#include <corelib/ncbitype.h>#include <assert.h>#include "njn_approx.hpp"#include "njn_doubletype.hpp"#include "njn_ioutil.hpp"#include "njn_vector.hpp"
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Classes | |
| class | Matrix< T > |
Enumerations | |
| enum | Format { HUMAN , MACHINE , FORMAT , GENERAL , SYMMETRIC , FORMAT } |
Functions | |
| Format | getFormat () |
| void | setFormat (Format format_) |
| Format | clearFormat () |
| template<typename T > | |
| bool | operator== (const Njn::Matrix< T > &matrix_, const Njn::Matrix< T > &matrix0_) |
| template<typename S , typename T > | |
| void | copy (Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_) |
| template<typename T > | |
| std::ostream & | operator<< (std::ostream &ostr_, const Njn::Matrix< T > &matrix_) |
| template<typename T > | |
| std::istream & | operator>> (std::istream &istr_, Njn::Matrix< T > &matrix_) |
| std::ostream & | operator<< (std::ostream &ostr_, Njn::MatrixIO::Format format_) |
| std::istream & | operator>> (std::istream &istr_, Njn::MatrixIO::Format format_) |
Enumeration Type Documentation
◆ Format
| enum Format |
| Enumerator | |
|---|---|
| HUMAN | |
| MACHINE | |
| FORMAT | |
| GENERAL | |
| SYMMETRIC | |
| FORMAT | |
Definition at line 115 of file njn_matrix.hpp.
Function Documentation
◆ clearFormat()
| Format clearFormat | ( | ) |
Referenced by Matrix< T >::in(), and Matrix< T >::out().
◆ copy()
| void copy | ( | Njn::Matrix< S > * | matrix_, |
| const Njn::Matrix< T > & | matrix0_ | ||
| ) |
Definition at line 613 of file njn_matrix.hpp.
Referenced by CSeq_loc_equiv::Add(), CBadResiduesException::SBadResiduePositions::AddBadIndexMap(), CPacked_seqint::AddIntervals(), CMsvcPrjProjectContext::AdditionalLinkerOptions(), CPacked_seqpnt::AddPoints(), CCleanup::AddProtein(), CAutofixReport::AddSubitems(), CAlignmentAssistant::AdjustBioseq(), CSymResolver::Append(), CSubmissionWizard::ApplySubmitCommand(), CSplignFormatter::AsSeqAlignSet(), AutofixCommand(), AutofixCommandHugeMode(), BitString(), Blast_HSPClone(), BlastBuildSearchResultSet(), BlastMemDup(), UpdateViewer::BlastNeighbor(), BlastSequenceBlkCopy(), UpdateViewer::BlastUpdate(), BOOST_AUTO_TEST_CASE(), CAutoDefAvailableModifier::CAutoDefAvailableModifier(), CBlastRPSAuxInfo::CBlastRPSAuxInfo(), CCharInSet::CCharInSet(), CCompartmentFinder< THit >::CCompartmentFinder(), CFlatSeqLoc::CFlatSeqLoc(), CWriteUtil::ChangeToPackedInt(), CSeq_loc::ChangeToPackedInt(), CLatLonCountryMap::CLatLonCountryMap(), CAlignCleanup::Cleanup(), CleanupCommand(), CleanupHugeFileCommand(), CleanVisString(), UngappedAlignedBlock::Clone(), UnalignedBlock::Clone(), SequenceDisplay::Clone(), NDirectNetStorageImpl::CObj::Clone(), BlockMultipleAlignment::Clone(), CMacroEditorContext::CMacroEditorContext(), CMsvcPrjProjectContext::CMsvcPrjProjectContext(), CollectDllsDepends(), CollectUserField(), CSimpleMakeFileContents::CollectValues(), TQueryMessages::Combine(), NVcfUtil::ConvertFromPreviousVCFModel(), DynProgProb::copy(), DynProgProbLim::copy(), LocalMaxStat::copy(), LocalMaxStatMatrix::copy(), CSyncQueue< Type, Container, Traits >::CopyTo(), CPacked_seqpnt::CPacked_seqpnt(), CSubjectsSequenceCoverage::Create(), CreateDllBuildTree(), CreateDllsList(), CMsvcPrjProjectContext::CreateLibsList(), CGraphTrack::CreateOverlay(), CSequenceEditingEventHandler::CreateSeqSubmit(), CTableDataAlnSummary::CTableDataAlnSummary(), CMSPeak::CullAll(), CMSPeak::CullChargeAndWhich(), CCleanup::DecodeXMLMarkChanged(), CMsvcPrjProjectContext::Defines(), deflate(), DensegConvert(), SAsnProjectMultipleT::DoCreate(), SAppProjectT::DoCreate(), SLibProjectT::DoCreate(), SMsvcProjectT::DoCreate(), SMakeProjectT::DoResolveDefs(), CRegistryReadView::DumpAll(), DynProgProb::DynProgProb(), AnnotateDialog::EditAnnotation(), splign_local::ElemToBuffer(), CCmdAddSeqEntry::Execute(), CSubmissionWizard::ExportTemplate(), CSymDustMasker::triplets::find_perfect(), CTextFsm< MatchType >::FindFail(), CSequenceEditingEventHandler::FixNonReciprocalLinks(), CFlatGeneSynonymsQVal::Format(), CGeneFinder::GeneMatchesXref(), CProjBulderApp::GenerateUnixProjects(), CNewCleanup_imp::GenerefBC(), xslt::xpath_object::get_as_bool(), xslt::xpath_object::get_as_float(), xslt::xpath_object::get_as_int(), xslt::xpath_object::get_as_string(), CFlatFileConfig::GetAllGenbankStrings(), CGnomonEngine::GetAnnot(), CPkgManager::GetBasePkgs(), CGeneModel::GetCdsDnaSequence(), CEditSequenceEnds::GetCommand(), CEditSeqEndsWithAlign::GetCommand(), CAppExplorerDataObject::GetDataHere(), CPhyloTree::GetExplicitlySelected(), CValidator::CCacheImpl::GetFeatFromCacheMulti(), CScorematPssmConverter::GetGaplessColumnWeights(), CGlyphContainer::GetHTMLActiveAreas(), CSelectionEvent::GetIndexed(), CScorematPssmConverter::GetInformationContent(), CProjectItemsTree::GetInternalDepends(), CScorematPssmConverter::GetIntervalSizes(), CMsvcSite::GetLibChoiceIncludes(), CMsvcSite::GetLibInclude(), CCassConnection::GetLocalPeersAddressList(), CUIToolRegistry::GetMRUToolNames(), CMacroEditorContext::GetncRNAClassTypes(), CScorematPssmConverter::GetNumMatchingSeqs(), CProjectService::GetObjProjects(), GetProtRefAnnot(), CPssm::GetQuerySequenceData(), CPhyloTree::GetSelected(), CBlastSequenceSource::GetSeq(), CEditSequence::GetSequence(), CScorematPssmConverter::GetSigma(), CRegistryReadView::GetStringList(), CGuiRegistry::GetStringList(), CSettingsSet::GetStringVec(), CNWAligner::GetTranscript(), CGeneralCommentField::GetVals(), gz_write(), gzwrite(), HEAP_Copy(), Vector< T >::in(), inflate(), inflateBack(), inflateCopy(), CTableDataFTable::Init(), CElementaryMatching::CBoolVector::Init(), CInputStreamSource::InitManifest(), CMsvcPrjProjectContext::IsConfigEnabled(), rapidjson::BaseReaderHandler< typename SchemaDocumentType::SchemaType::EncodingType >::Key(), rapidjson::internal::Hasher< Encoding, Allocator >::Key(), rapidjson::GenericSchemaValidator< SchemaDocumentType, OutputHandler, StateAllocator >::Key(), rapidjson::GenericDocument< Encoding, Allocator, StackAllocator >::Key(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::Key(), rapidjson::Writer< OutputStream, UTF8<>, UTF8<>, CrtAllocator, kWriteDefaultFlags >::Key(), CAsnObjectLoader::LoadFromStream(), CPkgManager::LoadPackages(), LocalMaxStat::LocalMaxStat(), LocalMaxStatMatrix::LocalMaxStatMatrix(), main(), MakeLeftHeader(), CNWFormatter::MakeSegments(), Matrix< T >::matrix(), Matrix< T >::Matrix(), mdb_page_split(), CTrackConfigManager::MergeTrackConfig(), Nlm_MemDup(), CAppPackagesDlg::OnOkClick(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::cast_from_other::operator()(), tree< T, tree_node_allocator >::pre_order_iterator::operator++(), tree< T, tree_node_allocator >::post_order_iterator::operator++(), tree< T, tree_node_allocator >::fixed_depth_iterator::operator++(), tree< T, tree_node_allocator >::sibling_iterator::operator++(), CConstResizingIterator< TSeq, TOut >::operator++(), CResizingIterator< TSeq, TVal >::operator++(), tree< T, tree_node_allocator >::pre_order_iterator::operator--(), tree< T, tree_node_allocator >::post_order_iterator::operator--(), tree< T, tree_node_allocator >::fixed_depth_iterator::operator--(), tree< T, tree_node_allocator >::sibling_iterator::operator--(), CNcbiArguments::operator=(), DynProgProb::operator=(), DynProgProbLim::operator=(), LocalMaxStat::operator=(), LocalMaxStatMatrix::operator=(), Matrix< T >::operator=(), Vector< T >::operator=(), CNewCleanup_imp::OrgrefBC(), PSSMWrapper::OutputPSSM(), rapidjson::GenericReader< SourceEncoding, TargetEncoding, StackAllocator >::ParseNumber(), rapidjson::GenericReader< SourceEncoding, TargetEncoding, StackAllocator >::ParseString(), PLibExclude::PLibExclude(), CPrefetchSeqDescr::PrefetchSeqDescr(), CEnumDataType::PrintJSONSchema(), CBiosampleChkApp::ProcessBioseqForUpdate(), PSourcesExclude::PSourcesExclude(), QSbuf_To_Single_Qscore_SeqGraph(), CBLASTToolManager::QuickLaunch(), CSplignTool::QuickLaunch(), rapidjson::BaseReaderHandler< typename SchemaDocumentType::SchemaType::EncodingType >::RawNumber(), rapidjson::GenericDocument< Encoding, Allocator, StackAllocator >::RawNumber(), rapidjson::GenericSchemaValidator< SchemaDocumentType, OutputHandler, StateAllocator >::RawNumber(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::RawNumber(), rapidjson::Writer< OutputStream, UTF8<>, UTF8<>, CrtAllocator, kWriteDefaultFlags >::RawNumber(), RemapAlignToLoc(), RemoveOverlaps(), CProjectTask::RemoveProjects(), CSymResolver::Resolve(), CProjSRCResolver::ResolveTo(), revcmp(), CAgpFastaComparator::Run(), CAlnBuildApp::Run(), s_AddPartToSegmentedBioseq(), s_AddProjItemToDll(), s_AddSitesToAnnot(), s_AnalyzeLibraryOrder(), s_BlastGapAlignStruct_Copy(), s_BlastGapAlignStruct_Free(), s_BlastScoreBlk_Copy(), s_BlastScoreBlk_Free(), s_BuildGetSeqPartsRequest(), s_CArgs_ReadFromFile(), s_CheckGiToGeneConsistency(), s_CleanVisString(), CSplign::s_ComputeStats(), s_CopyProtXrefToProtFeat(), s_CopyVector(), variation::CVariationUtil::s_FindLocationProperties(), CPubEquivCleaner::s_Flatten(), s_FormatRegularSequencePiece(), s_GetAuthorsString(), s_GetMaskLoc(), s_GetQuerySequenceData(), s_HTMLizeExperimentQual(), s_InitVDBVersion(), s_MoveNonDuplicatedItems(), s_Ncbi2naExpandRevCmp(), s_PcrPrimerSetCompare(), s_ReadConfig(), s_Render_Feat_Evidence(), CHitFilter< THit >::s_RunGreedy(), s_SetupWithMultipleQueriesAndSubjects(), SAlignIndividual::SAlignIndividual(), ScanSequence(), CNewCleanup_imp::SeqfeatBC(), xml::document::set_external_subset(), CAlignShadow::SetBox(), CVariation_ref::SetCNV(), CContainerTypeInfo::SetConstIteratorFunctions(), CClusterer::SetDistMatrix(), CBlastOptionsLocal::SetEffectiveSearchSpace(), CSearchResultSet::SetFilteredQueryRegions(), CRemoteBlast::SetGIList(), CCachedSeqDataForRemote::SetIdList(), CMultiAligner::SetInputMSAs(), CPrimitiveTypeInfo::SetIOFunctions(), CContainerTypeInfo::SetIteratorFunctions(), CSearchResults::SetMaskedQueryRegions(), CVariation_ref::SetMicrosatellite(), CRemoteBlast::SetNegativeGIList(), CMultiAligner::SetQueries(), CSearchResults::SetSubjectMasks(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), rapidjson::SkipWhitespace(), SNetScheduleExecutorImpl::SNetScheduleExecutorImpl(), rapidjson::GenericDocument< Encoding, Allocator, StackAllocator >::String(), rapidjson::GenericSchemaValidator< SchemaDocumentType, OutputHandler, StateAllocator >::String(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::String(), rapidjson::Writer< OutputStream, UTF8<>, UTF8<>, CrtAllocator, kWriteDefaultFlags >::String(), CSeqConvert_imp::Subseq(), test(), test0(), TestSignedSparseVector(), TestSparseVector(), CSplign::SAlignedCompartment::ToBuffer(), variation::CVariationUtil::TranslateNAtoAA(), updatewindow(), CSeqDB::ValidateMaskAlgorithms(), Vector< T >::Vector(), VectorRemoveElements(), CFileManifest::WriteManyFilePaths(), CTablePrinter::x_AddCellValue(), CExportStrategy::x_AddParameterToProgramOptions(), CApplyBsrcQualTreeItemData::x_AddParamPanel(), CApplyFeatQualTreeItemData::x_AddParamPanel(), CConvertBsrcTreeItemData::x_AddParamPanel(), CCopyBsrcTreeItemData::x_AddParamPanel(), CEditFeatQualTreeItemData::x_AddParamPanel(), CParseBsrcTreeItemData::x_AddParamPanel(), CParseToBsrcTreeItemData::x_AddParamPanel(), CParseBsrcToStructCommTreeItemData::x_AddParamPanel(), CRmvOutsideQualTreeItemData::x_AddParamPanel(), CRmvOutsideBsrcTreeItemData::x_AddParamPanel(), CRmvOutsideStrCommQualTreeItemData::x_AddParamPanel(), CRmvOutsideRNAQualTreeItemData::x_AddParamPanel(), CRmvOutsideProteinQualTreeItemData::x_AddParamPanel(), CRmvOutsideFeatQualTreeItemData::x_AddParamPanel(), CSwapBsrcTreeItemData::x_AddParamPanel(), CFeatureItem::x_AddQualsRegion(), CSeqDictionaryBuilder< Alphabet >::x_AddSequence(), CNWAligner::x_Align(), CTraversalMerger::CNodeLabeler::x_AppendDirectNodeLabel(), CSequenceUpdater::x_ChangeIDInFeature(), CMakeProfileDBApp::x_CheckDelta(), CCmdCleanup::x_CreateActionCmd(), CCmdPlaceProteinFeats::x_CreateActionCmd(), CVcfLoadingJob::x_CreateColumnarVCFProjectItem(), CProSplignTool::x_CreateLoadingJob(), CSplignTool::x_CreateLoadingJob(), CCleanupAlignmentsJob::x_CreateProjectItems(), CAppHitFilter::x_DoMultiple(), CAppHitFilter::x_DoPairwise(), CGenomeProjectItem::x_GatherInfo(), CInstancedAligner::x_GetDistanceInstances(), CValidError_align::x_GetIds(), CSplignApp::x_GetNextComp(), CSplignApp::x_GetNextPair(), CVDBBlastUtil::x_GetSRARunAccessions(), CRemoteBlast::x_Init(), CBlastPrelimSearch::x_Init(), CElementaryMatching::x_InitFilteringVector(), CMacroInterpreter::x_InterpretWhereFunctions(), x_json_value_init_string(), CSGAlignmentJob::x_LoadAlignmentFeats(), CSplign::x_LoadSequence(), CLDS2_DataLoader::x_LoadTSE(), CNewCleanup_imp::x_ModernizePCRPrimers(), CFeatureGraph::x_OnJobCompleted(), CPhyTreeView::x_OnSetSelection(), CAssignQueryTreeGetArgs::x_ProcessFunction(), CMakeBlastDBApp::x_ProcessInputData(), CNewCleanup_imp::x_ProtGBQualBC(), CAppNWA::x_ReadFastaFile(), IPhyloTreeRender::x_RenderCircularVbo(), IPhyloTreeRender::x_RenderSplineVbo(), CSplign::x_Run(), CNWAligner::x_Run(), CSplignApp::x_RunSplign(), CQuickLaunchList::x_Save(), CProSplignTool::x_SelectCompatibleInputObjects(), CSplignTool::x_SelectCompatibleInputObjects(), CLayeredLayout::x_SetObjectPos(), CInversionMergeAligner::x_SortAlignSet(), CMergeAligner::x_SortAlignSet(), CUnorderedSplitter::x_SortAlignSet(), CFeatureTableReader_Imp::x_TokenizeLenient(), CFeatureTableReader_Imp::x_TokenizeStrict(), CTraversalSpecFileParser::CTokenizer::x_TryToGetTokensIfNone(), CMakeProfileDBApp::x_UpdateDelta(), CValidError_bioseq::x_ValidateMultiplePubs(), and CVcfWriter::x_WriteInit().
◆ getFormat()
| Format getFormat | ( | ) |
Referenced by Matrix< T >::in(), and Matrix< T >::out().
◆ operator<<() [1/2]
| std::ostream & operator<< | ( | std::ostream & | ostr_, |
| const Njn::Matrix< T > & | matrix_ | ||
| ) |
Definition at line 640 of file njn_matrix.hpp.
◆ operator<<() [2/2]
|
inline |
Definition at line 647 of file njn_matrix.hpp.
References setFormat().
◆ operator==()
| bool operator== | ( | const Njn::Matrix< T > & | matrix_, |
| const Njn::Matrix< T > & | matrix0_ | ||
| ) |
Definition at line 626 of file njn_matrix.hpp.
References i.
◆ operator>>() [1/2]
| std::istream & operator>> | ( | std::istream & | istr_, |
| Njn::Matrix< T > & | matrix_ | ||
| ) |
Definition at line 644 of file njn_matrix.hpp.
◆ operator>>() [2/2]
|
inline |
Definition at line 653 of file njn_matrix.hpp.
References setFormat().
◆ setFormat()
| void setFormat | ( | Format | format_ | ) |
Referenced by operator<<(), and operator>>().
