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CAlnVec Class Reference

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#include <objtools/alnmgr/alnvec.hpp>

+ Inheritance diagram for CAlnVec:
+ Collaboration diagram for CAlnVec:

Public Types

enum  EConstants { kDefaultGenCode = 1 }
 
typedef CSeqVector::TResidue TResidue
 
typedef vector< intTResidueCount
 
typedef CSeq_data::E_Choice TCoding
 
- Public Types inherited from CAlnMap
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

 CAlnVec (const CDense_seg &ds, CScope &scope)
 
 CAlnVec (const CDense_seg &ds, TNumrow anchor, CScope &scope)
 
 ~CAlnVec (void)
 
CScopeGetScope (void) const
 
stringGetSeqString (string &buffer, TNumrow row, TSeqPos seq_from, TSeqPos seq_to) const
 
stringGetSeqString (string &buffer, TNumrow row, const CAlnMap::TRange &seq_rng) const
 
stringGetSegSeqString (string &buffer, TNumrow row, TNumseg seg, TNumseg offset=0) const
 
stringGetAlnSeqString (string &buffer, TNumrow row, const CAlnMap::TSignedRange &aln_rng) const
 
stringGetColumnVector (string &buffer, TSeqPos aln_pos, TResidueCount *residue_count=0, bool gaps_in_count=false) const
 
stringGetWholeAlnSeqString (TNumrow row, string &buffer, TSeqPosList *insert_aln_starts=0, TSeqPosList *insert_starts=0, TSeqPosList *insert_lens=0, unsigned int scrn_width=0, TSeqPosList *scrn_lefts=0, TSeqPosList *scrn_rights=0) const
 
const CBioseq_HandleGetBioseqHandle (TNumrow row) const
 
TResidue GetResidue (TNumrow row, TSeqPos aln_pos) const
 
TCoding GetNaCoding (void) const
 
TCoding GetAaCoding (void) const
 
void SetNaCoding (TCoding coding)
 
void SetAaCoding (TCoding coding)
 
void SetGapChar (TResidue gap_char)
 
void UnsetGapChar ()
 
bool IsSetGapChar () const
 
TResidue GetGapChar (TNumrow row) const
 
void SetEndChar (TResidue gap_char)
 
void UnsetEndChar ()
 
bool IsSetEndChar () const
 
TResidue GetEndChar () const
 
void SetGenCode (int gen_code, TNumrow row=-1)
 
void UnsetGenCode ()
 
bool IsSetGenCode () const
 
int GetGenCode (TNumrow row) const
 
CRef< CDense_segCreateConsensus (int &consensus_row) const
 
CRef< CDense_segCreateConsensus (int &consensus_row, const CSeq_id &consensus_id) const
 
CRef< CDense_segCreateConsensus (int &consensus_row, CBioseq &consensus_seq, const CSeq_id &consensus_id, vector< string > *consens=NULL) const
 
int CalculateScore (TNumrow row1, TNumrow row2) const
 
int CalculatePercentIdentity (TSeqPos aln_pos) const
 
void RetrieveSegmentSequences (size_t segment, vector< string > &segs) const
 
- Public Member Functions inherited from CAlnMap
 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 void TranslateNAToAA (const string &na, string &aa, int gen_code=kDefaultGenCode)
 
static int CalculateScore (const string &s1, const string &s2, bool s1_is_prot, bool s2_is_prot, int gen_code1=kDefaultGenCode, int gen_code2=kDefaultGenCode)
 
static unsigned char FromIupac (unsigned char c)
 
static unsigned char ToIupac (unsigned char c)
 
static void TransposeSequences (vector< string > &segs)
 
static void CollectNucleotideFrequences (const string &col, int base_count[], int numBases)
 
static void CollectProteinFrequences (const string &col, int base_count[], int numBases)
 
- Static Public Member Functions inherited from CAlnMap
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 Member Functions

CSeqVectorx_GetSeqVector (TNumrow row) const
 
CSeqVectorx_GetConsensusSeqVector (void) const
 
void CreateConsensus (vector< string > &consens) const
 
- Protected Member Functions inherited from CAlnMap
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

CRef< CScopem_Scope
 
TBioseqHandleCache m_BioseqHandlesCache
 
TSeqVectorCache m_SeqVectorCache
 
- Protected Attributes inherited from CAlnMap
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 CAlnMap Tparent
 
typedef map< TNumrow, CBioseq_HandleTBioseqHandleCache
 
typedef map< TNumrow, CRef< CSeqVector > > TSeqVectorCache
 

Private Member Functions

 CAlnVec (const CAlnVec &)
 
CAlnVecoperator= (const CAlnVec &)
 

Private Attributes

TResidue m_GapChar
 
bool m_set_GapChar
 
TResidue m_EndChar
 
bool m_set_EndChar
 
vector< intm_GenCodes
 
TCoding m_NaCoding
 
TCoding m_AaCoding
 

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...
 
- Protected Types inherited from CAlnMap
typedef vector< TSegTypeFlagsTRawSegTypes
 

Detailed Description

Definition at line 47 of file alnvec.hpp.

Member Typedef Documentation

◆ TBioseqHandleCache

Definition at line 50 of file alnvec.hpp.

◆ TCoding

Definition at line 110 of file alnvec.hpp.

◆ Tparent

typedef CAlnMap CAlnVec::Tparent
private

Definition at line 49 of file alnvec.hpp.

◆ TResidue

Definition at line 54 of file alnvec.hpp.

◆ TResidueCount

typedef vector<int> CAlnVec::TResidueCount

Definition at line 55 of file alnvec.hpp.

◆ TSeqVectorCache

Definition at line 51 of file alnvec.hpp.

Member Enumeration Documentation

◆ EConstants

Enumerator
kDefaultGenCode 

Definition at line 129 of file alnvec.hpp.

Constructor & Destructor Documentation

◆ CAlnVec() [1/3]

CAlnVec::CAlnVec ( const CDense_seg ds,
CScope scope 
)

Definition at line 59 of file alnvec.cpp.

◆ CAlnVec() [2/3]

CAlnVec::CAlnVec ( const CDense_seg ds,
TNumrow  anchor,
CScope scope 
)

Definition at line 70 of file alnvec.cpp.

◆ ~CAlnVec()

CAlnVec::~CAlnVec ( void  )

Definition at line 81 of file alnvec.cpp.

◆ CAlnVec() [3/3]

CAlnVec::CAlnVec ( const CAlnVec )
private

Member Function Documentation

◆ CalculatePercentIdentity()

int CAlnVec::CalculatePercentIdentity ( TSeqPos  aln_pos) const

Definition at line 1051 of file alnvec.cpp.

References column, GetColumnVector(), ITERATE, CAlnMap::m_NumRows, and max().

Referenced by CAlnVwrApp::View8().

◆ CalculateScore() [1/2]

int CAlnVec::CalculateScore ( const string s1,
const string s2,
bool  s1_is_prot,
bool  s2_is_prot,
int  gen_code1 = kDefaultGenCode,
int  gen_code2 = kDefaultGenCode 
)
static

◆ CalculateScore() [2/2]

int CAlnVec::CalculateScore ( TNumrow  row1,
TNumrow  row2 
) const

◆ CollectNucleotideFrequences()

void CAlnVec::CollectNucleotideFrequences ( const string col,
int  base_count[],
int  numBases 
)
static

Definition at line 558 of file alnvec.cpp.

References i.

Referenced by CreateConsensus().

◆ CollectProteinFrequences()

void CAlnVec::CollectProteinFrequences ( const string col,
int  base_count[],
int  numBases 
)
static

Definition at line 636 of file alnvec.cpp.

References i.

Referenced by CreateConsensus().

◆ CreateConsensus() [1/4]

CRef< CDense_seg > CAlnVec::CreateConsensus ( int consensus_row) const

Definition at line 817 of file alnvec.cpp.

Referenced by CreateConsensus().

◆ CreateConsensus() [2/4]

CRef< CDense_seg > CAlnVec::CreateConsensus ( int consensus_row,
CBioseq consensus_seq,
const CSeq_id consensus_id,
vector< string > *  consens = NULL 
) const

◆ CreateConsensus() [3/4]

CRef< CDense_seg > CAlnVec::CreateConsensus ( int consensus_row,
const CSeq_id consensus_id 
) const

◆ CreateConsensus() [4/4]

void CAlnVec::CreateConsensus ( vector< string > &  consens) const
protected

◆ FromIupac()

unsigned char CAlnVec::FromIupac ( unsigned char  c)
inlinestatic

Definition at line 444 of file alnvec.hpp.

Referenced by GetColumnVector(), and CTestSingleAln_All::RunTest().

◆ GetAaCoding()

TCoding CAlnVec::GetAaCoding ( void  ) const
inline

Definition at line 112 of file alnvec.hpp.

References m_AaCoding.

◆ GetAlnSeqString()

string & CAlnVec::GetAlnSeqString ( string buffer,
TNumrow  row,
const CAlnMap::TSignedRange aln_rng 
) const

◆ GetBioseqHandle()

const CBioseq_Handle & CAlnVec::GetBioseqHandle ( TNumrow  row) const

◆ GetColumnVector()

string & CAlnVec::GetColumnVector ( string buffer,
TSeqPos  aln_pos,
TResidueCount residue_count = 0,
bool  gaps_in_count = false 
) const

◆ GetEndChar()

CSeqVector::TResidue CAlnVec::GetEndChar ( ) const
inline

◆ GetGapChar()

CSeqVector::TResidue CAlnVec::GetGapChar ( TNumrow  row) const
inline

◆ GetGenCode()

int CAlnVec::GetGenCode ( TNumrow  row) const
inline

◆ GetNaCoding()

TCoding CAlnVec::GetNaCoding ( void  ) const
inline

Definition at line 111 of file alnvec.hpp.

References m_NaCoding.

◆ GetResidue()

CSeqVector::TResidue CAlnVec::GetResidue ( TNumrow  row,
TSeqPos  aln_pos 
) const
inline

◆ GetScope()

CScope & CAlnVec::GetScope ( void  ) const
inline

◆ GetSegSeqString()

string & CAlnVec::GetSegSeqString ( string buffer,
TNumrow  row,
TNumseg  seg,
TNumseg  offset = 0 
) const
inline

Definition at line 317 of file alnvec.hpp.

References buffer, GetSeqString(), CAlnMap::GetStart(), CAlnMap::GetStop(), offset, and row.

Referenced by s_ComputeTraceback(), and CAlnVwrApp::View7().

◆ GetSeqString() [1/2]

string & CAlnVec::GetSeqString ( string buffer,
TNumrow  row,
const CAlnMap::TRange seq_rng 
) const
inline

Definition at line 328 of file alnvec.hpp.

References buffer, CRange_Base::GetFrom(), GetSeqString(), CRange_Base::GetTo(), and row.

◆ GetSeqString() [2/2]

string & CAlnVec::GetSeqString ( string buffer,
TNumrow  row,
TSeqPos  seq_from,
TSeqPos  seq_to 
) const
inline

◆ GetWholeAlnSeqString()

string & CAlnVec::GetWholeAlnSeqString ( TNumrow  row,
string buffer,
TSeqPosList insert_aln_starts = 0,
TSeqPosList insert_starts = 0,
TSeqPosList insert_lens = 0,
unsigned int  scrn_width = 0,
TSeqPosList scrn_lefts = 0,
TSeqPosList scrn_rights = 0 
) const

◆ IsSetEndChar()

bool CAlnVec::IsSetEndChar ( ) const
inline

Definition at line 381 of file alnvec.hpp.

References m_set_EndChar.

Referenced by GetEndChar(), and CAlnVecPrinter::x_SetChars().

◆ IsSetGapChar()

bool CAlnVec::IsSetGapChar ( ) const
inline

Definition at line 352 of file alnvec.hpp.

References m_set_GapChar.

Referenced by GetGapChar(), and CAlnVecPrinter::x_SetChars().

◆ IsSetGenCode()

bool CAlnVec::IsSetGenCode ( ) const
inline

Definition at line 419 of file alnvec.hpp.

References m_GenCodes.

Referenced by GetGenCode(), and SetGenCode().

◆ operator=()

CAlnVec& CAlnVec::operator= ( const CAlnVec )
private

◆ RetrieveSegmentSequences()

void CAlnVec::RetrieveSegmentSequences ( size_t  segment,
vector< string > &  segs 
) const

◆ SetAaCoding()

void CAlnVec::SetAaCoding ( TCoding  coding)
inline

◆ SetEndChar()

void CAlnVec::SetEndChar ( TResidue  gap_char)
inline

◆ SetGapChar()

void CAlnVec::SetGapChar ( TResidue  gap_char)
inline

◆ SetGenCode()

void CAlnVec::SetGenCode ( int  gen_code,
TNumrow  row = -1 
)
inline

◆ SetNaCoding()

void CAlnVec::SetNaCoding ( TCoding  coding)
inline

Definition at line 113 of file alnvec.hpp.

References m_NaCoding.

◆ ToIupac()

unsigned char CAlnVec::ToIupac ( unsigned char  c)
inlinestatic

Definition at line 468 of file alnvec.hpp.

References data.

Referenced by CreateConsensus().

◆ TranslateNAToAA()

void CAlnVec::TranslateNAToAA ( const string na,
string aa,
int  gen_code = kDefaultGenCode 
)
static

◆ TransposeSequences()

void CAlnVec::TransposeSequences ( vector< string > &  segs)
static

Definition at line 527 of file alnvec.cpp.

References buf, NULL, and row.

Referenced by CreateConsensus().

◆ UnsetEndChar()

void CAlnVec::UnsetEndChar ( )
inline

Definition at line 375 of file alnvec.hpp.

References m_set_EndChar.

Referenced by CAlnVecPrinter::x_UnsetChars().

◆ UnsetGapChar()

void CAlnVec::UnsetGapChar ( )
inline

Definition at line 346 of file alnvec.hpp.

References m_set_GapChar.

Referenced by CAlnVecPrinter::x_UnsetChars().

◆ UnsetGenCode()

void CAlnVec::UnsetGenCode ( )
inline

Definition at line 413 of file alnvec.hpp.

References m_GenCodes.

Referenced by SetGenCode().

◆ x_GetConsensusSeqVector()

CSeqVector& CAlnVec::x_GetConsensusSeqVector ( void  ) const
protected

◆ x_GetSeqVector()

CSeqVector & CAlnVec::x_GetSeqVector ( TNumrow  row) const
protected

Member Data Documentation

◆ m_AaCoding

TCoding CAlnVec::m_AaCoding
private

Definition at line 197 of file alnvec.hpp.

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

◆ m_BioseqHandlesCache

TBioseqHandleCache CAlnVec::m_BioseqHandlesCache
mutableprotected

Definition at line 183 of file alnvec.hpp.

Referenced by GetBioseqHandle().

◆ m_EndChar

TResidue CAlnVec::m_EndChar
private

Definition at line 193 of file alnvec.hpp.

Referenced by GetEndChar(), and SetEndChar().

◆ m_GapChar

TResidue CAlnVec::m_GapChar
private

Definition at line 191 of file alnvec.hpp.

Referenced by GetGapChar(), and SetGapChar().

◆ m_GenCodes

vector<int> CAlnVec::m_GenCodes
private

Definition at line 195 of file alnvec.hpp.

Referenced by GetGenCode(), IsSetGenCode(), SetGenCode(), and UnsetGenCode().

◆ m_NaCoding

TCoding CAlnVec::m_NaCoding
private

Definition at line 196 of file alnvec.hpp.

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

◆ m_Scope

CRef<CScope> CAlnVec::m_Scope
mutableprotected

Definition at line 182 of file alnvec.hpp.

Referenced by GetScope().

◆ m_SeqVectorCache

TSeqVectorCache CAlnVec::m_SeqVectorCache
mutableprotected

Definition at line 184 of file alnvec.hpp.

Referenced by x_GetSeqVector().

◆ m_set_EndChar

bool CAlnVec::m_set_EndChar
private

Definition at line 194 of file alnvec.hpp.

Referenced by IsSetEndChar(), SetEndChar(), and UnsetEndChar().

◆ m_set_GapChar

bool CAlnVec::m_set_GapChar
private

Definition at line 192 of file alnvec.hpp.

Referenced by IsSetGapChar(), SetGapChar(), and UnsetGapChar().


The documentation for this class was generated from the following files:
Modified on Tue Jul 23 17:58:25 2024 by modify_doxy.py rev. 669887