NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | Friends | List of all members
CSparseAln Class Reference

Search Toolkit Book for CSparseAln

Sparse alignment. More...

#include <objtools/alnmgr/sparse_aln.hpp>

+ Inheritance diagram for CSparseAln:
+ Collaboration diagram for CSparseAln:

Public Types

enum  EConstants { kDefaultGenCode = 1 }
 
typedef CPairwiseAln::TRng TRng
 
typedef CPairwiseAln::TAlnRng TAlnRng
 
typedef CPairwiseAln::TAlnRngColl TAlnRngColl
 
typedef CAnchoredAln::TDim TDim
 Synonym of TNumrow. More...
 
typedef CSeq_data::E_Choice TCoding
 
typedef pair< int, intTFrames
 Get start and stop frames for the selected row/range. More...
 
- 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue 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

 CSparseAln (const CAnchoredAln &anchored_aln, objects::CScope &scope)
 Constructor. More...
 
virtual ~CSparseAln (void)
 Destructor. More...
 
void SetGapChar (TResidue gap_char)
 Gap character modifier. More...
 
CRef< objects::CScope > GetScope (void) const
 Scope accessor. More...
 
TDim GetDim (void) const
 Alignment dimension (number of sequence rows in the alignment) More...
 
TNumrow GetNumRows (void) const
 Synonym of the above. More...
 
const objects::CSeq_id & GetSeqId (TNumrow row) const
 Get seq-id for the row. More...
 
TRng GetAlnRange (void) const
 Get whole alignment range. More...
 
const TAlnRngCollGetAlignCollection (TNumrow row)
 Get pairwise alignment for the row. More...
 
bool IsSetAnchor (void) const
 Check if anchor is set - always true for sparse alignments. More...
 
TNumrow GetAnchor (void) const
 Get anchor row index. More...
 
TSignedRange GetSeqAlnRange (TNumrow row) const
 Get sequence range in alignment coords (strand ignored). More...
 
TSignedSeqPos GetSeqAlnStart (TNumrow row) const
 
TSignedSeqPos GetSeqAlnStop (TNumrow row) const
 
TRange GetSeqRange (TNumrow row) const
 Get sequence range in sequence coords. More...
 
TSeqPos GetSeqStart (TNumrow row) const
 
TSeqPos GetSeqStop (TNumrow row) const
 
bool IsPositiveStrand (TNumrow row) const
 Check direction of the row. More...
 
bool IsNegativeStrand (TNumrow row) const
 
TSignedSeqPos GetAlnPosFromSeqPos (TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const
 Map sequence position to alignment coordinates. More...
 
TSignedSeqPos GetSeqPosFromAlnPos (TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const
 
TCoding GetNaCoding (void) const
 Get sequence coding for nucleotides. More...
 
TCoding GetAaCoding (void) const
 Get sequence coding for proteins. More...
 
void SetNaCoding (TCoding coding)
 Set sequence coding for nucleotides. If not set, Iupacna coding is used. More...
 
void SetAaCoding (TCoding coding)
 Set sequence coding for proteins. If not set, Iupacaa coding is used. More...
 
stringGetSeqString (TNumrow row, string &buffer, TSeqPos seq_from, TSeqPos seq_to, bool force_translation=false) const
 Fetch sequence data for the given row and range. More...
 
stringGetSeqString (TNumrow row, string &buffer, const TRange &rq_seq_rng, bool force_translation=false) const
 Fetch sequence data for the given row and range. More...
 
stringGetAlnSeqString (TNumrow row, string &buffer, const TSignedRange &rq_aln_rng, bool force_translation=false) const
 Fetch alignment sequence data. More...
 
const objects::CBioseq_Handle & GetBioseqHandle (TNumrow row) const
 Get bioseq handle for the row. More...
 
virtual IAlnSegmentIteratorCreateSegmentIterator (TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flags) const
 Create segment iterator. More...
 
bool IsTranslated (void) const
 Wheather the alignment is translated (heterogenous), e.g. nuc-prot. More...
 
int GetBaseWidth (TNumrow row) const
 Get base width for the sequence (1 for nucleotides, 3 for proteins). More...
 
TSignedSeqPos AlnPosToNativeSeqPos (TNumrow row, TSignedSeqPos aln_pos) const
 Convert alignment (genomic) coordinate on the selected row to real sequence position. More...
 
int AlnPosToNativeFrame (TNumrow row, TSignedSeqPos aln_pos) const
 For protein sequences get frame for the specified coordinated. More...
 
TSignedSeqPos NativeSeqPosToAlnPos (TNumrow row, TSignedSeqPos seq_pos, int frame=0) const
 Convert sequence position to alignment (genomic) coordinate. More...
 
template<class _TRange >
_TRange AlnRangeToNativeSeqRange (TNumrow row, _TRange aln_range) const
 Convert alignment range (genomic coordinates) on the selected row to real sequence range. More...
 
template<class _TRange >
TFrames AlnRangeToNativeFrames (TNumrow row, _TRange aln_range) const
 
template<class _TRange >
_TRange NativeSeqRangeToAlnRange (TNumrow row, _TRange seq_range, TFrames frames=TFrames(0, 0)) const
 Convert sequence range to alignment range (genomic coordinates). More...
 
- 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 void TranslateNAToAA (const string &na, string &aa, int gen_code=kDefaultGenCode)
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 CAnchoredAln::TPairwiseAlnVector TPairwiseAlnVector
 

Protected Member Functions

void x_Build (const CAnchoredAln &src_align)
 
CSeqVectorx_GetSeqVector (TNumrow row) const
 
int x_GetGenCode (TNumrow row) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

CRef< CAnchoredAlnm_Aln
 
CRef< objects::CScope > m_Scope
 
TRng m_FirstRange
 
vector< TRngm_SecondRanges
 
TResidue m_GapChar
 
vector< objects::CBioseq_Handle > m_BioseqHandles
 
vector< CRef< CSeqVector > > m_SeqVectors
 
TCoding m_NaCoding
 
TCoding m_AaCoding
 
bool m_AnchorDirect
 

Friends

class CSparse_CI
 

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

Sparse alignment.

Definition at line 50 of file sparse_aln.hpp.

Member Typedef Documentation

Definition at line 54 of file sparse_aln.hpp.

Definition at line 55 of file sparse_aln.hpp.

Definition at line 133 of file sparse_aln.hpp.

Synonym of TNumrow.

Definition at line 56 of file sparse_aln.hpp.

typedef pair<int, int> CSparseAln::TFrames

Get start and stop frames for the selected row/range.

0 - no frame (native coordinates are genomic) 1..3 - frame value for protein coordinates

Definition at line 275 of file sparse_aln.hpp.

Definition at line 308 of file sparse_aln.hpp.

Definition at line 53 of file sparse_aln.hpp.

Member Enumeration Documentation

Enumerator
kDefaultGenCode 

Definition at line 216 of file sparse_aln.hpp.

Constructor & Destructor Documentation

CSparseAln::CSparseAln ( const CAnchoredAln anchored_aln,
objects::CScope &  scope 
)

Constructor.

Parameters
anchored_alnInput CAnchoredAln object. Should be built using BuildAln function for the alignment coordinates to be correct.
scopeCScope used to fetch sequence data.
See also
BuildAln

Definition at line 52 of file sparse_aln.cpp.

References x_Build().

CSparseAln::~CSparseAln ( void  )
virtual

Destructor.

Definition at line 64 of file sparse_aln.cpp.

Member Function Documentation

int CSparseAln::AlnPosToNativeFrame ( TNumrow  row,
TSignedSeqPos  aln_pos 
) const
inline

For protein sequences get frame for the specified coordinated.

For genomic sequences always returns 0.

Definition at line 242 of file sparse_aln.hpp.

References GetBaseWidth().

TSignedSeqPos CSparseAln::AlnPosToNativeSeqPos ( TNumrow  row,
TSignedSeqPos  aln_pos 
) const
inline

Convert alignment (genomic) coordinate on the selected row to real sequence position.

Definition at line 235 of file sparse_aln.hpp.

References GetBaseWidth().

template<class _TRange >
TFrames CSparseAln::AlnRangeToNativeFrames ( TNumrow  row,
_TRange  aln_range 
) const
inline

Definition at line 277 of file sparse_aln.hpp.

References GetBaseWidth().

Referenced by DumpSparseAln(), and CAlnTestApp::Run().

template<class _TRange >
_TRange CSparseAln::AlnRangeToNativeSeqRange ( TNumrow  row,
_TRange  aln_range 
) const
inline

Convert alignment range (genomic coordinates) on the selected row to real sequence range.

NOTE: Need to use template since there are many range types: TRng, TAlnRng, TRange, TSignedRange etc.

Definition at line 265 of file sparse_aln.hpp.

References GetBaseWidth().

Referenced by CheckSparseAln(), DumpSparseAln(), and CAlnTestApp::Run().

IAlnSegmentIterator * CSparseAln::CreateSegmentIterator ( TNumrow  row,
const TSignedRange range,
IAlnSegmentIterator::EFlags  flags 
) const
virtual
TCoding CSparseAln::GetAaCoding ( void  ) const
inline

Get sequence coding for proteins.

Definition at line 137 of file sparse_aln.hpp.

References m_AaCoding.

const CSparseAln::TAlnRngColl & CSparseAln::GetAlignCollection ( TNumrow  row)

Get pairwise alignment for the row.

Definition at line 257 of file sparse_aln.cpp.

References _ASSERT, GetDim(), CAnchoredAln::GetPairwiseAlns(), and m_Aln.

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

Map sequence position to alignment coordinates.

Parameters
rowAlignment row where the input position is defined.
seq_posInput position
dirIn case the input position can not be mapped to the alignment coordinates (e.g. the position is inside an unaligned range), try to search for the neares alignment position in the specified direction.
try_reverse_dirNot implemented

Definition at line 373 of file sparse_aln.cpp.

References _ASSERT, GetCollectionSearchDirection(), GetDim(), CAnchoredAln::GetPairwiseAlns(), and m_Aln.

Referenced by CSparseMultiDataSource::GetAlnFromSeq(), CSparseRowHandle::GetAlnPosFromSeqPos(), CSparseAlnGraphicDataSource::GetAlnPosFromSeqPos(), CSparseMultiDataSource::GetAlnPosFromSeqPos(), CSparseAlnGraphicDataSource::GetSeqPosFromSeqPos(), and CValidError_align::x_ValidateAlignPercentIdentity().

CSparseAln::TRng CSparseAln::GetAlnRange ( void  ) const
string & CSparseAln::GetAlnSeqString ( TNumrow  row,
string buffer,
const TSignedRange rq_aln_rng,
bool  force_translation = false 
) const
TNumrow CSparseAln::GetAnchor ( void  ) const
inline
int CSparseAln::GetBaseWidth ( TNumrow  row) const
inline
const CBioseq_Handle & CSparseAln::GetBioseqHandle ( TNumrow  row) const
CSparseAln::TDim CSparseAln::GetDim ( void  ) const
TCoding CSparseAln::GetNaCoding ( void  ) const
inline

Get sequence coding for nucleotides.

Definition at line 135 of file sparse_aln.hpp.

References m_NaCoding.

TNumrow CSparseAln::GetNumRows ( void  ) const
inline
CRef< CScope > CSparseAln::GetScope ( void  ) const

Scope accessor.

Definition at line 250 of file sparse_aln.cpp.

References m_Scope.

Referenced by CSparseMultiDataSource::GetAlignType().

CSparseAln::TSignedRange CSparseAln::GetSeqAlnRange ( TNumrow  row) const
TSignedSeqPos CSparseAln::GetSeqAlnStart ( TNumrow  row) const
TSignedSeqPos CSparseAln::GetSeqAlnStop ( TNumrow  row) const
const CSeq_id & CSparseAln::GetSeqId ( TNumrow  row) const
TSignedSeqPos CSparseAln::GetSeqPosFromAlnPos ( TNumrow  for_row,
TSeqPos  aln_pos,
ESearchDirection  dir = eNone,
bool  try_reverse_dir = true 
) const
CSparseAln::TRange CSparseAln::GetSeqRange ( TNumrow  row) const

Get sequence range in sequence coords.

Definition at line 306 of file sparse_aln.cpp.

References _ASSERT, GetDim(), GetSeqStart(), and GetSeqStop().

Referenced by CheckSparseAln(), DumpSparseAln(), and GetSeqString().

TSeqPos CSparseAln::GetSeqStart ( TNumrow  row) const
TSeqPos CSparseAln::GetSeqStop ( TNumrow  row) const
string & CSparseAln::GetSeqString ( TNumrow  row,
string buffer,
TSeqPos  seq_from,
TSeqPos  seq_to,
bool  force_translation = false 
) const

Fetch sequence data for the given row and range.

Parameters
rowAlignment row to fetch sequence for.
bufferOutput buffer.
seq_fromStart sequence position.
seq_toEnd sequence position.
force_translationForce nucleotide to protein sequence translation.
Returns
Reference to the output buffer.

Definition at line 496 of file sparse_aln.cpp.

Referenced by CheckSparseAln(), DumpSparseAln(), CSparseRowHandle::GetSeqString(), and CSparseMultiDataSource::GetSeqString().

string & CSparseAln::GetSeqString ( TNumrow  row,
string buffer,
const TRange rq_seq_rng,
bool  force_translation = false 
) const

Fetch sequence data for the given row and range.

Parameters
rowAlignment row to fetch sequence for.
bufferOutput buffer.
seq_rngSequence range.
force_translationForce nucleotide to protein sequence translation.
Returns
Reference to the output buffer.

Definition at line 505 of file sparse_aln.cpp.

References _ASSERT, buffer, GetDim(), COpenRange< Position >::GetFrom(), CAnchoredAln::GetPairwiseAlns(), CSeqVector::GetSeqData(), GetSeqRange(), COpenRange< Position >::GetToOpen(), IsPositiveStrand(), COpenRange< Position >::IsWhole(), m_Aln, m_GapChar, CSeqVector::size(), size, TranslateNAToAA(), x_GetGenCode(), and x_GetSeqVector().

bool CSparseAln::IsNegativeStrand ( TNumrow  row) const
bool CSparseAln::IsPositiveStrand ( TNumrow  row) const
bool CSparseAln::IsSetAnchor ( void  ) const
inline

Check if anchor is set - always true for sparse alignments.

Definition at line 92 of file sparse_aln.hpp.

Referenced by CSparseMultiDataSource::IsSetAnchor().

bool CSparseAln::IsTranslated ( void  ) const

Wheather the alignment is translated (heterogenous), e.g. nuc-prot.

Definition at line 329 of file sparse_aln.cpp.

References GetDim(), CAnchoredAln::GetPairwiseAlns(), and m_Aln.

TSignedSeqPos CSparseAln::NativeSeqPosToAlnPos ( TNumrow  row,
TSignedSeqPos  seq_pos,
int  frame = 0 
) const
inline

Convert sequence position to alignment (genomic) coordinate.

Optional frame can be used with protein positions.

Definition at line 250 of file sparse_aln.hpp.

References GetBaseWidth().

template<class _TRange >
_TRange CSparseAln::NativeSeqRangeToAlnRange ( TNumrow  row,
_TRange  seq_range,
TFrames  frames = TFrames(0, 0) 
) const
inline

Convert sequence range to alignment range (genomic coordinates).

Optional frames argument can be provided for protein ranges. NOTE: Need to use template since there are many range types: TRng, TAlnRng, TRange, TSignedRange etc.

Definition at line 290 of file sparse_aln.hpp.

References GetBaseWidth().

void CSparseAln::SetAaCoding ( TCoding  coding)
inline

Set sequence coding for proteins. If not set, Iupacaa coding is used.

Definition at line 141 of file sparse_aln.hpp.

References m_AaCoding.

void CSparseAln::SetGapChar ( TResidue  gap_char)

Gap character modifier.

Definition at line 244 of file sparse_aln.cpp.

References m_GapChar.

Referenced by CSparseMultiDataSource::SetGapChar(), CTreeBuilderJob::x_CreateProjectItems(), and CTreeBuilderJob::x_Divergence().

void CSparseAln::SetNaCoding ( TCoding  coding)
inline

Set sequence coding for nucleotides. If not set, Iupacna coding is used.

Definition at line 139 of file sparse_aln.hpp.

References m_NaCoding.

void CSparseAln::TranslateNAToAA ( const string na,
string aa,
int  gen_code = kDefaultGenCode 
)
static
void CSparseAln::x_Build ( const CAnchoredAln src_align)
protected

Definition at line 99 of file sparse_aln.cpp.

References _ASSERT, CAlignRangeCollection< TAlnRange >::begin(), COpenRange< Position >::CombineWith(), SGapRange::direct, CAlignRangeCollection< TAlnRange >::empty(), CAlignRangeCollection< TAlnRange >::end(), CAlignRangeCollection< TAlnRange >::fInvalid, CAlignRangeCollection< TAlnRange >::fOverlap, SGapRange::from, CAlignRangeCollection< TAlnRange >::fUnsorted, CAnchoredAln::GetAnchorRow(), CAnchoredAln::GetDim(), CAlignRange< Position >::GetFirstFrom(), CPairwiseAln::GetFirstId(), CAlignRange< Position >::GetFirstToOpen(), CAlignRangeCollection< TAlnRange >::GetFlags(), CAlignRangeCollection< TAlnRange >::GetInsertions(), CAlignRange< Position >::GetLength(), CAnchoredAln::GetPairwiseAlns(), CAnchoredAln::GetScore(), CAlignRange< Position >::GetSecondFrom(), CPairwiseAln::GetSecondId(), CAlignRange< Position >::GetSecondToOpen(), i, SGapRange::idx, CAlignRange< Position >::IsDirect(), CAlignRange< Position >::IsFirstDirect(), SGapRange::len, m_Aln, m_AnchorDirect, m_BioseqHandles, m_FirstRange, m_SecondRanges, m_SeqVectors, NON_CONST_ITERATE, CAlignRangeCollection< TAlnRange >::push_back(), CRef< C, Locker >::Reset(), SGapRange::row, SGapRange::second_from, CAnchoredAln::SetAnchorRow(), CAnchoredAln::SetDim(), CAlignRange< Position >::SetDirect(), CAlignRange< Position >::SetFirstDirect(), CAlignRange< Position >::SetFirstFrom(), CAlignRange< Position >::SetLength(), CAnchoredAln::SetPairwiseAlns(), CAnchoredAln::SetScore(), CAlignRange< Position >::SetSecondFrom(), SGapRange::shift, and CAlignRangeCollExtender< TColl >::UpdateIndex().

Referenced by CSparseAln().

int CSparseAln::x_GetGenCode ( TNumrow  row) const
protected
CSeqVector & CSparseAln::x_GetSeqVector ( TNumrow  row) const
protected

Friends And Related Function Documentation

friend class CSparse_CI
friend

Definition at line 302 of file sparse_aln.hpp.

Referenced by CreateSegmentIterator().

Member Data Documentation

TCoding CSparseAln::m_AaCoding
protected

Definition at line 319 of file sparse_aln.hpp.

Referenced by GetAaCoding(), SetAaCoding(), and x_GetSeqVector().

CRef<CAnchoredAln> CSparseAln::m_Aln
protected
bool CSparseAln::m_AnchorDirect
protected

Definition at line 321 of file sparse_aln.hpp.

Referenced by GetAlnSeqString(), IsNegativeStrand(), IsPositiveStrand(), and x_Build().

vector<objects::CBioseq_Handle> CSparseAln::m_BioseqHandles
mutableprotected

Definition at line 315 of file sparse_aln.hpp.

Referenced by GetBioseqHandle(), and x_Build().

TRng CSparseAln::m_FirstRange
protected

Definition at line 312 of file sparse_aln.hpp.

Referenced by GetAlnRange(), and x_Build().

TResidue CSparseAln::m_GapChar
protected

Definition at line 314 of file sparse_aln.hpp.

Referenced by GetAlnSeqString(), GetSeqString(), and SetGapChar().

TCoding CSparseAln::m_NaCoding
protected

Definition at line 318 of file sparse_aln.hpp.

Referenced by GetNaCoding(), SetNaCoding(), and x_GetSeqVector().

CRef<objects::CScope> CSparseAln::m_Scope
mutableprotected

Definition at line 311 of file sparse_aln.hpp.

Referenced by GetBioseqHandle(), and GetScope().

vector<TRng> CSparseAln::m_SecondRanges
protected

Definition at line 313 of file sparse_aln.hpp.

Referenced by GetSeqStart(), GetSeqStop(), and x_Build().

vector<CRef<CSeqVector> > CSparseAln::m_SeqVectors
mutableprotected

Definition at line 316 of file sparse_aln.hpp.

Referenced by x_Build(), and x_GetSeqVector().


The documentation for this class was generated from the following files:
Modified on Sun Jun 25 17:47:18 2017 by modify_doxy.py rev. 533848