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USING_SCOPE (objects) bool GetSeqID (const CRef< CSeq_align > &seqAlign, CRef< CSeq_id > &SeqID, bool getSlave=true) bool ChangeSeqIdInSeqAlign (CRef< CSeq_align > &sa, const CRef< CSeq_id > &newSeqId, bool onMaster) int MapPositionToMaster (int childPos, const CSeq_align &align) int MapPositionToChild (int masterPos, const CSeq_align &align) int MapPosition (const CSeq_align &seqAlign, int Position, CoordMapDir mapDir) bool IsPositionAligned (const CSeq_align &seqAlign, int Position, bool onMaster) bool IsPositionAligned (const TDendiag *&dd, int Position, bool onMaster) int GetAlignedPositions (const CRef< CSeq_align > &align1, const CRef< CSeq_align > &align2, vector< int > &alignedPositions, bool onMaster) int GetNumAlignedResidues (const CRef< CSeq_align > &align) int GetLowerBound (const CRef< CSeq_align > &seqAlign, bool onMaster) int GetUpperBound (const CRef< CSeq_align > &seqAlign, bool onMaster) void SetAlignedResiduesOnSequence (const CRef< CSeq_align > &align, const string &sequenceString, char *&pAlignedRes, bool isMaster=false) bool CheckSeqIdInDD (const CRef< CSeq_align > &seqAlign) int GetBlockNumberForResidue (int residue, const CRef< CSeq_align > &seqAlign, bool onMaster, vector< int > *starts=NULL, vector< int > *lengths=NULL) int GetBlockCount (const CRef< CSeq_align > &seqAlign) int GetBlockLengths (const CRef< CSeq_align > &seqAlign, vector< int > &lengths) int GetBlockStarts (const CRef< CSeq_align > &seqAlign, vector< int > &starts, bool onMaster) int GetBlockStartsForMaster (const CRef< CSeq_align > &seqAlign, vector< int > &starts) bool GetDDSetFromSeqAlign (const CSeq_align &align, const TDendiag *&dd) bool GetDDSetFromSeqAlign (CSeq_align &align, TDendiag *&dd) void MakeDDFromSeqLoc (CSeq_loc *pAl, TDendiag *pDD) void MakeSeqLocFromDD (const TDendiag *pDD, CSeq_loc *pAl) void AddIntervalToDD (TDendiag *pDD, CRef< CSeq_id > seqID1, CRef< CSeq_id > seqID2, TSeqPos st1, TSeqPos st2, TSeqPos lll) bool GetFirstOrLastDenDiag (const CRef< CSeq_align > &seqAlign, bool firstOrLast, CRef< CDense_diag > &dd) bool GetDenDiagSet (const CRef< CSeq_annot > &seqAnnot, int row, const TDendiag *&pDenDiagSet) bool SetDenDiagSet (CRef< CSeq_annot > &seqAnnot, int row, TDendiag *&pddSet) bool EraseRow (CRef< CSeq_annot > &seqAnnot, int row) CRef< CSeq_align > ExtractFirstSeqAlign (CRef< CSeq_align > seqAlign) CRef< CSeq_align > Denseg2DenseDiagList (const CRef< CSeq_align > &denseSegSeqAlign) void Denseg2DenseDiagList (const CDense_seg &ds, TDendiag &ddl) int GetPssmIdFromSeqAlign (const CRef< CSeq_align > &seqAlign, string &err) TGi GetMasterGIFromSeqAlign (const CRef< CSeq_align > &seqAlign, string &err) bool GetPendingSeqId (CCdCore *pCD, int irow, CRef< CSeq_id > &seqID) ◆ TDendiag ◆ TDendiag_cit ◆ TDendiag_it ◆ AddIntervalToDD() ◆ ChangeSeqIdInSeqAlign() ◆ CheckSeqIdInDD() ◆ Denseg2DenseDiagList() [1/2] ◆ Denseg2DenseDiagList() [2/2] ◆ EraseRow() ◆ ExtractFirstSeqAlign() ◆ GetAlignedPositions() ◆ GetBlockCount() ◆ GetBlockLengths() ◆ GetBlockNumberForResidue() ◆ GetBlockStarts()Definition at line 418 of file cuAlign.cpp.
References count, GetBlockCount(), GetDDSetFromSeqAlign(), CRef< C, Locker >::NotEmpty(), and NULL.
Referenced by BlockModel::BlockModel(), GetAlignedPositions(), GetAlignmentColumnsForCD(), GetBlockNumberForResidue(), GetBlockStartsForMaster(), and CCdCore::GetBlockStartsForRow().
◆ GetBlockStartsForMaster() ◆ GetDDSetFromSeqAlign() [1/2]Definition at line 439 of file cuAlign.cpp.
References CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::GetSegs(), and CSeq_align_Base::C_Segs::IsDendiag().
Referenced by CheckSeqIdInDD(), GetBlockLengths(), GetBlockStarts(), GetFirstOrLastDenDiag(), GetLowerBound(), GetNumAlignedResidues(), GetUpperBound(), AlignmentCollection::IsNonOverlapping(), IsPositionAligned(), MapPosition(), and SetAlignedResiduesOnSequence().
◆ GetDDSetFromSeqAlign() [2/2] ◆ GetDenDiagSet() ◆ GetFirstOrLastDenDiag() ◆ GetLowerBound() ◆ GetMasterGIFromSeqAlign()Definition at line 806 of file cuAlign.cpp.
References CRef< C, Locker >::Empty(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_id_Base::GetGi(), CDense_seg_Base::GetIds(), CSeq_align_Base::GetSegs(), CSeq_align_Base::GetType(), CSeq_align_Base::C_Segs::IsDendiag(), CSeq_align_Base::C_Segs::IsDenseg(), CSeq_id_Base::IsGi(), CRef< C, Locker >::NotEmpty(), and ZERO_GI.
◆ GetNumAlignedResidues() ◆ GetPendingSeqId() ◆ GetPssmIdFromSeqAlign()Definition at line 784 of file cuAlign.cpp.
References CRef< C, Locker >::Empty(), GetCDDPssmIdFromSeqId(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetDim(), CDense_seg_Base::GetIds(), CSeq_align_Base::GetSegs(), CSeq_align_Base::GetType(), CSeq_align_Base::C_Segs::IsDendiag(), CSeq_align_Base::C_Segs::IsDenseg(), and CSeq_align_Base::IsSetDim().
◆ GetSeqID() ◆ GetUpperBound() ◆ IsPositionAligned() [1/2] ◆ IsPositionAligned() [2/2] ◆ MakeDDFromSeqLoc() ◆ MakeSeqLocFromDD() ◆ MapPosition() ◆ MapPositionToChild() ◆ MapPositionToMaster() ◆ SetAlignedResiduesOnSequence()Definition at line 290 of file cuAlign.cpp.
References CRef< C, Locker >::Empty(), GetDDSetFromSeqAlign(), GetFirstOrLastDenDiag(), GetNumAlignedResidues(), i, IsPositionAligned(), CRef< C, Locker >::NotEmpty(), and NULL.
Referenced by AlignmentCollection::GetAlignedResiduesForRow(), and SetAlignedResiduesForCD().
◆ SetDenDiagSet() ◆ USING_SCOPE()RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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