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CAlnMap Class Reference

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#include <objtools/alnmgr/alnmap.hpp>

+ Inheritance diagram for CAlnMap:
+ Collaboration diagram for CAlnMap:

Classes

class  CAlnChunk
 
class  CAlnChunkVec
 
class  CNumSegWithOffset
 

Public Types

enum  ESegTypeFlags {
  fSeq = 0x0001 , fNotAlignedToSeqOnAnchor = 0x0002 , fInsert = fSeq | fNotAlignedToSeqOnAnchor , fUnalignedOnRight = 0x0004 ,
  fUnalignedOnLeft = 0x0008 , fNoSeqOnRight = 0x0010 , fNoSeqOnLeft = 0x0020 , fEndOnRight = 0x0040 ,
  fEndOnLeft = 0x0080 , fUnaligned = 0x0100 , fUnalignedOnRightOnAnchor = 0x0200 , fUnalignedOnLeftOnAnchor = 0x0400 ,
  fTypeIsSet = (TSegTypeFlags) 0x80000000
}
 
enum  EGetChunkFlags {
  fAllChunks = 0x0000 , fIgnoreUnaligned = 0x0001 , fInsertSameAsSeq = 0x0002 , fDeletionSameAsGap = 0x0004 ,
  fIgnoreAnchor = fInsertSameAsSeq | fDeletionSameAsGap , fIgnoreGaps = 0x0008 , fChunkSameAsSeg = 0x0010 , fSkipUnalignedGaps = 0x0020 ,
  fSkipDeletions = 0x0040 , fSkipAllGaps = fSkipUnalignedGaps | fSkipDeletions , fSkipInserts = 0x0080 , fSkipAlnSeq = 0x0100 ,
  fSeqOnly = fSkipAllGaps | fSkipInserts , fInsertsOnly = fSkipAllGaps | fSkipAlnSeq , fAlnSegsOnly = fSkipInserts | fSkipUnalignedGaps , fDoNotTruncateSegs = 0x0200 ,
  fAddUnalignedChunks = 0x0400
}
 
enum  ESegmentTrimFlag { eSegment_Include , eSegment_Trim , eSegment_Remove }
 
typedef unsigned int TSegTypeFlags
 
typedef CDense_seg::TDim TDim
 
typedef TDim TNumrow
 
typedef CRange< TSeqPosTRange
 
typedef CRange< TSignedSeqPosTSignedRange
 
typedef CDense_seg::TNumseg TNumseg
 
typedef list< TSeqPosTSeqPosList
 
typedef int TGetChunkFlags
 
typedef TNumseg TNumchunk
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Public Types inherited from IAlnExplorer
enum  EAlignType {
  fDNA = 0x01 , fProtein = 0x02 , fMixed = 0x04 , fHomogenous = fDNA | fProtein ,
  fInvalid = 0x80000000
}
 
enum  ESearchDirection {
  eNone , eBackwards , eForward , eLeft ,
  eRight
}
 Position search options. More...
 
enum  ESortState { eUnSorted , eAscending , eDescending , eNotSupported }
 
typedef int TNumrow
 
typedef objects::CSeqVector::TResidue TResidue
 
typedef CRange< TSeqPosTRange
 
typedef CRange< TSignedSeqPosTSignedRange
 

Public Member Functions

 CAlnMap (const CDense_seg &ds)
 
 CAlnMap (const CDense_seg &ds, TNumrow anchor)
 
CRef< CSeq_alignCreateAlignFromRange (const vector< TNumrow > &selected_rows, TSignedSeqPos aln_from, TSignedSeqPos aln_to, ESegmentTrimFlag seg_flag=eSegment_Trim)
 
 ~CAlnMap (void)
 
const CDense_segGetDenseg (void) const
 
TNumseg GetNumSegs (void) const
 
TDim GetNumRows (void) const
 
const CSeq_idGetSeqId (TNumrow row) const
 
bool IsPositiveStrand (TNumrow row) const
 
bool IsNegativeStrand (TNumrow row) const
 
int StrandSign (TNumrow row) const
 
int GetWidth (TNumrow row) const
 
TSignedSeqPos GetSeqAlnStart (TNumrow row) const
 
TSignedSeqPos GetSeqAlnStop (TNumrow row) const
 
TSignedRange GetSeqAlnRange (TNumrow row) const
 
TSeqPos GetSeqStart (TNumrow row) const
 
TSeqPos GetSeqStop (TNumrow row) const
 
TRange GetSeqRange (TNumrow row) const
 
TSignedSeqPos GetStart (TNumrow row, TNumseg seg, int offset=0) const
 
TSignedSeqPos GetStop (TNumrow row, TNumseg seg, int offset=0) const
 
TSignedRange GetRange (TNumrow row, TNumseg seg, int offset=0) const
 
TSeqPos GetLen (TNumseg seg, int offset=0) const
 
TSeqPos GetSeqLen (TNumrow row, TNumseg seg, int offset=0) const
 
TSegTypeFlags GetSegType (TNumrow row, TNumseg seg, int offset=0) const
 
TSegTypeFlags GetTypeAtAlnPos (TNumrow row, TSeqPos aln_pos) const
 
TSeqPos GetAlnStart (TNumseg seg) const
 
TSeqPos GetAlnStop (TNumseg seg) const
 
TSeqPos GetAlnStart (void) const
 
TSeqPos GetAlnStop (void) const
 
bool IsSetAnchor (void) const
 
TNumrow GetAnchor (void) const
 
void SetAnchor (TNumrow anchor)
 
void UnsetAnchor (void)
 
TNumseg GetSeg (TSeqPos aln_pos) const
 
TNumseg GetRawSeg (TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const
 
TSignedSeqPos GetAlnPosFromSeqPos (TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const
 
TSignedSeqPos GetSeqPosFromSeqPos (TNumrow for_row, TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const
 
TSignedSeqPos GetSeqPosFromAlnPos (TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const
 
void GetResidueIndexMap (TNumrow row0, TNumrow row1, TRange aln_rng, vector< TSignedSeqPos > &result, TRange &rng0, TRange &rng1) const
 
CRef< CAlnChunkVecGetAlnChunks (TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const
 
CRef< CAlnChunkVecGetSeqChunks (TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Static Public Member Functions

static bool IsTypeInsert (TSegTypeFlags type)
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 

Protected Types

typedef vector< TSegTypeFlagsTRawSegTypes
 

Protected Member Functions

void x_GetChunks (CAlnChunkVec *vec, TNumrow row, TNumseg left_seg, TNumseg right_seg, TGetChunkFlags flags) const
 
 CAlnMap (const CAlnMap &value)
 
CAlnMapoperator= (const CAlnMap &value)
 
void x_Init (void)
 
void x_CreateAlnStarts (void)
 
TRawSegTypesx_GetRawSegTypes () const
 
TSegTypeFlags x_GetRawSegType (TNumrow row, TNumseg seg, int hint_idx=-1) const
 
TSegTypeFlags x_SetRawSegType (TNumrow row, TNumseg seg) const
 
void x_SetRawSegTypes (TNumrow row) const
 
CNumSegWithOffset x_GetSegFromRawSeg (TNumseg seg) const
 
TNumseg x_GetRawSegFromSeg (TNumseg seg) const
 
TSignedSeqPos x_GetRawStart (TNumrow row, TNumseg seg) const
 
TSignedSeqPos x_GetRawStop (TNumrow row, TNumseg seg) const
 
TSeqPos x_GetLen (TNumrow row, TNumseg seg) const
 
const TNumsegx_GetSeqLeftSeg (TNumrow row) const
 
const TNumsegx_GetSeqRightSeg (TNumrow row) const
 
TSignedSeqPos x_FindClosestSeqPos (TNumrow row, TNumseg seg, ESearchDirection dir, bool try_reverse_dir) const
 
bool x_SkipType (TSegTypeFlags type, TGetChunkFlags flags) const
 
bool x_CompareAdjacentSegTypes (TSegTypeFlags left_type, TSegTypeFlags right_type, TGetChunkFlags flags) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

CConstRef< CDense_segm_DS
 
TNumrow m_NumRows
 
TNumseg m_NumSegs
 
const CDense_seg::TIdsm_Ids
 
const CDense_seg::TStartsm_Starts
 
const CDense_seg::TLensm_Lens
 
const CDense_seg::TStrandsm_Strands
 
const CDense_seg::TScoresm_Scores
 
const CDense_seg::TWidthsm_Widths
 
TNumrow m_Anchor
 
vector< TNumsegm_AlnSegIdx
 
vector< TNumsegm_SeqLeftSegs
 
vector< TNumsegm_SeqRightSegs
 
CDense_seg::TStarts m_AlnStarts
 
vector< CNumSegWithOffsetm_NumSegWithOffsets
 
TRawSegTypesm_RawSegTypes
 

Private Types

typedef CObject TParent
 

Friends

CConstRef< CAlnChunkCAlnChunkVec::operator[] (TNumchunk i) const
 

Additional Inherited Members

- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 

Detailed Description

Definition at line 44 of file alnmap.hpp.

Member Typedef Documentation

◆ TDim

Definition at line 68 of file alnmap.hpp.

◆ TGetChunkFlags

Definition at line 110 of file alnmap.hpp.

◆ TNumchunk

Definition at line 112 of file alnmap.hpp.

◆ TNumrow

Definition at line 69 of file alnmap.hpp.

◆ TNumseg

Definition at line 72 of file alnmap.hpp.

◆ TParent

typedef CObject CAlnMap::TParent
private

Definition at line 46 of file alnmap.hpp.

◆ TRange

Definition at line 70 of file alnmap.hpp.

◆ TRawSegTypes

typedef vector<TSegTypeFlags> CAlnMap::TRawSegTypes
protected

Definition at line 342 of file alnmap.hpp.

◆ TSegTypeFlags

typedef unsigned int CAlnMap::TSegTypeFlags

Definition at line 50 of file alnmap.hpp.

◆ TSeqPosList

Definition at line 73 of file alnmap.hpp.

◆ TSignedRange

Definition at line 71 of file alnmap.hpp.

Member Enumeration Documentation

◆ 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.

Constructor & Destructor Documentation

◆ CAlnMap() [1/3]

CAlnMap::CAlnMap ( const CDense_seg ds)
inline

Definition at line 428 of file alnmap.hpp.

References x_CreateAlnStarts(), and x_Init().

◆ CAlnMap() [2/3]

CAlnMap::CAlnMap ( const CDense_seg ds,
TNumrow  anchor 
)
inline

Definition at line 447 of file alnmap.hpp.

References SetAnchor(), and x_Init().

◆ ~CAlnMap()

CAlnMap::~CAlnMap ( void  )
inline

Definition at line 466 of file alnmap.hpp.

References m_RawSegTypes.

◆ CAlnMap() [3/3]

CAlnMap::CAlnMap ( const CAlnMap value)
protected

Member Function Documentation

◆ CreateAlignFromRange()

CRef< CSeq_align > CAlnMap::CreateAlignFromRange ( const vector< TNumrow > &  selected_rows,
TSignedSeqPos  aln_from,
TSignedSeqPos  aln_to,
ESegmentTrimFlag  seg_flag = eSegment_Trim 
)

◆ GetAlnChunks()

CRef< CAlnMap::CAlnChunkVec > CAlnMap::GetAlnChunks ( TNumrow  row,
const TSignedRange range,
TGetChunkFlags  flags = fAlnSegsOnly 
) const

◆ GetAlnPosFromSeqPos()

TSignedSeqPos CAlnMap::GetAlnPosFromSeqPos ( TNumrow  row,
TSeqPos  seq_pos,
ESearchDirection  dir = eNone,
bool  try_reverse_dir = true 
) const

◆ GetAlnStart() [1/2]

TSeqPos CAlnMap::GetAlnStart ( TNumseg  seg) const
inline

◆ GetAlnStart() [2/2]

TSeqPos CAlnMap::GetAlnStart ( void  ) const
inline

◆ GetAlnStop() [1/2]

TSeqPos CAlnMap::GetAlnStop ( TNumseg  seg) const
inline

◆ GetAlnStop() [2/2]

TSeqPos CAlnMap::GetAlnStop ( void  ) const
inline

◆ GetAnchor()

CAlnMap::TNumrow CAlnMap::GetAnchor ( void  ) const
inline

Definition at line 530 of file alnmap.hpp.

References m_Anchor.

Referenced by CAlnPos_CI::operator++(), and CAlnPos_CI::operator--().

◆ GetDenseg()

const CDense_seg & CAlnMap::GetDenseg ( void  ) const
inline

◆ GetLen()

TSeqPos CAlnMap::GetLen ( TNumseg  seg,
int  offset = 0 
) const
inline

◆ GetNumRows()

CAlnMap::TDim CAlnMap::GetNumRows ( void  ) const
inline

◆ GetNumSegs()

CAlnMap::TNumseg CAlnMap::GetNumSegs ( void  ) const
inline

◆ GetRange()

CAlnMap::TSignedRange CAlnMap::GetRange ( TNumrow  row,
TNumseg  seg,
int  offset = 0 
) const
inline

◆ GetRawSeg()

CAlnMap::TNumseg CAlnMap::GetRawSeg ( TNumrow  row,
TSeqPos  seq_pos,
ESearchDirection  dir = eNone,
bool  try_reverse_dir = true 
) const

◆ GetResidueIndexMap()

void CAlnMap::GetResidueIndexMap ( TNumrow  row0,
TNumrow  row1,
TRange  aln_rng,
vector< TSignedSeqPos > &  result,
TRange rng0,
TRange rng1 
) const

◆ GetSeg()

CAlnMap::TNumseg CAlnMap::GetSeg ( TSeqPos  aln_pos) const

◆ GetSegType()

CAlnMap::TSegTypeFlags CAlnMap::GetSegType ( TNumrow  row,
TNumseg  seg,
int  offset = 0 
) const
inline

◆ GetSeqAlnRange()

CAlnMap::TSignedRange CAlnMap::GetSeqAlnRange ( TNumrow  row) const
inline

Definition at line 691 of file alnmap.hpp.

References GetSeqAlnStart(), GetSeqAlnStop(), and row.

Referenced by CAlignFormatUtil::GetAlignLengths().

◆ GetSeqAlnStart()

TSignedSeqPos CAlnMap::GetSeqAlnStart ( TNumrow  row) const

◆ GetSeqAlnStop()

TSignedSeqPos CAlnMap::GetSeqAlnStop ( TNumrow  row) const

◆ GetSeqChunks()

CRef< CAlnMap::CAlnChunkVec > CAlnMap::GetSeqChunks ( TNumrow  row,
const TSignedRange range,
TGetChunkFlags  flags = fAlnSegsOnly 
) const

◆ GetSeqId()

const CSeq_id & CAlnMap::GetSeqId ( TNumrow  row) const
inline

◆ GetSeqLen()

TSeqPos CAlnMap::GetSeqLen ( TNumrow  row,
TNumseg  seg,
int  offset = 0 
) const
inline

Definition at line 628 of file alnmap.hpp.

References offset, row, x_GetLen(), and x_GetRawSegFromSeg().

Referenced by GetRange(), and GetStop().

◆ GetSeqPosFromAlnPos()

TSignedSeqPos CAlnMap::GetSeqPosFromAlnPos ( TNumrow  for_row,
TSeqPos  aln_pos,
ESearchDirection  dir = eNone,
bool  try_reverse_dir = true 
) const

◆ GetSeqPosFromSeqPos()

TSignedSeqPos CAlnMap::GetSeqPosFromSeqPos ( TNumrow  for_row,
TNumrow  row,
TSeqPos  seq_pos,
ESearchDirection  dir = eNone,
bool  try_reverse_dir = true 
) const

◆ GetSeqRange()

CAlnMap::TRange CAlnMap::GetSeqRange ( TNumrow  row) const
inline

Definition at line 684 of file alnmap.hpp.

References GetSeqStart(), GetSeqStop(), and row.

Referenced by s_MapSlaveFeatureToMaster().

◆ GetSeqStart()

TSeqPos CAlnMap::GetSeqStart ( TNumrow  row) const
inline

◆ GetSeqStop()

TSeqPos CAlnMap::GetSeqStop ( TNumrow  row) const
inline

◆ GetStart()

TSignedSeqPos CAlnMap::GetStart ( TNumrow  row,
TNumseg  seg,
int  offset = 0 
) const
inline

◆ GetStop()

TSignedSeqPos CAlnMap::GetStop ( TNumrow  row,
TNumseg  seg,
int  offset = 0 
) const
inline

◆ GetTypeAtAlnPos()

CAlnMap::TSegTypeFlags CAlnMap::GetTypeAtAlnPos ( TNumrow  row,
TSeqPos  aln_pos 
) const
inline

Definition at line 730 of file alnmap.hpp.

References GetSeg(), GetSegType(), and row.

◆ GetWidth()

int CAlnMap::GetWidth ( TNumrow  row) const
inline

◆ IsNegativeStrand()

bool CAlnMap::IsNegativeStrand ( TNumrow  row) const
inline

Definition at line 607 of file alnmap.hpp.

References IsPositiveStrand(), and row.

Referenced by s_MapSlaveFeatureToMaster().

◆ IsPositiveStrand()

bool CAlnMap::IsPositiveStrand ( TNumrow  row) const
inline

◆ IsSetAnchor()

bool CAlnMap::IsSetAnchor ( void  ) const
inline

◆ IsTypeInsert()

bool CAlnMap::IsTypeInsert ( TSegTypeFlags  type)
inlinestatic

Definition at line 723 of file alnmap.hpp.

References fInsert.

Referenced by CAlnMapPrinter::Chunks(), and CAlnMapPrinter::Segments().

◆ operator=()

CAlnMap& CAlnMap::operator= ( const CAlnMap value)
protected

◆ SetAnchor()

void CAlnMap::SetAnchor ( TNumrow  anchor)

◆ StrandSign()

int CAlnMap::StrandSign ( TNumrow  row) const
inline

◆ UnsetAnchor()

void CAlnMap::UnsetAnchor ( void  )

Definition at line 63 of file alnmap.cpp.

References m_AlnSegIdx, m_Anchor, m_NumSegWithOffsets, m_RawSegTypes, and x_CreateAlnStarts().

Referenced by SetAnchor().

◆ x_CompareAdjacentSegTypes()

bool CAlnMap::x_CompareAdjacentSegTypes ( TSegTypeFlags  left_type,
TSegTypeFlags  right_type,
TGetChunkFlags  flags 
) const
inlineprotected

Definition at line 1112 of file alnmap.cpp.

References flags.

Referenced by x_GetChunks().

◆ x_CreateAlnStarts()

void CAlnMap::x_CreateAlnStarts ( void  )
protected

Definition at line 49 of file alnmap.cpp.

References GetNumSegs(), i, len, m_AlnStarts, and m_Lens.

Referenced by CAlnMap(), and UnsetAnchor().

◆ x_FindClosestSeqPos()

TSignedSeqPos CAlnMap::x_FindClosestSeqPos ( TNumrow  row,
TNumseg  seg,
ESearchDirection  dir,
bool  try_reverse_dir 
) const
protected

◆ x_GetChunks()

void CAlnMap::x_GetChunks ( CAlnChunkVec vec,
TNumrow  row,
TNumseg  left_seg,
TNumseg  right_seg,
TGetChunkFlags  flags 
) const
protected

◆ x_GetLen()

TSeqPos CAlnMap::x_GetLen ( TNumrow  row,
TNumseg  seg 
) const
inlineprotected

◆ x_GetRawSegFromSeg()

CAlnMap::TNumseg CAlnMap::x_GetRawSegFromSeg ( TNumseg  seg) const
inlineprotected

◆ x_GetRawSegType()

CAlnMap::TSegTypeFlags CAlnMap::x_GetRawSegType ( TNumrow  row,
TNumseg  seg,
int  hint_idx = -1 
) const
inlineprotected

◆ x_GetRawSegTypes()

CAlnMap::TRawSegTypes & CAlnMap::x_GetRawSegTypes ( ) const
inlineprotected

Definition at line 699 of file alnmap.hpp.

References m_NumRows, m_NumSegs, and m_RawSegTypes.

Referenced by x_GetRawSegType(), and x_SetRawSegTypes().

◆ x_GetRawStart()

TSignedSeqPos CAlnMap::x_GetRawStart ( TNumrow  row,
TNumseg  seg 
) const
inlineprotected

Definition at line 554 of file alnmap.hpp.

References m_NumRows, m_Starts, and row.

Referenced by GetSeqChunks(), x_FindClosestSeqPos(), and x_GetRawStop().

◆ x_GetRawStop()

TSignedSeqPos CAlnMap::x_GetRawStop ( TNumrow  row,
TNumseg  seg 
) const
inlineprotected

Definition at line 584 of file alnmap.hpp.

References row, x_GetLen(), and x_GetRawStart().

Referenced by GetSeqChunks(), and x_FindClosestSeqPos().

◆ x_GetSegFromRawSeg()

CAlnMap::CNumSegWithOffset CAlnMap::x_GetSegFromRawSeg ( TNumseg  seg) const
inlineprotected

Definition at line 539 of file alnmap.hpp.

References IsSetAnchor(), and m_NumSegWithOffsets.

Referenced by GetAlnPosFromSeqPos(), and CAlnMap::CAlnChunkVec::operator[]().

◆ x_GetSeqLeftSeg()

const CAlnMap::TNumseg & CAlnMap::x_GetSeqLeftSeg ( TNumrow  row) const
protected

◆ x_GetSeqRightSeg()

const CAlnMap::TNumseg & CAlnMap::x_GetSeqRightSeg ( TNumrow  row) const
protected

◆ x_Init()

void CAlnMap::x_Init ( void  )
protected

Definition at line 42 of file alnmap.cpp.

References GetNumRows(), m_SeqLeftSegs, and m_SeqRightSegs.

Referenced by CAlnMap().

◆ x_SetRawSegType()

CAlnMap::TSegTypeFlags CAlnMap::x_SetRawSegType ( TNumrow  row,
TNumseg  seg 
) const
protected

◆ x_SetRawSegTypes()

void CAlnMap::x_SetRawSegTypes ( TNumrow  row) const
protected

◆ x_SkipType()

bool CAlnMap::x_SkipType ( TSegTypeFlags  type,
TGetChunkFlags  flags 
) const
inlineprotected

Friends And Related Function Documentation

◆ CAlnChunkVec::operator[]

CConstRef<CAlnChunk> CAlnChunkVec::operator[] ( TNumchunk  i) const
friend

Member Data Documentation

◆ m_AlnSegIdx

vector<TNumseg> CAlnMap::m_AlnSegIdx
protected

◆ m_AlnStarts

CDense_seg::TStarts CAlnMap::m_AlnStarts
protected

◆ m_Anchor

TNumrow CAlnMap::m_Anchor
protected

◆ m_DS

CConstRef<CDense_seg> CAlnMap::m_DS
protected

Definition at line 369 of file alnmap.hpp.

Referenced by CAlnVec::CreateConsensus(), and GetDenseg().

◆ m_Ids

const CDense_seg::TIds& CAlnMap::m_Ids
protected

Definition at line 372 of file alnmap.hpp.

Referenced by CreateAlignFromRange(), CAlnVec::CreateConsensus(), and GetSeqId().

◆ m_Lens

const CDense_seg::TLens& CAlnMap::m_Lens
protected

◆ m_NumRows

TNumrow CAlnMap::m_NumRows
protected

◆ m_NumSegs

TNumseg CAlnMap::m_NumSegs
protected

◆ m_NumSegWithOffsets

vector<CNumSegWithOffset> CAlnMap::m_NumSegWithOffsets
protected

Definition at line 383 of file alnmap.hpp.

Referenced by SetAnchor(), UnsetAnchor(), and x_GetSegFromRawSeg().

◆ m_RawSegTypes

TRawSegTypes* CAlnMap::m_RawSegTypes
mutableprotected

Definition at line 384 of file alnmap.hpp.

Referenced by SetAnchor(), UnsetAnchor(), x_GetRawSegTypes(), and ~CAlnMap().

◆ m_Scores

const CDense_seg::TScores& CAlnMap::m_Scores
protected

Definition at line 376 of file alnmap.hpp.

◆ m_SeqLeftSegs

vector<TNumseg> CAlnMap::m_SeqLeftSegs
mutableprotected

Definition at line 380 of file alnmap.hpp.

Referenced by x_GetSeqLeftSeg(), and x_Init().

◆ m_SeqRightSegs

vector<TNumseg> CAlnMap::m_SeqRightSegs
mutableprotected

Definition at line 381 of file alnmap.hpp.

Referenced by x_GetSeqRightSeg(), and x_Init().

◆ m_Starts

const CDense_seg::TStarts& CAlnMap::m_Starts
protected

◆ m_Strands

const CDense_seg::TStrands& CAlnMap::m_Strands
protected

Definition at line 375 of file alnmap.hpp.

Referenced by CreateAlignFromRange(), CAlnVec::CreateConsensus(), and IsPositiveStrand().

◆ m_Widths

const CDense_seg::TWidths& CAlnMap::m_Widths
protected

Definition at line 377 of file alnmap.hpp.

Referenced by CreateAlignFromRange(), and GetWidth().


The documentation for this class was generated from the following files:
Modified on Mon May 27 04:35:02 2024 by modify_doxy.py rev. 669887