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NCBI C++ ToolKit: CAlnMap Class Reference

#include <objtools/alnmgr/alnmap.hpp>

Definition at line 44 of file alnmap.hpp.

◆ TDim ◆ TGetChunkFlags ◆ TNumchunk ◆ TNumrow ◆ TNumseg ◆ TParent ◆ TRange ◆ TRawSegTypes ◆ TSegTypeFlags ◆ TSeqPosList ◆ TSignedRange ◆ EGetChunkFlags Enumerator fAllChunks fIgnoreUnaligned fInsertSameAsSeq fDeletionSameAsGap fIgnoreAnchor fIgnoreGaps fChunkSameAsSeg fSkipUnalignedGaps fSkipDeletions fSkipAllGaps fSkipInserts fSkipAlnSeq fSeqOnly fInsertsOnly fAlnSegsOnly fDoNotTruncateSegs fAddUnalignedChunks

Definition at line 76 of file alnmap.hpp.

◆ ESegmentTrimFlag Enumerator eSegment_Include eSegment_Trim eSegment_Remove

Definition at line 120 of file alnmap.hpp.

◆ ESegTypeFlags Enumerator fSeq fNotAlignedToSeqOnAnchor fInsert fUnalignedOnRight fUnalignedOnLeft fNoSeqOnRight fNoSeqOnLeft fEndOnRight fEndOnLeft fUnaligned fUnalignedOnRightOnAnchor fUnalignedOnLeftOnAnchor fTypeIsSet

Definition at line 51 of file alnmap.hpp.

◆ CAlnMap() [1/3] ◆ CAlnMap() [2/3] ◆ ~CAlnMap() CAlnMap::~CAlnMap ( void ) inline ◆ CAlnMap() [3/3] ◆ CreateAlignFromRange()

Definition at line 1404 of file alnmap.cpp.

References _ASSERT, eSegment_Remove, eSegment_Trim, CSeq_align_Base::eType_partial, GetAlnStart(), GetAlnStop(), GetLen(), GetSeg(), GetStart(), i, len, m_Ids, m_NumRows, m_NumSegs, m_Strands, m_Widths, r(), CRef< C, Locker >::Reset(), row, CDense_seg_Base::SetDim(), CSeq_align_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), CSeq_align_Base::SetType(), and CDense_seg::SetWidths().

◆ GetAlnChunks()

Definition at line 1002 of file alnmap.cpp.

References fDoNotTruncateSegs, flags, GetAlnStart(), GetAlnStop(), CRange_Base::GetFrom(), GetNumSegs(), GetSeg(), CRange_Base::GetTo(), m_NumSegs, row, x_GetChunks(), and x_GetRawSegFromSeg().

Referenced by CAlnMapPrinter::Chunks(), CAlignFormatUtil::GetAlignLengths(), CAlnVec::GetAlnSeqString(), and CSampleAlnmgrApplication::Run().

◆ GetAlnPosFromSeqPos()

Definition at line 527 of file alnmap.cpp.

References delta(), IAlnExplorer::eBackwards, IAlnExplorer::eForward, IAlnExplorer::eLeft, IAlnExplorer::eNone, IAlnExplorer::eRight, CAlnMap::CNumSegWithOffset::GetAlnSeg(), GetAlnStart(), GetAlnStop(), GetNumSegs(), CAlnMap::CNumSegWithOffset::GetOffset(), GetRawSeg(), GetWidth(), IsPositiveStrand(), len, m_AlnStarts, m_Lens, m_NumRows, m_Starts, plus(), row, x_GetLen(), and x_GetSegFromRawSeg().

Referenced by s_GetGermlineTranslation(), s_MapSlaveFeatureToMaster(), s_MaskQuerySeq(), CAlnVwrApp::View10(), and CIgBlast::x_AnnotateDomain().

◆ GetAlnStart() [1/2] ◆ GetAlnStart() [2/2] TSeqPos CAlnMap::GetAlnStart ( void ) const inline ◆ GetAlnStop() [1/2]

Definition at line 488 of file alnmap.hpp.

References m_AlnStarts, m_Lens, and x_GetRawSegFromSeg().

Referenced by CAlnPos_CI::CAlnPos_CI(), CContigAssembly::CAlnStats::CAlnStats(), CAlnMapPrinter::Chunks(), CAlnVecPrinter::ClustalStyle(), CAlignFormatUtil::GetAlignmentLength(), CAlnMap::CAlnChunkVec::operator[](), CAlnVecPrinter::PopsetStyle(), CTestSingleAln_All::RunTest(), s_CalculateMatchingColumns(), s_MaskQuerySeq(), CAlnMapPrinter::Segments(), CAlnVwrApp::View10(), CAlnVwrApp::View9(), COligoSpecificityCheck::x_FindMatchInfoForAlignment(), CMultiAlnPrinter::x_PrintNexus(), and CMultiAlnPrinter::x_PrintPhylipInterleaved().

◆ GetAlnStop() [2/2] TSeqPos CAlnMap::GetAlnStop ( void ) const inline ◆ GetAnchor() ◆ GetDenseg() ◆ GetLen()

Definition at line 621 of file alnmap.hpp.

References m_Lens, offset, and x_GetRawSegFromSeg().

Referenced by CreateAlignFromRange(), CAlnMapPrinter::CsvTable(), CScoreBuilder::GetBlastScoreDenseg(), CAlnVec::GetColumnVector(), CAlnPos_CI::operator++(), CAlnPos_CI::operator--(), CAlnVwrApp::View7(), CGff3Writer::xAssignAlignmentDensegTarget(), and CGff3FlybaseWriter::xAssignAlignmentDensegTarget().

◆ GetNumRows()

Definition at line 517 of file alnmap.hpp.

References m_NumRows.

Referenced by CBuildAlnVecJob::Build(), CPhyTreeCalc::CalcBioTree(), CAlnPos_CI::CAlnPos_CI(), CAlignFormatUtil::GetAlignLengths(), CAlnVec::GetColumnVector(), s_GetCountIdentityMismatch(), s_GetTails(), CAlnVec::SetGenCode(), CAlnVwrApp::View10(), CAlnVwrApp::View7(), CAlnVwrApp::View8(), CPhyTreeCalc::x_CalcDivergenceMatrix(), CPhyTreeCalc::x_ComputeTree(), CTreeBuilderJob::x_CreateProjectItems(), CPhyTreeCalc::x_CreateValidAlign(), CCIGAR_Formatter::x_FormatDensegRows(), CApplyRNAITSDlg::x_GetRow(), CCIGAR_Formatter::x_GetRowById(), x_Init(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CMultiAlnPrinter::x_PrintNexus(), CMultiAlnPrinter::x_PrintPhylipInterleaved(), CMultiAlnPrinter::x_PrintPhylipSequential(), and CGff3Writer::xWriteAlignDenseg().

◆ GetNumSegs()

Definition at line 510 of file alnmap.hpp.

References IsSetAnchor(), m_AlnSegIdx, and m_NumSegs.

Referenced by CAlnVecPrinter::ClustalStyle(), CAlnMapPrinter::CsvTable(), GetAlnChunks(), GetAlnPosFromSeqPos(), GetAlnStop(), CScoreBuilder::GetBlastScoreDenseg(), CAlnVecPrinter::PopsetStyle(), CTestSingleAln_All::RunTest(), s_GetCountIdentityMismatch(), s_MaskQuerySeq(), CAlnMapPrinter::Segments(), CAlnVwrApp::View7(), x_CreateAlnStarts(), CCIGAR_Formatter::x_FormatLine(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegTarget(), and CGff3FlybaseWriter::xAssignAlignmentDensegTarget().

◆ GetRange() ◆ GetRawSeg()

Definition at line 400 of file alnmap.cpp.

References IAlnExplorer::eBackwards, IAlnExplorer::eForward, IAlnExplorer::eLeft, IAlnExplorer::eNone, IAlnExplorer::eRight, GetSeqStart(), GetSeqStop(), IsPositiveStrand(), last(), m_NumRows, m_NumSegs, m_Starts, plus(), row, and x_GetLen().

Referenced by GetAlnPosFromSeqPos(), GetSeqChunks(), and GetSeqPosFromSeqPos().

◆ GetResidueIndexMap()

Definition at line 757 of file alnmap.cpp.

References _ASSERT, delta(), GetAlnStop(), CRange_Base::GetFrom(), CRange_Base::GetTo(), NStr::IntToString(), IsPositiveStrand(), IsSetAnchor(), m_Lens, m_NumRows, m_NumSegs, m_Starts, NCBI_THROW, result, CRange_Base::SetFrom(), CRange_Base::SetTo(), ncbi::grid::netcache::search::fields::size, and string.

Referenced by CAlnVwrApp::View9().

◆ GetSeg() ◆ GetSegType() ◆ GetSeqAlnRange() ◆ GetSeqAlnStart() ◆ GetSeqAlnStop() ◆ GetSeqChunks()

Definition at line 1039 of file alnmap.cpp.

References fDoNotTruncateSegs, flags, CRange_Base::GetFrom(), GetRawSeg(), GetSeqStart(), GetSeqStop(), CRange_Base::GetTo(), IsPositiveStrand(), m_NumSegs, row, x_GetChunks(), x_GetRawStart(), and x_GetRawStop().

Referenced by COligoSpecificityCheck::x_NW_alignment().

◆ GetSeqId()

Definition at line 645 of file alnmap.hpp.

References m_Ids, and row.

Referenced by CBuildAlnVecJob::Build(), CAlnMapPrinter::CAlnMapPrinter(), CDisplaySeqalign::DisplaySeqalign(), CAlnVec::GetBioseqHandle(), s_DoNWalign(), CCIGAR_Formatter::x_FormatDensegRows(), CCIGAR_Formatter::x_FormatLine(), CApplyRNAITSDlg::x_GetRow(), CCIGAR_Formatter::x_GetRowById(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CMultiAlnPrinter::x_PrintNexus(), CMultiAlnPrinter::x_PrintPhylipInterleaved(), CMultiAlnPrinter::x_PrintPhylipSequential(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegMethod(), CGff3Writer::xAssignAlignmentDensegSeqId(), CGff3FlybaseWriter::xAssignAlignmentDensegSeqId(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CGff3Writer::xAssignAlignmentDensegType(), and CGff3Writer::xWriteAlignDenseg().

◆ GetSeqLen() ◆ GetSeqPosFromAlnPos()

Definition at line 663 of file alnmap.cpp.

References delta(), IAlnExplorer::eNone, GetAlnStart(), GetAlnStop(), GetSeg(), GetStart(), GetWidth(), IsPositiveStrand(), x_FindClosestSeqPos(), x_GetLen(), and x_GetRawSegFromSeg().

Referenced by CContigAssembly::BestLocalSubAlignment(), CAlnVec::GetResidue(), CApplyRNAITSDlg::GetRNAITSList_AlignCoordFromDlg(), CAlnVecPrinter::PopsetStyle(), CTestSingleAln_All::RunTest(), s_MapSlaveFeatureToMaster(), and CAlnVwrApp::View10().

◆ GetSeqPosFromSeqPos()

Definition at line 688 of file alnmap.cpp.

References delta(), GetRawSeg(), GetWidth(), m_NumRows, m_Starts, offset, row, StrandSign(), x_FindClosestSeqPos(), and x_GetLen().

Referenced by CAlnVwrApp::View10(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateDomain(), CIgBlast::x_FillJDomain(), and COligoSpecificityCheck::x_NW_alignment().

◆ GetSeqRange() ◆ GetSeqStart()

Definition at line 665 of file alnmap.hpp.

References IsPositiveStrand(), m_NumRows, m_Starts, row, x_GetSeqLeftSeg(), and x_GetSeqRightSeg().

Referenced by GetRawSeg(), GetSeqChunks(), GetSeqRange(), CTestSingleAln_All::RunTest(), s_GetGermlineTranslation(), s_GetTails(), CBlastTabularInfo::SetFields(), CIgBlastTabularInfo::SetIgAnnotation(), CDisplaySeqalign::x_CalcUrlLinksParams(), CGff3Writer::xAssignAlignmentDensegLocation(), and CGff3FlybaseWriter::xAssignAlignmentDensegLocation().

◆ GetSeqStop()

Definition at line 675 of file alnmap.hpp.

References IsPositiveStrand(), m_NumRows, m_Starts, row, x_GetLen(), x_GetSeqLeftSeg(), and x_GetSeqRightSeg().

◆ GetStart()

Definition at line 614 of file alnmap.hpp.

References m_NumRows, m_Starts, offset, row, and x_GetRawSegFromSeg().

Referenced by CreateAlignFromRange(), CAlnMapPrinter::CsvTable(), CScoreBuilder::GetBlastScoreDenseg(), CAlnVec::GetColumnVector(), GetRange(), CAlnVec::GetSegSeqString(), CAlnPos_CI::GetSeqPos(), GetSeqPosFromAlnPos(), GetStop(), CTestSingleAln_All::RunTest(), s_GetCountIdentityMismatch(), CAlnMapPrinter::Segments(), CAlnVwrApp::View7(), CIgBlast::x_AnnotateDomain(), CGff3Writer::xAssignAlignmentDensegTarget(), and CGff3FlybaseWriter::xAssignAlignmentDensegTarget().

◆ GetStop() ◆ GetTypeAtAlnPos() ◆ GetWidth()

Definition at line 560 of file alnmap.hpp.

References _ASSERT, m_NumRows, m_Widths, and row.

Referenced by CAlnVecPrinter::ClustalStyle(), GetAlnPosFromSeqPos(), CAlnVec::GetAlnSeqString(), CAlnVec::GetColumnVector(), CAlnVec::GetResidue(), GetSeqPosFromAlnPos(), GetSeqPosFromSeqPos(), CAlnVec::GetSeqString(), CAlnVec::GetWholeAlnSeqString(), CAlnMap::CAlnChunkVec::operator[](), CAlnVecPrinter::PopsetStyle(), and x_GetLen().

◆ IsNegativeStrand() ◆ IsPositiveStrand()

Definition at line 600 of file alnmap.hpp.

References eNa_strand_minus, m_Strands, and row.

Referenced by CAlnVec::CalculateScore(), GetAlnPosFromSeqPos(), CAlnVec::GetAlnSeqString(), CAlnVec::GetColumnVector(), GetRawSeg(), CAlnVec::GetResidue(), GetResidueIndexMap(), GetSeqChunks(), CAlnPos_CI::GetSeqPos(), GetSeqPosFromAlnPos(), GetSeqStart(), GetSeqStop(), CAlnVec::GetSeqString(), CAlnVec::GetWholeAlnSeqString(), IsNegativeStrand(), CAlnMap::CAlnChunkVec::operator[](), CAlnVec::RetrieveSegmentSequences(), s_DoNWalign(), s_GetTails(), s_MapSlaveFeatureToMaster(), StrandSign(), x_FindClosestSeqPos(), CAlnVec::x_GetSeqVector(), COligoSpecificityCheck::x_NW_alignment(), x_SetRawSegType(), and x_SetRawSegTypes().

◆ IsSetAnchor() bool CAlnMap::IsSetAnchor ( void ) const inline ◆ IsTypeInsert() ◆ operator=() ◆ SetAnchor() void CAlnMap::SetAnchor ( TNumrow anchor )

Definition at line 79 of file alnmap.cpp.

References i, len, m_AlnSegIdx, m_AlnStarts, m_Anchor, m_Lens, m_NumRows, m_NumSegs, m_NumSegWithOffsets, m_RawSegTypes, m_Starts, NCBI_THROW, offset, and UnsetAnchor().

Referenced by BuildAlignDataSource(), CAlnMap(), CAlnVwrApp::Run(), CSampleAlnmgrApplication::Run(), and CAlnMrgApp::ViewMergedAln().

◆ StrandSign() ◆ UnsetAnchor() void CAlnMap::UnsetAnchor ( void ) ◆ x_CompareAdjacentSegTypes() ◆ x_CreateAlnStarts() void CAlnMap::x_CreateAlnStarts ( void ) protected ◆ x_FindClosestSeqPos()

Definition at line 598 of file alnmap.cpp.

References _ASSERT, IAlnExplorer::eBackwards, IAlnExplorer::eForward, IAlnExplorer::eLeft, IAlnExplorer::eNone, IAlnExplorer::eRight, NStr::IntToString(), IsPositiveStrand(), m_NumSegs, msg(), NCBI_THROW, row, x_GetRawStart(), and x_GetRawStop().

Referenced by GetSeqPosFromAlnPos(), and GetSeqPosFromSeqPos().

◆ x_GetChunks()

Definition at line 1145 of file alnmap.cpp.

References _ASSERT, Critical(), fAddUnalignedChunks, fIgnoreGaps, flags, fSeq, fUnalignedOnRight, int, CAlnMap::CAlnChunkVec::m_LeftDelta, m_NumRows, CAlnMap::CAlnChunkVec::m_RightDelta, CAlnMap::CAlnChunkVec::m_StartSegs, CAlnMap::CAlnChunkVec::m_StopSegs, NCBI_THROW, row, test_type(), type, x_CompareAdjacentSegTypes(), x_GetRawSegType(), and x_SkipType().

Referenced by GetAlnChunks(), and GetSeqChunks().

◆ x_GetLen()

Definition at line 571 of file alnmap.hpp.

References _ASSERT, GetWidth(), len, m_Lens, and row.

Referenced by GetAlnPosFromSeqPos(), GetRawSeg(), GetSeqLen(), GetSeqPosFromAlnPos(), GetSeqPosFromSeqPos(), GetSeqStop(), CAlnMap::CAlnChunkVec::operator[](), x_GetRawStop(), x_SetRawSegType(), and x_SetRawSegTypes().

◆ x_GetRawSegFromSeg() ◆ x_GetRawSegType() ◆ x_GetRawSegTypes() ◆ x_GetRawStart() ◆ x_GetRawStop() ◆ x_GetSegFromRawSeg() ◆ x_GetSeqLeftSeg() ◆ x_GetSeqRightSeg() ◆ x_Init() void CAlnMap::x_Init ( void ) protected ◆ x_SetRawSegType()

Definition at line 125 of file alnmap.cpp.

References fEndOnLeft, fEndOnRight, flags, fNoSeqOnLeft, fNoSeqOnRight, fNotAlignedToSeqOnAnchor, fSeq, fUnalignedOnLeft, fUnalignedOnLeftOnAnchor, fUnalignedOnRight, fUnalignedOnRightOnAnchor, IsPositiveStrand(), IsSetAnchor(), m_Anchor, m_NumRows, m_NumSegs, m_Starts, row, and x_GetLen().

◆ x_SetRawSegTypes() void CAlnMap::x_SetRawSegTypes ( TNumrow row ) const protected

Definition at line 235 of file alnmap.cpp.

References _ASSERT, fEndOnLeft, fEndOnRight, flags, fNoSeqOnLeft, fNoSeqOnRight, fNotAlignedToSeqOnAnchor, fSeq, fTypeIsSet, fUnalignedOnLeft, fUnalignedOnLeftOnAnchor, fUnalignedOnRight, fUnalignedOnRightOnAnchor, IsPositiveStrand(), IsSetAnchor(), m_Anchor, m_NumRows, m_NumSegs, m_Starts, plus(), row, types, x_GetLen(), and x_GetRawSegTypes().

Referenced by x_GetRawSegType().

◆ x_SkipType() ◆ CAlnChunkVec::operator[] ◆ m_AlnSegIdx vector<TNumseg> CAlnMap::m_AlnSegIdx protected ◆ m_AlnStarts ◆ m_Anchor ◆ m_DS ◆ m_Ids ◆ m_Lens

Definition at line 374 of file alnmap.hpp.

Referenced by CAlnVec::CalculateScore(), CAlnVec::CreateConsensus(), GetAlnPosFromSeqPos(), GetAlnStop(), GetLen(), GetResidueIndexMap(), GetSeg(), CAlnVec::GetWholeAlnSeqString(), CAlnVec::RetrieveSegmentSequences(), SetAnchor(), x_CreateAlnStarts(), and x_GetLen().

◆ m_NumRows

Definition at line 370 of file alnmap.hpp.

Referenced by CAlnVec::CalculatePercentIdentity(), CAlnVec::CalculateScore(), CreateAlignFromRange(), CAlnVec::CreateConsensus(), GetAlnPosFromSeqPos(), CAlnVec::GetColumnVector(), GetNumRows(), GetRawSeg(), GetResidueIndexMap(), GetSeqAlnStart(), GetSeqAlnStop(), GetSeqPosFromSeqPos(), GetSeqStart(), GetSeqStop(), GetStart(), CAlnVec::GetWholeAlnSeqString(), GetWidth(), CAlnMap::CAlnChunkVec::operator[](), CAlnVec::RetrieveSegmentSequences(), SetAnchor(), x_GetChunks(), x_GetRawSegType(), x_GetRawSegTypes(), x_GetRawStart(), x_GetSeqLeftSeg(), x_GetSeqRightSeg(), x_SetRawSegType(), and x_SetRawSegTypes().

◆ m_NumSegs

Definition at line 371 of file alnmap.hpp.

Referenced by CAlnVec::CalculateScore(), CreateAlignFromRange(), CAlnVec::CreateConsensus(), GetAlnChunks(), GetNumSegs(), GetRawSeg(), GetResidueIndexMap(), GetSeqChunks(), CAlnVec::GetWholeAlnSeqString(), CAlnMap::CAlnChunkVec::operator[](), SetAnchor(), x_FindClosestSeqPos(), x_GetRawSegTypes(), x_GetSeqLeftSeg(), x_GetSeqRightSeg(), x_SetRawSegType(), and x_SetRawSegTypes().

◆ m_NumSegWithOffsets ◆ m_RawSegTypes ◆ m_Scores ◆ m_SeqLeftSegs vector<TNumseg> CAlnMap::m_SeqLeftSegs mutableprotected ◆ m_SeqRightSegs vector<TNumseg> CAlnMap::m_SeqRightSegs mutableprotected ◆ m_Starts

Definition at line 373 of file alnmap.hpp.

Referenced by CAlnVec::CalculateScore(), CAlnVec::CreateConsensus(), GetAlnPosFromSeqPos(), GetRawSeg(), GetResidueIndexMap(), GetSeqAlnStart(), GetSeqAlnStop(), GetSeqPosFromSeqPos(), GetSeqStart(), GetSeqStop(), GetStart(), CAlnVec::GetWholeAlnSeqString(), CAlnMap::CAlnChunkVec::operator[](), CAlnVec::RetrieveSegmentSequences(), SetAnchor(), x_GetRawStart(), x_GetSeqLeftSeg(), x_GetSeqRightSeg(), x_SetRawSegType(), and x_SetRawSegTypes().

◆ m_Strands ◆ m_Widths

The documentation for this class was generated from the following files:

include/objtools/alnmgr/alnmap.hpp
src/objtools/alnmgr/alnmap.cpp

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