NCBI C++ ToolKit
Classes | Enumerations | Functions
njn_matrix.hpp File Reference
#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

enum Format
Enumerator
HUMAN 
MACHINE 
FORMAT 
GENERAL 
SYMMETRIC 
FORMAT 

Definition at line 115 of file njn_matrix.hpp.

Function Documentation

Format clearFormat ( )
template<typename S , typename T >
void copy ( Njn::Matrix< S > *  matrix_,
const Njn::Matrix< T > &  matrix0_ 
)

Definition at line 612 of file njn_matrix.hpp.

References i.

Referenced by CSeq_loc_equiv::Add(), CBadResiduesException::SBadResiduePositions::AddBadIndexMap(), CPacked_seqint::AddIntervals(), CMsvcPrjProjectContext::AdditionalLinkerOptions(), CPacked_seqpnt::AddPoints(), AddProtein(), CAlignmentAssistant::AdjustBioseq(), CSymResolver::Append(), CSplignFormatter::AsSeqAlignSet(), AutofixCommand(), BitString(), Blast_HSPClone(), BlastBuildSearchResultSet(), BlastMemDup(), UpdateViewer::BlastNeighbor(), UpdateViewer::BlastUpdate(), BOOST_AUTO_TEST_CASE(), BUF_PeekAtCB(), CAlignCollapser::CAlignCollapser(), CBlastRPSAuxInfo::CBlastRPSAuxInfo(), CCharInSet::CCharInSet(), CCompartmentFinder< THit >::CCompartmentFinder(), CFlatSeqLoc::CFlatSeqLoc(), CReferenceItem::ChangeMedlineAuthorsToISO(), CWriteUtil::ChangeToPackedInt(), CSeq_loc::ChangeToPackedInt(), wgsparse::CheckKeywords(), CLatLonCountryMap::CLatLonCountryMap(), CAlignCleanup::Cleanup(), CleanupCommand(), CleanVisString(), BlockMultipleAlignment::Clone(), SequenceDisplay::Clone(), UngappedAlignedBlock::Clone(), UnalignedBlock::Clone(), CMsvcPrjProjectContext::CMsvcPrjProjectContext(), CollectDllsDepends(), CollectUserField(), CSimpleMakeFileContents::CollectValues(), TQueryMessages::Combine(), LocalMaxStatMatrix::copy(), DynProgProbLim::copy(), LocalMaxStat::copy(), DynProgProb::copy(), CSyncQueue< Type, Container, Traits >::CopyTo(), CPacked_seqpnt::CPacked_seqpnt(), CSubjectsSequenceCoverage::Create(), CreateDllBuildTree(), CreateDllsList(), CMsvcPrjProjectContext::CreateLibsList(), CGraphTrack::CreateOverlay(), CTableDataAlnSummary::CTableDataAlnSummary(), CMSPeak::CullAll(), CMSPeak::CullChargeAndWhich(), CCleanup::DecodeXMLMarkChanged(), CMsvcPrjProjectContext::Defines(), DensegConvert(), SAppProjectT::DoCreate(), SLibProjectT::DoCreate(), SAsnProjectMultipleT::DoCreate(), SMsvcProjectT::DoCreate(), SMakeProjectT::DoResolveDefs(), CGuiRegistry::CReadView::DumpAll(), DynProgProb::DynProgProb(), AnnotateDialog::EditAnnotation(), splign_local::ElemToBuffer(), CCmdAddSeqEntry::Execute(), CSymDustMasker::triplets::find_perfect(), CTextFsm< MatchType >::FindFail(), 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(), CEditSeqEndsWithAlign::GetCommand(), CEditSequenceEnds::GetCommand(), CAppExplorerDataObject::GetDataHere(), CPhyloTree::GetExplicitlySelected(), CValidator::CCacheImpl::GetFeatFromCacheMulti(), CScorematPssmConverter::GetGaplessColumnWeights(), CGlyphContainer::GetHTMLActiveAreas(), CSelectionEvent::GetIndexed(), CScorematPssmConverter::GetInformationContent(), CProjectItemsTree::GetInternalDepends(), CScorematPssmConverter::GetIntervalSizes(), CMsvcSite::GetLibChoiceIncludes(), CMsvcSite::GetLibInclude(), CUIToolRegistry::GetMRUToolNames(), CScorematPssmConverter::GetNumMatchingSeqs(), CProjectService::GetObjProjects(), CGuiRegistry::CReadView::GetOctetString(), CGuiRegistry::GetOctetString(), CGuiRegistry::CReadView::GetOctetStringVec(), CGuiRegistry::GetOctetStringVec(), CPssm::GetQuerySequenceData(), CPhyloTree::GetSelected(), ISequenceSource::GetSeq(), CEditSequence::GetSequence(), CScorematPssmConverter::GetSigma(), CGuiRegistry::GetStringList(), CSettingsSet::GetStringVec(), CNWAligner::GetTranscript(), CGeneralCommentField::GetVals(), gzwrite(), HEAP_Copy(), Vector< T >::in(), inflate(), inflateBack(), inflateCopy(), CTableDataFTable::Init(), CElementaryMatching::CBoolVector::Init(), CInputStreamSource::InitManifest(), CMsvcPrjProjectContext::IsConfigEnabled(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator >::Key(), rapidjson::Writer< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::Key(), CAsnObjectLoader::LoadFromStream(), CPkgManager::LoadPackages(), LocalMaxStat::LocalMaxStat(), LocalMaxStatMatrix::LocalMaxStatMatrix(), main(), CChainer::CChainerImpl::MakeChains(), MakeLeftHeader(), CNWFormatter::MakeSegments(), Matrix< T >::matrix(), Matrix< T >::Matrix(), mdb_page_split(), CTrackConfigManager::MergeTrackConfig(), Nlm_MemDup(), CAppPackagesDlg::OnOkClick(), DeBruijn::IntegerTemplate< T1, T2, T3, T4, T5 >::cast_from_other::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++(), 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--(), Vector< T >::operator=(), Matrix< T >::operator=(), LocalMaxStatMatrix::operator=(), DynProgProbLim::operator=(), LocalMaxStat::operator=(), DynProgProb::operator=(), CNcbiArguments::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(), CSplignTool::QuickLaunch(), CBLASTToolManager::QuickLaunch(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator >::RawNumber(), rapidjson::Writer< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::RawNumber(), RemapAlignToLoc(), RemoveOverlaps(), CProjectTask::RemoveProjects(), NStr::Replace(), NStr::ReplaceInPlace(), CSymResolver::Resolve(), CProjSRCResolver::ResolveTo(), revcmp(), CDiscRepApp::Run(), CAgpFastaComparator::Run(), CAlnBuildApp::Run(), s_AddPartToSegmentedBioseq(), s_AddProjItemToDll(), s_AddSitesToAnnot(), s_AnalyzeLibraryOrder(), s_BlastGapAlignStruct_Copy(), s_BlastScoreBlk_Copy(), s_BuildGetSeqPartsRequest(), s_CArgs_ReadFromFile(), s_CheckGiToGeneConsistency(), CSplign::s_ComputeStats(), s_CopyProtXrefToProtFeat(), s_CopyVector(), variation::CVariationUtil::s_FindLocationProperties(), s_FormatRegularSequencePiece(), s_GetAuthorsString(), s_GetMaskLoc(), s_GetQuerySequenceData(), s_HTMLizeExperimentQual(), s_MoveNonDuplicatedItems(), s_Ncbi2naExpandRevCmp(), s_PcrPrimerSetCompare(), s_Render_Feat_Evidence(), CHitFilter< THit >::s_RunGreedy(), s_SetupWithMultipleQueriesAndSubjects(), SAlignIndividual::SAlignIndividual(), 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(), CContainerTypeInfo::SetIteratorFunctions(), CSearchResults::SetMaskedQueryRegions(), CVariation_ref::SetMicrosatellite(), CRemoteBlast::SetNegativeGIList(), CMultiAligner::SetQueries(), CSearchResults::SetSubjectMasks(), rapidjson::SkipWhitespace(), SNetScheduleExecutorImpl::SNetScheduleExecutorImpl(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator >::String(), rapidjson::Writer< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::String(), CSeqConvert_imp::Subseq(), TestSparseVector(), CSplign::SAlignedCompartment::ToBuffer(), variation::CVariationUtil::TranslateNAtoAA(), updatewindow(), CSeqDB::ValidateMaskAlgorithms(), Vector< T >::Vector(), VectorRemoveElements(), CFileManifest::WriteManyFilePaths(), CTablePrinter::x_AddCellValue(), CExportStrategy::x_AddParameterToProgramOptions(), CFeatureItem::x_AddQualsRegion(), CNWAligner::x_Align(), CTraversalMerger::CNodeLabeler::x_AppendDirectNodeLabel(), CFastaReader::x_ApplyAllMods(), CSequenceUpdater::x_ChangeIDInFeature(), CAsn2FlatApp::x_CreateCancelBenchmarkCallback(), CProSplignTool::x_CreateLoadingJob(), CSplignTool::x_CreateLoadingJob(), CCleanupAlignmentsJob::x_CreateProjectItems(), CAppHitFilter::x_DoMultiple(), CAppHitFilter::x_DoPairwise(), CNewCleanup_imp::x_FlattenPubEquiv(), CGenomeProjectItem::x_GatherInfo(), CReferenceItem::x_GatherInfo(), CInstancedAligner::x_GetDistanceInstances(), CValidError_align::x_GetIds(), CSplignApp::x_GetNextComp(), CSplignApp::x_GetNextPair(), CBlastPrelimSearch::x_Init(), CRemoteBlast::x_Init(), CElementaryMatching::x_InitFilteringVector(), 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(), CImportFeatTable::x_PlaceProteinSpecificFeats(), CMakeBlastDBApp::x_ProcessInputData(), CNewCleanup_imp::x_ProtGBQualBC(), CAppNWA::x_ReadFastaFile(), CNWAligner::x_Run(), CSplign::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(), CFeature_table_reader_imp::x_TokenizeLenient(), CFeature_table_reader_imp::x_TokenizeStrict(), CTraversalSpecFileParser::CTokenizer::x_TryToGetTokensIfNone(), CMakeProfileDBApp::x_UpdateDelta(), CValidError_bioseq::x_ValidateMultiplePubs(), and CVcfWriter::x_WriteInit().

Format getFormat ( )
template<typename T >
std::ostream & operator<< ( std::ostream &  ostr_,
const Njn::Matrix< T > &  matrix_ 
)

Definition at line 639 of file njn_matrix.hpp.

std::ostream & operator<< ( std::ostream &  ostr_,
Njn::MatrixIO::Format  format_ 
)
inline

Definition at line 646 of file njn_matrix.hpp.

References setFormat().

template<typename T >
bool operator== ( const Njn::Matrix< T > &  matrix_,
const Njn::Matrix< T > &  matrix0_ 
)

Definition at line 625 of file njn_matrix.hpp.

References i.

template<typename T >
std::istream & operator>> ( std::istream &  istr_,
Njn::Matrix< T > &  matrix_ 
)

Definition at line 643 of file njn_matrix.hpp.

std::istream & operator>> ( std::istream &  istr_,
Njn::MatrixIO::Format  format_ 
)
inline

Definition at line 652 of file njn_matrix.hpp.

References setFormat().

void setFormat ( Format  format_)

Referenced by operator<<(), and operator>>().

Modified on Sat Sep 23 14:27:13 2017 by modify_doxy.py rev. 546573