularLabelMinAngle(), CScope_Impl::x_ClearCacheOnNewData(), CLinearSelHandler::x_ClipPosByRange(), CAlignMarkHandler::x_ClipPosByRange(), CTextSelHandler::x_ClipPosByRange(), CCompareSeq_locs::x_Compare(), CQualScoreWriter::x_ComposeHeaderEnding(), IPhyloTreeRender::x_ComputeEdgeHighlight(), CBDB_Cache::x_ComputeExpTime(), CCompareSeq_locs::x_ComputeOverlapValues(), CBoundaryShapeTri::x_ComputeTriParms(), CPSGS_Dispatcher::x_ConcludeIDGetNARequestStatus(), CValidError_bioseq::x_CountAdjacentNs(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), CTableDataValidate::x_CountRows(), CWGSSeqIterator::x_CreateFeaturesChunk(), CSGAnnotJob::x_CreateHistFromGraph(), CElementaryMatching::x_CreateIndex(), CSGAlignStatJob::x_CreatePileUpGraphs(), CSplignJob::x_CreateProjectItems(), CSelectionControl::x_DeleteItem(), CBlastFormat::x_DisplayDeflines(), CDisplaySeqalign::x_DisplayMpvAnchor(), CSplitter::x_DoDistributeEvenly(), CSplitter::x_DoDragSeparator(), COrfSearchJob::x_DoSearch(), CNamedGroup::x_Draw(), CAlnStatGlyph::x_DrawBarGraph(), CHistogramGlyph::x_DrawDataPoints(), CAlnStatGlyph::x_DrawDensityTable(), CFeatGlyph::x_DrawFeatureBar(), CHistogramGlyph::x_DrawGraph(), CHistogramGlyph::x_DrawHeatMap(), CAlignGlyph::x_DrawInserts(), CHistogramGlyph::x_DrawLogRuler(), CAttribMenu::x_DrawMenu(), CAlignGlyph::x_DrawMultiAlign(), CSelectionHelper::x_DrawSelectionArea(), CTranslationGlyph::x_DrawSequence(), CHistogramGlyph::x_DrawSmoothCurve(), CMapItem::x_DrawText(), CSequenceTextGraph::x_DrawVariations(), CId2ReaderBase::x_DumpReply(), CTreeQueryExec::x_EvalAdvance(), CCompartApp::CCompartment::x_EvalExons(), CMergeTree::x_EvalGap(), CSGAlignStatJob::x_Execute(), CSGFeatureJob::x_Execute(), CVcfFeatureJob::x_Execute(), CBlastFastaInputSource::x_FastaToSeqLoc(), CCgiEntryReader::x_FillBuffer(), CIgBlast::x_FillJDomain(), CInstancedAligner::x_FilterInstances(), IPhyloTreeRender::x_FindBestSize(), CObjectConverter::x_FindRelationByName(), CMultiAligner::x_FindRPSHits(), x_FindRSite(), CTraceGraph::x_FindSampleToLeft(), CTraceGlyph::x_FindSampleToLeft(), CTraceGraph::x_FindSampleToRight(), CTraceGlyph::x_FindSampleToRight(), CSequenceAmbigTrimmer::x_FindWhereToTrim(), CSpaceShrinker::x_FinishMoves(), CGBProjectHandle::x_FixIdGenerator(), CDisplaySeqalign::x_FormatAlnHSPLinks(), CCIGAR_Formatter::x_FormatLine(), variation_ref::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_fuzzy_pos(), CPSG_Request_Resolve::x_GetAbsPathRef(), CSeqDBVol::x_GetAmbigSeq(), CAlnVecRow::x_GetBaseHeight(), CGC_Sequence::x_GetChildren(), CInstancedAligner::x_GetDistanceInstances(), CDisplaySeqalign::x_GetDomainInfo(), CVecscreen::x_GetEdgeRanges(), CBoundaryShapeRoundedRect::x_GetEdges(), CAnnotObject_Less::x_GetExtremes(), CDisplaySeqalign::x_GetFeatureInfo(), CFileLoadWizard::x_GetFileSelectPanel(), CDiagConsoleCache::x_GetItem(), CSeqMap_CI_SegmentInfo::x_GetLevelPos(), CVecscreen::x_GetMatchType(), CVariantDescriptors::x_GetMaxFeatLengthForClinVar(), x_GetMaxMin(), CRuler::x_GetMaxNum(), CAlnStatGlyph::x_GetMaxTotal(), CSplignApp::x_GetNextComp(), CSplignApp::x_GetNextPair(), CFileLoadManager::x_GetOptionsPanel(), CRuler::x_GetOriginMetricSizeV(), CRelaxedLookupDlg::x_GetPubIds(), CWGSSeqIterator::x_GetQualityAnnot(), CCSraShortReadIterator::x_GetQualityGraph(), x_GetSequence(), CCorrectRNAStrandDlg::x_GetStatusSMART(), CTL_BCPInCmd::x_GetStringValue(), CDrawTextOStream::x_GetStyles(), CMapItem::x_GetTextAreaWidth(), CMacroLabel::x_GetTextWidth(), CRuler::x_GetTicksLabelsSizeV(), CPubseqGatewayApp::x_GetTimeSeries(), CSeqMap_CI_SegmentInfo::x_GetTopOffset(), CBoundaryShapeRoundedRect::x_GetTris(), CSchedulerEngine::x_GetWaitPeriod(), CHistogramGlyph::x_HighestValueBelowMax(), CNcbiApplicationAPI::x_HonorStandardSettings(), CSeqVector_CI::x_IncSeg(), CSeq_align_Mapper_Base::x_Init(), CGencollIdMapper::x_Init_SeqLocMappers(), CElementaryMatching::x_InitFilteringVector(), CSeqVector_CI::x_InitSeg(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CTaxFormat::x_InitTextFormatInfo(), CSelectionControl::x_InsertItem(), CSelectionControl::x_InsertItems(), CAlnMultiRenderer::x_InvalidateRows(), CVectorTrimPanel::x_IsCompleteCut(), CGencollIdMapper::x_IsLoc_Int_InAGap(), CLayeredLayout::x_LayerByPos(), CLayeredLayout::x_LayerBySize(), CBamRefSeqInfo::x_LoadRangesCov(), CBamRefSeqInfo::x_LoadRangesScan(), CBamRefSeqInfo::x_LoadRangesStat(), CCSRARefSeqInfo::x_LoadRangesStat(), CSGSeqGraphJob::x_LoadSeqTable(), CGraphTrack::x_LoadSettings(), CHTMLPage::x_LoadTemplate(), CHTMLPage::x_LoadTemplateLib(), CVDBGraphSeqIterator::x_MakeGraph(), CHistogramGlyph::x_MapValue(), CMinPanelContainer::x_MeasureItem(), CAlnGraphic::x_MergeDifferentSeq(), CAlnGraphic::x_MergeSameSeq(), CInstancedAligner::x_MinCoverageCheck(), CAlnMultiHeaderHandler::x_MoveColumnSeparator(), CSelListController< Item >::x_MoveSelectionBy(), CSelectionControl::x_MoveSelectionBy(), CAnnot_Collector::x_NoMoreObjects(), CSeqDB_BitSet::x_Normalize(), COligoSpecificityCheck::x_NW_alignment(), CPSGS_CassBlobBase::x_OnBlobPropSlimTSE(), CPSGS_CassBlobBase::x_OnBlobPropSmartTSE(), CMouseZoomHandler::x_OnChangeScale(), CMouseZoomHandler::x_OnEndZoomRect(), CGraphTrack::x_OnJobCompleted(), CGraphOverlay::x_OnLayoutChanged(), CGraphTrack::x_OnLayoutChanged(), CAlignmentTrack::x_OnLayoutIconClicked(), CWorkspaceAutoSaver::x_OnSave(), CGlWidgetBase::x_OnScrollX(), CGlWidgetBase::x_OnScrollY(), CAlignmentTrack::x_OnStatIconClicked(), CPhyloTreeMaxIdCalculator::x_OnStep(), CPhyloTreeMaxDirectChildDist::x_OnStep(), CPhyloTreeMaxChildDist::x_OnStep(), CPhyloTreeDistFromRoot::x_OnStep(), CPhyloTreeLabelRange::x_OnStep(), CPhyloTreeCalculator::x_OnStep(), CCache< TKey, TValue, THandler, TLock, TSize >::x_PackElementIndex(), CGFFReader::x_ParseFeatureInterval(), CAlignedFeatureGraph::x_PlaceCluster(), CAlnSpanVertModel::x_PopulateRows(), CArgDescriptions::x_PostCheck(), CDisplaySeqalign::x_PrepareRowData(), CSeq_loc_Mapper_Base::x_PreserveDestinationLocs(), CBlastFormat::x_PrintAirrRearrangement(), CIgBlastTabularInfo::x_PrintIgGenes(), CBlastFormat::x_PrintIgTabularReport(), CBlastTabularInfo::x_PrintQueryAndDbNames(), CGapStatsApplication::x_PrintSummaryView(), CBlastFormat::x_PrintTaxReport(), CSplignApp::x_ProcessPair(), CCorrectRNAStrandDlg::x_ProcessRNAStrandLine(), CStreamUtils::x_Pushback(), CConn_Streambuf::x_Read(), CRWStreambuf::x_Read(), CMultiAligner::x_RealignBlocks(), CTableImportDataSource::x_RecomputeRowFields(), CAlnVecRow::x_RenderAveragableScores(), CAlignGlyph::x_RenderAveragableScores(), CRuler::x_RenderBackground(), CTraceGlyph::x_RenderConfGraph(), CTraceGraph::x_RenderConfGraph(), CTraceGlyph::x_RenderCurveSegment(), CTraceGraph::x_RenderCurveSegment(), IImageGrabber::x_RenderGuides(), CAlnVecRow::x_RenderInserts(), CTraceGlyph::x_RenderIntensityGraphs(), CTraceGraph::x_RenderIntensityGraphs(), CLegend::x_RenderItems(), CAlnMultiRenderer::x_RenderItems(), CMinimapHandler::x_RenderMinimap(), IPhyloTreeRender::x_RenderNodeHighlight(), IPhyloTreeRender::x_RenderNodeVbo(), CTextSelHandler::x_RenderOpSymbol(), CRuler::x_RenderOriginAndMetric(), CTextSelHandler::x_RenderRange(), CRuler::x_RenderScale(), IPhyloTreeRender::x_RenderScaleMarker(), CAlnVecRow::x_RenderSequence(), CTraceGlyph::x_RenderSignalGraph(), CTraceGraph::x_RenderSignalGraph(), CLayoutTrack::x_RenderTitleBar(), CAlnVecRow::x_RenderUnaligned(), CBlastFormat::x_ReverseQuery(), CSplign::x_Run(), CSplign::x_RunOnCompartment(), CPosToIndex::x_SaveMaximumIndex(), COligoSpecificityCheck::x_SavePrimerInfo(), CSeqDBImpl::x_ScanTotals(), CAnnot_Collector::x_SearchMapped(), CAnnot_Collector::x_SearchRange(), CSeqGraphicPane::x_SelectByRect(), CHitMatrixGraph::x_SelectByRect(), CSelectionControl::x_SelectTo(), ILayoutPolicy::x_SeparateObjects(), variation_ref::CHgvsParser::x_SeqPntToStr(), COligoSpecificityCheck::x_SequencesMappedToSameTarget(), CMonotonicCounterSeries::x_SerializeOneSeries(), CProcessorRequestTimeSeries::x_SerializeOneSeries(), CPhyloSaveSelectiondlg::x_SetClusterIds(), CHugeAsnReader::x_SetFeatIdHooks(), CColumnLayout::x_SetObjectPos(), CLayeredLayout::x_SetObjectPos(), CSplign::x_SetPattern(), CIgBlast::x_SetupDJSearch(), CDataLoadersUtil::x_SetupGenbankDataLoader(), CCrossAlnRenderer::x_SetupModelLimits(), CIgBlast::x_SetupNoOverlapDSearch(), CScriptPanel::x_ShiftBottomLabels(), CSplitter::x_ShrinkCell(), COligoSpecificityTemplate::x_SortHit(), CSplitter::x_SplitPositionsToSizes(), CNCActiveSyncControl::x_StartScanSlots(), CAnnot_Collector::x_StopSearchLimits(), CSparseGraph::x_Sync(), CHistogramBinning::x_TryForEvenBins(), CSeqTextPane::x_UnderlineInterval(), CAlignGlyph::x_UpdateBoundingBox(), CLinkedFeatsGroup::x_UpdateBoundingBox(), CFeatureTrack::x_UpdateData(), CGeneModelTrack::x_UpdateData(), CGraphOverlay::x_UpdateLegend(), CHistogramGlyph::x_UpdateLegend(), CAlignMarkHandler::x_UpdateMarks(), COperationTiming::x_UpdateMaxReqsStat(), CAlnMultiModel::x_UpdateMinScale(), x_UpdateRanges(), CHitMatrixDataSource::x_UpdateScoreMap(), CGlWidgetBase::x_UpdateScrollbars(), CSingleFeatValidator::x_ValidateGeneXRef(), CValidError_graph::x_ValidateGraphValues(), CValidError_graph::x_ValidateMaxValues(), NStr::x_VerifyFloatLimits(), NStr::x_VerifyIntLimits(), SPSG_CV< deque< string > >::x_WaitUntil(), CScoringJob::x_WindowAvgScores(), CQualScoreWriter::x_WriteHeader(), CElementaryMatching::x_WriteIndexFile(), CFastaOstream::x_WriteSequence(), CGff3Writer::xAssignFeatureEndpoints(), CGtfWriter::xAssignFeaturesCds(), CAlnScannerNexus::xProcessMatrix(), CPushback_Streambuf::xsgetn(), CRWStreambuf::xsputn(), CConn_Streambuf::xsputn(), CForeignContaminationScreenReportReader::xTrimExt(), CGtfAnnotAssembler::xUpdateGene(), CGff3Writer::xWriteFeatureCds(), and CCassQueryList::Yield().
◆ max3()
Definition at line 106 of file njn_function.hpp.
◆ min()
- Examples
- /home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp, and /home/coremake/doxygen/cxx/include/util/data_histogram.hpp.
Definition at line 107 of file njn_function.hpp.
Referenced by _mm_cvtps_pi16(), _mm_cvtps_pi8(), _mm_minpos_epu16(), CSeq_annot_SplitInfo::Add(), CSeqsRange::Add(), CTMgr_LengthStats::Add(), CTMgr_PositionStats::Add(), SBaseStats::add_stat(), CAlignCollapser::AddAlignment(), NAdapterSearch::CPairedEndAdapterDetector::CConsensusPattern::AddExemplar(), AddInsertWithGaps(), CRasterizer< A >::AddInterval(), CProteinAlignText::AddProtText(), CDensityMap< CntType >::AddRange(), CBamFileRangeSet::AddRanges(), CDensityMap< CntType >::AddRanges(), CSAM_CIGAR_Formatter::AddRow(), CSubjectMap_Factory::AddSequenceChunk(), CSubjectMap_Factory_TBase::AddSequenceChunk(), CPdf::AddShadedTris(), CFeatureGenerator::SImplementation::AdjustAlignment(), CwxTableListCtrl::ApplyFiltering(), AreAbuttingOnProduct(), CModelCompare::AreSimilar(), CHitMatrixGraph::AssignColorsByScore(), CFastaReader::AssignMolType(), BDB_LStringCompare(), BOOST_AUTO_TEST_CASE(), CGridCellWrapStringRenderer::BreakLines(), CCompactLayout::BuildLayout(), CSimpleLayout::BuildLayout(), COverlayLayout::BuildLayout(), CachedTaxonomyLookupCommand(), CalcDistanceSquare(), CPhyloTreePS::CalcForces(), CChain::CalculateDropLimits(), IPhyloTreeRender::CalculateExtents(), CalculateFormattingParams(), CScatterGraph::CalculateLimits(), CQueueDataBase::CalculateRuntimePrecision(), CChain::CalculateSupportAndWeightFromMembers(), CSeqVector_CI::CanGetRange(), CChain::CChain(), CGeneralScoreMatrix::CGeneralScoreMatrix(), CGraphTrack::CGraphTrack(), CExonSelectorApplication::ChainExons(), check_match_limit(), CChainer::CChainerImpl::CheckCompatibility(), CFastaReader::CheckDataLine(), CheckSourceFeatCoverage(), CHitGlyph::CHitGlyph(), CAlignCollapser::CleanSelfTranscript(), CChain::ClipLowCoverageUTR(), CAlignCollapser::ClipNotSupportedFlanks(), BlockModel::clipToRange(), CLorentz::ClosingScore(), CAlnVecPrinter::ClustalStyle(), CMergeNode::CMergeNode(), CNumberValidator::CNumberValidator(), NTweakExon::Collapse(), CollapseExonStructure(), CDepthCollection::CollapseOnDepth(), SBamIndexRefIndex::CollectEstimatedCoverage(), CTableImportListCtrl::ColumnWidthsUpdated(), CChainer::CChainerImpl::CombineCompatibleChains(), CombineCorrectionsAndIndels(), CGlRect< TVPUnit >::CombineWith(), NStr::CommonPrefixSize(), NStr::CommonSuffixSize(), CTempString::compare(), CFile::Compare(), CBDB_FieldLString::Compare(), compile_time_bits::Compare(), CAuthListValidator::compare_lastnames(), NStr::CompareCase(), CMultiAlignerTest::CompareDomainHits(), NStr::CompareNocase(), compile_time_bits::CompareNocase(), CDiscrepancyContext::CompareRefs(), CReadBlastApp::complete_overlap(), CTL_Connection::CompleteBlobDescriptor(), CTL_Connection::CompleteBlobDescriptors(), CId2Compressor::Compress(), CLZOCompression::CompressBuffer(), ComputeNormalizedProteinEntropy(), CBoundaryShapeRectBase::ComputeShape(), CBoundaryShapeRectBase::ComputeShapeWithLabels(), CBoundaryShapeTri::ComputeShapeWithLabels(), convert_1_to_4(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertStdsegToPairwiseAln(), CTempString::Copy(), CBDB_BufferManager::CopyFieldsFrom(), CObjectOStreamAsnBinary::CopyStringValue(), CPmidValidator::CPmidValidator(), CPSGS_CDDProcessor::CPSGS_CDDProcessor(), CRanges::CRanges(), CRasterizer< A >::CRasterizer(), CreateAlignRow(), variation_ref::CVariationUtil::CreateFlankLocs(), variation::CVariationUtil::CreateFlankLocs(), CDirEntry::CreateRelativePath(), CMSMatchedPeakSetMap::CreateSeries(), CDeltaHelper::CreateSSR(), CPagerView::CreateSubNodes(), CSemaphore::CSemaphore(), CSeqTextVariationGraph::CSeqTextVariationGraph(), CWGSFeatureIterator::CWGSFeatureIterator(), SH2S_IoStream::DataSourceRead(), CLZOCompression::DecompressBuffer(), CSelListModelImpl< Item >::DeleteItems(), CSampleNetCacheClient::DemoPartialRead(), CDBConnectionFactory::DispatchServerName(), CMostAffinityJob< TImpl >::Done(), CTaxValidationAndCleanup::DoTaxonomyUpdate(), CGlDrawScale::Draw(), CExpandGlyph::Draw(), CJob::Dump(), EditDistance(), EffectiveExonLength(), CMultAlign::EmitSequenceFromRead(), CNamespace::EqualLevels(), SBamIndexRefIndex::EstimateDataSizeByAlnStartPos(), CMacroEngineParallel::Exec(), CRemoteAppLauncher::ExecRemoteApp(), CCassandraFullscanRunner::Execute(), CGnomonAnnotator::ExtendJustThisChain(), CTableImportDataSource::ExtractFixedFields(), CIStreamBuffer::FillBuffer(), FillSetClearIntervals(), FillSets(), FillSetsIntervals(), FillSetsRandom(), FillSetsRandomMethod(), FillSetsRandomOne(), FillSparseIntervals(), CAlignCollapser::FilterAlignments(), CEntrez2Client::FilterIds(), DeBruijn::CDBGraphDigger::FilterNeighbors(), bm::sparse_vector_scanner< SV, S_FACTOR >::find_ge(), find_minlength(), CCompactSAMApplication::FindCompactAligns(), FindCompartments(), COMSSASearch::FindMinMaxSearchSettingId(), COMSSASearch::FindMinMaxSpectrumNumber(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CSeqTextDataSource::FindSequenceFragment(), CSeqTextDataSource::FindSequenceFragmentList(), variation::FindSSRLoc(), FindStartsStops(), CInternalStopFinder::FindStartStopRanges(), DeBruijn::FindValleyAndPeak(), CReadBlastApp::fit_blast(), CSubSource::FixDateFormat(), flat2asn_range_func(), FloatingPointSpinCtrl::FloatingPointSpinCtrl(), CLZOCompressor::Flush(), CLZODecompressor::Flush(), CGenbankFormatter::FormatLocus(), CExonSelectorApplication::FormatPaired(), FormatPaired(), CGenbankFormatter::FormatSequence(), FSetPix2(), fta_check_feat_overlap(), CCassandraFilteredPlan::Generate(), generate_sparse_bvector(), CNCDistributionConf::GenerateBlobKey(), CRegularGridGen::GenerateGrid(), CScore_IndelToSplice::Get(), CScore_SymmetricOverlap::Get(), CScore_StartStopCodon::Get(), SItemTypeAndReason::Get(), CWGSDb_Impl::SAmbiguityInfo::Get2naLengthBlock(), CWGSDb_Impl::SAmbiguityInfo::Get2naLengthExact(), CWGSDb_Impl::SAmbiguityInfo::Get4naLengthBlock(), SBaseStats::get_min_max(), CNCBlobStorage::GetAllowedDBSize(), CAlnVecMultiDataSource::GetAlnFromSeq(), CSparseMultiDataSource::GetAlnFromSeq(), SBamIndexRefIndex::GetAlnOverStarts(), CCSraRefSeqIterator::GetAlnOverStarts(), CCSraRefSeqIterator::GetAlnOverToOpen(), CSparseAlignment::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CSeqDBVol::GetAmbigPartialSeq(), CVDBGraphSeqIterator::GetAnnot(), CQuerySet::GetBestRank(), CSQLITE_Statement::GetBlob(), GetBlobReader(), CPhyloNodeData::GetBoundingRect(), CVDBGraphDataLoader_Impl::GetChunkOnce(), CNCMMReserve::GetChunks(), CPhyloTreeDataSource::GetClosestLen(), CAlignCollapser::GetCollapsedAlgnments(), CTraceGraph::GetColorByValue(), CTraceGlyph::GetColorByValue(), CQualityScoringMethod::GetColorForScore(), CConservationScoringMethod::GetColorForScore(), CSimpleScoringMethod::GetColorForScore(), CColumnScoringMethod::GetColorForScore(), CMatrixScoringMethod::GetColorForScore(), CNonSynonymousScoringMethod::GetColorForScore(), SHitColoringParams::GetColorNorm(), CRgbaGradColorTable::GetColorTexCoord(), CTableImportListCtrl::GetColumnsCombinedCharWidth(), CWGSSeqIterator::SWGSContigGapInfo::GetDataLength(), CPhyloNodeData::GetDefaultNodeSize(), CCharHistogram::GetDelimiterProbablities(), CHitElemGlyph::GetDistPixels(), CDictionaryUtil::GetEditDistance(), CSNPDbSeqIterator::GetEntry(), AMatrix_base::GetExtremalEntries(), CSeqTextDataSource::GetFeatureData(), CRR_Row< TTraits >::GetFieldsMetaInfo(), GetFirstItemOffset(), GetFloatingPointDialog::GetFloatingPointDialog(), CWGSSeqIterator::SWGSContigGapInfo::GetGapLength(), CRgbaGradColorTable::GetIndex(), CPosToIndex::GetIndexForPosition(), CAnnotType_Index::GetIndexRange(), CPager::GetItemInfo(), CPhyloNodeData::GetLabelRect(), CHandleRange::GetLeft(), CGraphTrack::GetLegend(), SBamIndexRefIndex::GetLimitRange(), CHistogramGlyph::GetMin(), CAlignShadow::GetMin(), CSeqDBVolSet::GetMinLength(), GetMRNATranslationProblems(), CExonSelectorApplication::GetNextExon(), CPhyloNodeData::GetNodeOverhang(), CCompareSeq_locs::GetOverlap(), CSeqVector::GetPackedSeqData(), CAlignFormatUtil::GetPercentMatch(), CAlignRange< Position >::GetPositionMin(), CAlignShadow::GetQueryMin(), CPager::GetRange(), CCSraShortReadIterator::GetReadRange(), CApplyRNAITSDlg::GetRNAITSList_AlignCoordFromDlg(), CApplyRNAITSDlg::GetRNAITSList_SeqCoordFromDlg(), CCodingPropensity::GetScore(), CEditScript::GetScore(), CSGSegmentMapJob::GetSegmentMapLevels(), CPhyloTree::GetSelectedBoundary(), CHitMatrixRenderer::GetSelectedHitElemsRect(), CSNPDbFeatIterator::GetSeq_feat(), CAlignFormatUtil::GetSeqAlignCoverageParams(), CSeqVector_CI::GetSeqData(), CAlnVecMultiDataSource::GetSeqFromAln(), CSparseMultiDataSource::GetSeqFromAln(), CSraRun::GetSequenceLength(), GetSequenceProtein(), CCassConnection::GetSizeEstimates(), CSeqDBAtlas::GetSliceSize(), CNCDistributionConf::GetSlotByRnd(), CAdvancedAlignCleanup::GetSplignCompartments(), CSraRun::GetSpotEntry(), CSeq_bond::GetStart(), CAlignShadow::GetSubjMin(), CIncreasingTime::GetTime(), CCassConnection::GetTokenRanges(), CFeatGlyph::GetTooltip(), CSequenceTrack::GetTooltip(), CSeq_feat::GetTypeSortingOrder(), CNetBlastMonitoringJob::GetWaitPeriod(), CTextUtil::GetWordFrequencies(), CBDB_Cache::GetWriteStream(), GlbAlign(), CTableColumnTypeGuesser::GuessColumn(), CSeq_loc_CI_Impl::HasEquivBreak(), CSGSegmentMapJob::HasSegmentMap(), CAttribIntMenuItem::Inc(), CAttribFloatMenuItem::Inc(), CCalcTextPosOStream::Indent(), inflate_table(), SNgHttp2_Session::Init(), CSeqScores::Init(), CAlignCollapser::InitContig(), CHistogramData::InitDataPoints(), CTableDataListCtrl::InitDataSource(), InitSplicedsegFromPairwiseAln(), CNcbiTestApplication::InitTestFramework(), InRange(), CSelListModelImpl< Item >::InsertItems(), IntegerSpinCtrl::IntegerSpinCtrl(), interlocked_dec_min(), interlocked_inc_min(), CAlignRange< Position >::IntersectSecondWith(), CGlRect< TVPUnit >::IntersectWith(), CAlignRange< Position >::IntersectWith(), CCddInputData::CHit::IntersectWith(), CSeqDB_BitSet::IntersectWith(), IntervalsCheck(), CGene::IsAlternative(), CGeneModel::isCompatible(), CBlobRecord::IsDataEqual(), CSubSource::IsISOFormatTime(), CSplignTrim::JoinExons(), CGroupMapWidget::CGroupItem::Layout(), CMapItem::Layout(), LclAlign(), CMatrixScoringMethod::Load(), CJob::LoadFromDump(), CCSRARefSeqInfo::LoadRefSeqMainEntry(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), CInterProcessLock::Lock(), CWorkerNodeIdleThread::Main(), CSeqAnnotFromFasta::MakeAsIsSeqAnnot(), CChainer::CChainerImpl::MakeChains(), MakeCompartment(), CEditScript::MakeEditScript(), CBamIndex::MakeEstimatedCoverageAnnot(), Map(), CMappingRange::Map_Range(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), match(), CReadBlastApp::match_na(), CReferenceItem::Matches(), CNCBlobStorage::MeasureDB(), gfx::TimSort< RandomAccessIterator, LessFunction >::mergeHi(), CInstance::MergeIn(), gfx::TimSort< RandomAccessIterator, LessFunction >::mergeLo(), CFeatureGenerator::SImplementation::MergeSeq_locs(), mu::Parser::Min(), mu::ParserInt::Min(), SAutoMinMaxLimits< T, is_signed >::min(), ncbi::boost_fp_impl::tt_detail::fpt_limits< FPT >::min_value(), CDepthCollection::MinDepthForRange(), DeBruijn::CDBGraph::MinFraction(), UnalignedBlock::MinResidues(), MutationOperationsTest(), NCBI_PARAM_DEF_EX(), NcbiStreamCopyHead(), SSNP_Info::NoMore(), CPSGS_ThreadPool_Controller::OnEvent(), CTableImportListCtrl::OnGetItemText(), CAttribTableDelimitersPanel::OnListctrlColLeftClick(), CAttribTableColumnIdPanel::OnMergeIDColsClick(), CWidgetHandle::OnMove(), CGradientPanel::OnPaint(), SUvNgHttp2_TlsImpl::OnRecv(), CQueryParsePanel::OnSearchctrlTextEnter(), CSeqGraphicPane::OnSearchTip(), CHitMatrixWidget::OnSetEqualScale(), CPhyloTreeWidget::OnSetEqualScale(), CGoQualLessThan::operator()(), CLessThanNoCaseViaUpper::operator()(), CInitPSNodes::operator()(), CCalcSlantedTree::operator()(), FSetPix2::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::cast_from_other::operator()(), CDense_seg::OrderAdjacentGaps(), Overlap(), CReadBlastApp::overlaps(), CReadBlastApp::overlaps_prot_na(), CSeq_id_General_Id_Info::Pack(), CLogLatencies::Parse(), pcre_printint(), pcre_study(), CIStreamBuffer::PeekFindChar(), CSRSearch::Pos2Index(), CGnomonAnnotator::Predict(), CAttribTableDelimitersPanel::PreviewData(), CTabularFormatter_AlignStart::Print(), CTabularFormatter_PercentId::Print(), CTabularFormatter_PercentCoverage::Print(), CTabularFormatter_NearestGap::Print(), bm::chrono_taker< TOut >::print_duration(), CLZOCompressor::Process(), CLZODecompressor::Process(), CTransparentProcessor::Process(), QSbuf_ParseScores(), random_minmax(), RangeRandomFillTest(), CBGZFStream::Read(), CMMapByteSourceReader::Read(), CMemoryByteSourceReader::Read(), CResultZBtSrcX::Read(), AsnMemoryRead::Read(), CBamIndex::Read(), CGlimmerReader::Read(), CSQLITE3_Cache::Read(), SAffinityDictDump::Read(), SGroupDictDump::Read(), SQueueDescriptionDump::Read(), SLinkedSectionDump::Read(), SJobEventsDump::Read(), SJobIODump::Read(), SJobDump::Read(), CCgiEntryReader::Read(), CStringReader::Read(), CBDB_CacheIReader::Read(), CMemoryReader::Read(), CNlmZipReader::Read(), CTransmissionReader::Read(), CDataChunkReader::Read(), SNetStorageObjectRPC::SIState::Read(), read_repeat_counts(), CObjectIStreamAsnBinary::ReadBitString(), SH2S_ReaderWriter::ReadImpl(), CNCMMCentral::ReallocMemory(), CTableImportDataSource::RecomputeHeaders(), CHMM_State::RegionStart(), CReaderAllocatedConnection::Release(), CTrackContainer::RemoveEmptyTracks(), CExonSelectorApplication::Exon::RemoveLeftIndels(), CExonSelectorApplication::Exon::RemoveRightIndels(), SequenceViewerWidget_SequenceArea::RemoveRubberband(), CHistogramGraph::Render(), CRuler::Render(), CLinearSelHandler::Render(), CHitElemGlyph::Render(), CPieGraph::Render(), CPhyloNodeData::Render(), CPhyloNodeData::RenderRotated(), CAsnElementPrimitive::RenderValue(), CAsnOctetStringBlock::RenderValue(), IBoundaryShape::RenderVbo(), CChainer::CChainerImpl::ReplicatePStops(), CGnomonEngine::ResetRange(), CNcbiMatrix< T >::Resize(), CTempString::rfind(), CRgbaColor::RgbToHsv(), CSeqAlignCmp::Run(), CSplign::Run(), CDemoApp::Run(), s_BuiltInSM(), s_CitMatches(), s_CollectBestOverlaps(), s_CompareProtProdToTrans(), s_ConvertValue(), variation_ref::CVariationUtil::s_CountMatches(), variation::CVariationUtil::s_CountMatches(), s_CreateRotatedFont(), s_Distance(), s_DoNWalign(), s_FillFromPage(), s_FillPool(), s_FindBestSubRange(), s_GetAlignmentMismatches(), CAdapterSearchApplication::s_GetCoverage(), s_GetMinMax(), s_GetNumDbsPerChunk(), CHitFilter< THit >::s_GetOverlap(), s_GetPolyA_genomic_priming(), CGlPane::s_GetShift(), s_IsRawResponse(), s_MaskQuerySeq(), s_PopIdPart(), s_Read(), s_ReallocMemory(), s_SeqAlignSetToXMLHsps(), s_SeqDBMaskSequence(), s_SetAirrAlignmentInfo(), s_SetAmbiguitiesBlocks(), CSeqTextPane::ScrollToPosition(), CMergeTree::Search(), CCSraAlignIterator::Select(), CMultAlign::SelectAligns(), CCompactSAMApplication::SelectBestLocations(), CExonSelectorApplication::SelectBestLocations(), CScriptPanel::SelectMacros(), CWGSFeatureIterator::SelectRowRange(), CAutoDefExonListClause::SeqLocIntersect(), SerializationTest(), CIgBlastTabularInfo::SetAirrFormatData(), FloatingPointTextCtrl::SetAllowedRange(), IntegerTextCtrl::SetAllowedRange(), CHistogramGlyph::SetAxisMinFixed(), CHistogramGlyph::SetAxisRange(), CMSPeak::SetComputedCharge(), CChain::SetConfirmedEnds(), CChain::SetConsistentCoverage(), CBlastTabularInfo::SetFields(), CChainer::CChainerImpl::SetFlagsForChains(), CIdHandler::SetId(), CIgBlastTabularInfo::SetIgAnnotation(), CIgBlastTabularInfo::SetIgCDR3FWR4Annotation(), CCSraShortReadIterator::SetLastSpotId(), CGffFeatureRecord::SetLocation(), CStreamDiagHandler_Base::SetLogName(), CAlnMultiModel::SetMasterRow(), CDensityMap< score_type >::SetMin(), CBDB_FieldSimpleInt< Uint2 >::SetMinVal(), CBDB_FieldSimpleFloat< float >::SetMinVal(), CDBUDRandomMapper::SetPreference(), CDB_Binary::SetValue(), CDB_LongBinary::SetValue(), SHitColoringParams::SetValueRange(), CAlnMultiModel::SetVisible(), CwxAlnStatOptionsDlg::SetZoomLevel(), CByteStreamBuf::showmanyc(), SimpleGapFillSets(), CAlignCompare::SAlignment::Slice(), CSelListModelImpl< Item >::SLM_SelectTo(), gfx::TimSort< RandomAccessIterator, LessFunction >::sort(), CAlignFormatUtil::SortHitByMasterStartAscending(), CAlignFormatUtil::SortHspByMasterStartAscending(), CAlignFormatUtil::SortHspBySubjectStartAscending(), SortMixLoc(), SortPrimerHitByMismatchAscending(), SortPrimerHitInGroupByMismatchAscending(), NParamsBuilder::SParallelProcessing< SInteractiveParams >::SParallelProcessing(), SpecificHostCleanupCommand(), CCassandraFullscanPlan::SplitTokenRangesForLimits(), SPSG_Request::StateData(), CFeatureGenerator::SImplementation::StitchSmallHoles(), sx_CalcFeatChunkPages(), CSeqVectorTypes::sx_GetConvertTable(), sx_HasNonZero(), sx_Round(), CHitFilter< THit >::sx_TM(), CTableImportListCtrl::SynchDataSourceColumnWidths(), TaxonomyLookupCommand(), tds_fix_column_size(), fix_pub::TenAuthorsCompare(), fix_pub::TenAuthorsProcess(), TestSparseVector_Stress(), CutShortPartialExons::transform_align(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CProteinAlignText::TranslateDNA(), variation::CVariationUtil::TranslateNAtoAA(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), CFeatureGenerator::SImplementation::TrimLeftExon(), CFeatureGenerator::SImplementation::TrimRightExon(), CLabel::TruncateLabel(), TruncTextLength(), CPhyloTreePS::Update(), CGeneGroup::Update(), CPhyloTreePS::UpdateAndSynch(), CTableImportListCtrl::UpdateColumnWidths(), CAlignRangeCollExtender< TAlnRngColl >::UpdateIndex(), CPrintSetupDlg::UpdateMargins(), CTreeCollisionModel2D::UpdateScaled(), CTreeCollisionModel2D::UpdateVisibility(), CValidError_imp::ValidateOrgRefs(), CValidError_bioseqset::ValidatePopSet(), CValidError_imp::ValidateSpecificHost(), CValidError_imp::ValidateStrain(), CChain::ValidPolyA(), CProjectItemsTree::VerifyExternalDepends(), CCgiStreamWrapperWriter::Write(), CSQLITE_Blob::Write(), CObjectOStreamJson::WriteBase64Bytes(), CObjectOStreamXml::WriteBase64Bytes(), CPhrap_Contig::x_AddAlignRanges(), CSGAnnotJob::x_AddGraphToMap(), CWGSSeqIterator::x_AddQualityChunkInfo(), CFeatureGenerator::SImplementation::x_AddSelectMarkup(), SAccGuide::x_AddSpecial(), CSplicedAligner16::x_Align(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateDomain(), x_Append2To2(), x_AppendAnyTo2(), x_AppendAnyTo4(), x_AppendAnyTo8(), x_AppendRandomTo2(), CPhyloTreePS::x_ApplyNeighborCellForces(), CPhyloTreePS::x_ApplyRepulsiveForces(), CPhyloTreePS::x_ApplyRepulsiveForcesHashed(), CGvfWriteRecord::x_AssignAttributeEndRange(), CGvfWriteRecord::x_AssignAttributeStartRange(), x_BlastEffectiveLengthsOptions_cmp(), CMultiAligner::x_BuildAlignment(), CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CMacroFunction_StringConstraints::x_BuildNoCaseStringConstraint(), CWGSDb_Impl::SAmbiguityInfo::x_Calculate4na(), CScoringJob::x_CalculateAlignmentScores(), CWGSDb_Impl::SAmbiguityInfo::x_CalculateAmbiguityMask(), CMatrixScoringMethod::x_CalculateConsensusRange(), CMapControl::x_CalculateLayout(), CMatrixScoringMethod::x_CalculateNonConsensusRange(), CMapItem::x_CalculateRealTextWidth(), CHitClustering::x_CanCombine(), CSeqVector_CI::x_CheckBackward(), CSeqVector_CI::x_CheckForward(), CNCActiveSyncControl::x_CheckSlotTheirSync(), CScope_Impl::x_ClearCacheOnNewData(), CLinearSelHandler::x_ClipPosByRange(), CAlignMarkHandler::x_ClipPosByRange(), CTextSelHandler::x_ClipPosByRange(), CElementaryMatching::x_CompartPair(), CElementaryMatching::x_CompartVolume(), CQualScoreWriter::x_ComposeHeaderEnding(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), IPhyloTreeRender::x_ComputeEdgeHighlight(), CCompareSeq_locs::x_ComputeOverlapValues(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), CWGSSeqIterator::x_CreateFeaturesChunk(), CSGAnnotJob::x_CreateHistFromGraph(), CMessageSlotPopupWindow::x_CreateMessageSlotPanel(), CSGAlignStatJob::x_CreatePileUpGraphs(), CSeqVector_CI::x_DecSeg(), SNCBlobVerData::x_DeleteVersion(), CCgiEntryReaderContext::x_DelimitedRead(), CShowBlastDefline::x_DisplayDefline(), CDisplaySeqalign::x_DisplayMpvAnchor(), CNCMessageHandler::x_DoCmd_Remove(), CSplitter::x_DoDragSeparator(), CAlnMultiHeaderHandler::x_DoMoveColumn(), CAppHitFilter::x_DoMultiple(), COrfSearchJob::x_DoSearch(), CTranslationGlyph::x_Draw(), CSeqGraphicRenderer::x_Draw(), CFeatGlyph::x_DrawAdditionalInfo(), CVcfGlyph::x_DrawAdditionalInfo(), CAlignGlyph::x_DrawAlignRowSequence(), CFeatGlyph::x_DrawFeatureBar(), CHistogramGlyph::x_DrawGraph(), CHistogramGlyph::x_DrawHeatMap(), CSeqGlyph::x_DrawInnerLabelColumns(), CAlignGlyph::x_DrawInserts(), CFeatGlyph::x_DrawLabelWithYPinned(), CVcfGlyph::x_DrawLabelWithYPinned(), CCdsGlyph::x_DrawProtSeqWithMapping(), CGlTube< Curve >::x_DrawRecursive(), CFeatGlyph::x_DrawRNAProductSequence(), CSelectionHelper::x_DrawSelectionArea(), CTranslationGlyph::x_DrawSequence(), CHistogramGlyph::x_DrawSmoothCurve(), CMapItem::x_DrawText(), CSequenceTextGraph::x_DrawVariations(), SNCBlobVerData::x_ExecuteWriteAll(), CIgBlast::x_ExtendAlign3end(), CIgBlast::x_ExtendAlign5end(), CCgiEntryReader::x_FillBuffer(), CIgBlast::x_FillJDomain(), CTextPanel::x_FillSeqList(), IPhyloTreeRender::x_FindBestSize(), CIndexDeltaSumCache::x_FindDeltaSum2(), CTableImportDataSource::x_FindHeaderRows(), x_FindRSite(), CTraceGraph::x_FindSampleToLeft(), CTraceGlyph::x_FindSampleToLeft(), CTraceGraph::x_FindSampleToRight(), CTraceGlyph::x_FindSampleToRight(), CSequenceAmbigTrimmer::x_FindWhereToTrim(), variation_ref::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_fuzzy_pos(), CContigAssembly::x_GatherIdentStats(), CBaseCountItem::x_GatherInfo(), CFlatGatherer::x_GatherSequence(), CSeqDBVol::x_GetAmbigSeq(), CSeqTable_sparse_index::x_GetBitSetCache(), CNCMessageHandler::x_GetBlobTTL(), CInt4DeltaSumCache::x_GetDeltaSum2(), CInt8DeltaSumCache::x_GetDeltaSum2(), CIndexDeltaSumCache::x_GetDeltaSum2(), CDisplaySeqalign::x_GetDomainInfo(), CVecscreen::x_GetEdgeRanges(), CBoundaryShapeRoundedRect::x_GetEdges(), CAnnotObject_Less::x_GetExtremes(), CDisplaySeqalign::x_GetFeatureInfo(), CWorkerNodeIdleThread::x_GetInterval(), CSeqMap_CI_SegmentInfo::x_GetLevelEnd(), CAsn2FlatApp::x_GetLocation(), CVecscreen::x_GetMatchType(), x_GetMaxMin(), CTL_Connection::x_GetNativeBlobDescriptor(), x_GetNextAttribute(), CMMapByteSourceReader::x_GetNextChunkAt(), CSplignApp::x_GetNextComp(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), CSnpPtisClient_Impl::x_GetPrimarySnpTrack(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CWGSSeqIterator::x_GetQualityAnnot(), CGencollIdMapper::x_GetRole(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps(), x_GetSequence(), CPoolBalancer::x_GetServer(), CDrawTextOStream::x_GetStyles(), CSeqMap_CI_SegmentInfo::x_GetTopOffset(), CBoundaryShapeRoundedRect::x_GetTris(), CSchedulerEngine::x_GetWaitPeriod(), CSplitter::x_GrowCell(), CTempString::x_Init(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CBamRefSeqInfo::x_InitAlignIterator(), CSeqVector_CI::x_InitSeg(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CSeq_loc_Mapper_Base::x_InitSparse(), CSelectionControl::x_InsertItems(), CVectorTrimPanel::x_IsCompleteCut(), COligoSpecificityCheck::x_IsPcrLengthInRange(), CTSE_Split_Info::x_LoadChunks(), CPSGS_SNPProcessor::x_LoadConfig(), CPSGS_WGSProcessor::x_LoadConfig(), CBamRefSeqInfo::x_LoadRangesScan(), CBamRefSeqInfo::x_LoadRangesStat(), CCSRARefSeqInfo::x_LoadRangesStat(), CSGSeqGraphJob::x_LoadSeqTable(), CGraphTrack::x_LoadSettings(), CHistogramGlyph::x_LowesetValueBelowMin(), CVDBGraphSeqIterator::x_MakeGraph(), CVDBGraphSeqIterator::x_MakeTable(), CAlnMultiWidget::x_MakeVisibleHorz(), x_MatchSubHits(), CMinPanelContainer::x_MeasureItem(), CAlnGraphic::x_MergeDifferentSeq(), CAlnGraphic::x_MergeSameSeq(), CAlnMultiHeaderHandler::x_MoveColumnSeparator(), CSelListController< Item >::x_MoveSelectionBy(), CSelectionControl::x_MoveSelectionBy(), CSelListController< Item >::x_MoveSelLineByPage(), CSeqDB_BitSet::x_Normalize(), CWGSSeqIterator::x_NormalizeSeqRange(), COligoSpecificityCheck::x_NW_alignment(), CMouseZoomHandler::x_OnChangeScale(), CMouseZoomHandler::x_OnEndZoomRect(), CGraphTrack::x_OnJobCompleted(), CGraphOverlay::x_OnLayoutChanged(), CGraphTrack::x_OnLayoutChanged(), CGlWidgetBase::x_OnScrollX(), CGlWidgetBase::x_OnScrollY(), CPhyloTreeMaxChildDist::x_OnStep(), CPhyloTreeLabelRange::x_OnStep(), CTableImportDataSource::x_ParseEntry(), CTableImportDataSource::x_ParseQuotedEntry(), CAlignedFeatureGraph::x_PlaceCluster(), CHistogramGlyph::x_PointToWorld(), x_PredictAGSites(), x_PredictSignalSeq(), CAlnMultiCGIApplication::x_PreProcess(), CIgBlastTabularInfo::x_PrintIgGenes(), CMultiAlnPrinter::x_PrintNexus(), CMultiAlnPrinter::x_PrintPhylipInterleaved(), CAnnotObject_Info::x_ProcessAlign(), CCompartApp::x_ProcessPair(), CNCMessageHandler::x_ProlongBlobDeadTime(), SPSG_BlobReader::x_Read(), CPagedFile::x_ReadPage(), CMultiAligner::x_RealignBlocks(), CGlPreviewSetupWidget::x_Render(), CAlnVecRow::x_RenderAveragableScores(), CAlignGlyph::x_RenderAveragableScores(), CRuler::x_RenderBackground(), CTraceGlyph::x_RenderConfGraph(), CTraceGraph::x_RenderConfGraph(), CTraceGlyph::x_RenderCurveSegment(), CTraceGraph::x_RenderCurveSegment(), CAlignedFeatureGraph::x_RenderFeature(), CSequenceTrack::x_RenderGaps(), IImageGrabber::x_RenderGuides(), CTraceGlyph::x_RenderIntensityGraphs(), CTraceGraph::x_RenderIntensityGraphs(), CMinimapHandler::x_RenderMinimap(), IPhyloTreeRender::x_RenderNodeVbo(), CTextSelHandler::x_RenderOpSymbol(), CRuler::x_RenderOriginAndMetric(), CTextSelHandler::x_RenderRange(), CRuler::x_RenderScale(), CAlnVecRow::x_RenderSequence(), CSeqGraphicPane::x_RenderTooltipConnector(), CRNAValidator::x_ReportRNATranslationProblems(), CSplign::x_Run(), CInstancedAligner::x_RunMMGlobal(), CSplign::x_RunOnCompartment(), COligoSpecificityCheck::x_SavePrimerInfo(), CSeqDBImpl::x_ScanTotals(), CElementaryMatching::x_Search(), CMergeTree::x_Search_Iter(), CMergeTree::x_Search_Recur(), CAnnot_Collector::x_SearchRange(), CSequenceSearchJob::x_SearchSequence(), CSeqMap_CI::x_Select(), CSeqGraphicPane::x_SelectByRect(), CHitMatrixGraph::x_SelectByRect(), CSelectionControl::x_SelectTo(), ILayoutPolicy::x_SeparateObjects(), COligoSpecificityCheck::x_SequencesMappedToSameTarget(), CColumnLayout::x_SetObjectPos(), CLayeredLayout::x_SetObjectPos(), CCrossAlnRenderer::x_SetupModelLimits(), CIgBlast::x_SetupNoOverlapDSearch(), CScriptPanel::x_ShiftBottomLabels(), CSplitter::x_SplitPositionsToSizes(), CBDB_Cache::x_Store(), CSplitQueryTestFixture::x_TestCContextTranslator(), CSeqTextPane::x_UnderlineInterval(), CClonePlacementGlyph::x_UpdateBoundingBox(), CFeatGlyph::x_UpdateBoundingBox(), CLinkedFeatsGroup::x_UpdateBoundingBox(), CSegmentGlyph::x_UpdateBoundingBox(), CVcfGlyph::x_UpdateBoundingBox(), CSeqVector_CI::x_UpdateCacheDown(), CSeqVector_CI::x_UpdateCacheUp(), CGraphOverlay::x_UpdateLegend(), CHistogramGlyph::x_UpdateLegend(), CAlignMarkHandler::x_UpdateMarks(), x_UpdateRanges(), CHitMatrixDataSource::x_UpdateScoreMap(), CGlWidgetBase::x_UpdateScrollbars(), CValidError_graph::x_ValidateGraphValues(), CValidError_graph::x_ValidateMinValues(), NStr::x_VerifyIntLimits(), CScoringJob::x_WindowAvgScores(), CNCActiveHandler::x_WriteBlobData(), CQualScoreWriter::x_WriteHeader(), CBlastDbBlob::x_WriteRaw(), CFastaOstream::x_WriteSequence(), CGff3Writer::xAssignFeatureEndpoints(), CCompressionStreambuf::xsgetn(), CCompressionStreambuf::xsputn(), CForeignContaminationScreenReportReader::xTrimExt(), CGtfAnnotAssembler::xUpdateGene(), and CAsyncWriteCache::~CAsyncWriteCache().
◆ minus()
Referenced by CSeq_loc::GetCircularLength(), CAlignCollapser::GetCollapsedAlgnments(), CFeatureGenePanel::GetLocationForGene(), GetSequenceNucleotideBothStrands(), rapidjson::internal::DiyFp::NormalizedBoundaries(), rapidjson::GenericReader< SourceEncoding, TargetEncoding, StackAllocator >::ParseNumber(), s_FindBestPairs(), CIgBlastTabularInfo::SetMinusStrand(), CPaintSequence::UpdateData(), CGuiObjectInfoSeq_feat::x_AddExtraInfo(), and CValidError_align::x_ValidateSeqLength().
◆ natsToBits()
◆ natsToHartleys()
◆ negative()
Definition at line 109 of file njn_function.hpp.
References T.
Referenced by CLabelRna::AddNewMrnaCommand(), double_to_string(), CRenderingContext::DrawGreaterLessSign(), CTranslationGlyph::GetTooltip(), SChunkTranslator::Init(), CTraceData::Init(), CRangeListImpl::Parse(), parse_numeric(), CFastaDeflineReader::ParseRange(), s_SetRangesForMixedAlignments(), smp_from_string(), smp_to_string(), string_to_int(), string_to_int8(), string_to_numeric(), string_to_uint8(), tds_convert_char(), CAlignMarkHandler::x_AlnRangeFromSeqRange(), CWigGraph::x_DecodeSign(), CTranslationGlyph::x_Draw(), CHistogramGlyph::x_DrawLinearRuler(), CHistogramGlyph::x_DrawLogRuler(), CTranslationGlyph::x_DrawSequence(), CArgDescriptions::x_Find(), CFindITSParser::x_ParseLine(), CSFTranslationJob::x_Translate(), CAlignMarkHandler::x_UpdateSelection(), CBedReader::xSetFeatureLocationBlock(), and CBedReader::xSetFeatureLocationRna().
◆ plus()
Referenced by CSimpleMakeFileContents::CollectValues(), CDense_seg::FillUnaligned(), CAlnMixSegments::FillUnalignedRegions(), CAlnMap::GetAlnPosFromSeqPos(), CAlignCollapser::GetCollapsedAlgnments(), CAlnVec::GetColumnVector(), CAlnMap::GetRawSeg(), GetSequenceNucleotideBothStrands(), CAlnVec::GetWholeAlnSeqString(), rapidjson::internal::DiyFp::NormalizedBoundaries(), s_FindBestPairs(), CPaintSequence::UpdateData(), CDense_seg::Validate(), and CAlnMap::x_SetRawSegTypes().
◆ positive()
Definition at line 108 of file njn_function.hpp.
References T.
Referenced by CSeqDBIdSet::Compute(), CSparseAlignment::GetAlnSeqString(), CSparseAlignment::GetSeqString(), s_DisplayIdentityInfo(), CDisplaySeqalign::x_FillIdentityInfo(), CAlignMarkHandler::x_InitDeltaMap(), and CFeatureGraph::x_StartJob().
◆ prob()
Definition at line 123 of file njn_function.hpp.
Referenced by Blast_ReadAaComposition(), descendingLadderEpochRepeat(), CAlignFormatUtil::PrintPhiInfo(), s_BlastEvenGapLinkHSPs(), s_Trim(), and DynProgProbLim::update().
◆ probability()
Definition at line 122 of file njn_function.hpp.
◆ psqrt()
Definition at line 113 of file njn_function.hpp.
Referenced by LocalMaxStatMatrix::getR().
◆ signum()
Definition at line 110 of file njn_function.hpp.
Referenced by newtonRaphson(), SGridWorkerNodeImpl::Run(), CNetStorageServer::SetShutdownFlag(), CNetScheduleServer::SetShutdownFlag(), CUvSignal::Start(), and Threaded_Server_SignalHandler().
◆ square()
Definition at line 114 of file njn_function.hpp.
Referenced by gf2_matrix_square().
