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CBlastTabular Class Reference

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#include <algo/align/util/blast_tabular.hpp>

+ Inheritance diagram for CBlastTabular:
+ Collaboration diagram for CBlastTabular:

Public Types

typedef CAlignShadow TParent
 
typedef TParent::TCoord TCoord
 
typedef int(* SCORE_FUNC) (const CRef< objects::CSeq_id > &id)
 Construct CBlastTabular from m8 line, use score_func to select seq-id from FASTA-style ids. More...
 
- Public Types inherited from CAlignShadow
typedef CConstRef< objects::CSeq_id > TId
 
typedef TSeqPos TCoord
 
typedef string TTranscript
 
- 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 Member Functions

 CBlastTabular (void)
 
 CBlastTabular (const objects::CSeq_align &seq_align, bool save_xcript=false)
 
 CBlastTabular (const TId &idquery, TCoord qstart, bool qstrand, const TId &idsubj, TCoord sstart, bool sstrand, const string &xcript)
 
 CBlastTabular (const char *m8, bool force_local_ids=false)
 
 CBlastTabular (const char *m8, SCORE_FUNC score_func)
 
void SetLength (TCoord length)
 
TCoord GetLength (void) const
 
void SetMismatches (TCoord mismatches)
 
TCoord GetMismatches (void) const
 
void SetGaps (TCoord gaps)
 
TCoord GetGaps (void) const
 
void SetRawScore (TCoord score)
 
TCoord GetRawScore (void) const
 
void SetEValue (double evalue)
 
double GetEValue (void) const
 
void SetIdentity (float identity)
 
float GetIdentity (void) const
 
void SetScore (float score)
 
float GetScore (void) const
 
virtual void Modify (Uint1 where, TCoord new_pos)
 
- Public Member Functions inherited from CAlignShadow
 CAlignShadow (void)
 
 CAlignShadow (const objects::CSeq_align &seq_align, bool save_xcript=false)
 Create the object from a seq-align structure. More...
 
 CAlignShadow (const TId &idquery, TCoord qstart, bool qstrand, const TId &idsubj, TCoord sstart, bool sstrand, const string &xcript)
 Create the object from a transcript. More...
 
virtual ~CAlignShadow ()
 
const TIdGetId (Uint1 where) const
 
const TIdGetQueryId (void) const
 
const TIdGetSubjId (void) const
 
void SetId (Uint1 where, const TId &id)
 
void SetQueryId (const TId &id)
 
void SetSubjId (const TId &id)
 
bool GetStrand (Uint1 where) const
 
bool GetQueryStrand (void) const
 
bool GetSubjStrand (void) const
 
void SetStrand (Uint1 where, bool strand)
 
void SetQueryStrand (bool strand)
 
void SetSubjStrand (bool strand)
 
void FlipStrands (void)
 
void SwapQS (void)
 
const TCoordGetBox (void) const
 
void SetBox (const TCoord box[4])
 
TCoord GetMin (Uint1 where) const
 
TCoord GetMax (Uint1 where) const
 
TCoord GetQueryMin (void) const
 
TCoord GetQueryMax (void) const
 
TCoord GetSubjMin (void) const
 
TCoord GetSubjMax (void) const
 
void SetMax (Uint1 where, TCoord pos)
 
void SetMin (Uint1 where, TCoord pos)
 
void SetQueryMin (TCoord pos)
 
void SetQueryMax (TCoord pos)
 
void SetSubjMin (TCoord pos)
 
void SetSubjMax (TCoord pos)
 
TCoord GetQuerySpan (void) const
 
TCoord GetSubjSpan (void) const
 
TCoord GetStart (Uint1 where) const
 
TCoord GetStop (Uint1 where) const
 
TCoord GetQueryStart (void) const
 
TCoord GetQueryStop (void) const
 
TCoord GetSubjStart (void) const
 
TCoord GetSubjStop (void) const
 
void SetStop (Uint1 where, TCoord pos)
 
void SetStart (Uint1 where, TCoord pos)
 
void SetQueryStart (TCoord pos)
 
void SetQueryStop (TCoord pos)
 
void SetSubjStart (TCoord pos)
 
void SetSubjStop (TCoord pos)
 
void Shift (Int4 shift_query, Int4 shift_subj)
 
const TTranscriptGetTranscript (void) 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
 

Protected Member Functions

template<class F >
void x_Deserialize (const char *m8, F seq_id_extractor)
 
virtual void x_PartialSerialize (CNcbiOstream &os) const
 
virtual void x_PartialDeserialize (const char *m8)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Static Protected Member Functions

static void sx_MineSegment (size_t where, const objects::CStd_seg::TLoc &locs, TSeqPos *delta, TSeqPos *prev)
 

Protected Attributes

TCoord m_Length
 
TCoord m_Mismatches
 
TCoord m_Gaps
 
TCoord m_RawScore
 
double m_EValue
 
float m_Identity
 
float m_Score
 
- Protected Attributes inherited from CAlignShadow
std::pair< TId, TIdm_Id
 
TCoord m_Box [4]
 
TTranscript m_Transcript
 

Additional Inherited Members

- Static Public Member Functions inherited from CAlignShadow
static string s_RunLengthEncode (const string &in)
 
static string s_RunLengthDecode (const string &in)
 
- 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)
 
- 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 43 of file blast_tabular.hpp.

Member Typedef Documentation

◆ SCORE_FUNC

typedef int(* CBlastTabular::SCORE_FUNC) (const CRef< objects::CSeq_id > &id)

Construct CBlastTabular from m8 line, use score_func to select seq-id from FASTA-style ids.

Definition at line 63 of file blast_tabular.hpp.

◆ TCoord

Definition at line 48 of file blast_tabular.hpp.

◆ TParent

Definition at line 47 of file blast_tabular.hpp.

Constructor & Destructor Documentation

◆ CBlastTabular() [1/5]

CBlastTabular::CBlastTabular ( void  )
inline

Definition at line 51 of file blast_tabular.hpp.

◆ CBlastTabular() [2/5]

CBlastTabular::CBlastTabular ( const objects::CSeq_align &  seq_align,
bool  save_xcript = false 
)

◆ CBlastTabular() [3/5]

CBlastTabular::CBlastTabular ( const TId idquery,
TCoord  qstart,
bool  qstrand,
const TId idsubj,
TCoord  sstart,
bool  sstrand,
const string xcript 
)

Definition at line 233 of file blast_tabular.cpp.

References i, m_EValue, m_Gaps, m_Length, m_Mismatches, m_RawScore, m_Score, and SetIdentity().

◆ CBlastTabular() [4/5]

CBlastTabular::CBlastTabular ( const char *  m8,
bool  force_local_ids = false 
)

Definition at line 306 of file blast_tabular.cpp.

References x_Deserialize().

◆ CBlastTabular() [5/5]

CBlastTabular::CBlastTabular ( const char *  m8,
SCORE_FUNC  score_func 
)

Definition at line 314 of file blast_tabular.cpp.

References x_Deserialize().

Member Function Documentation

◆ GetEValue()

double CBlastTabular::GetEValue ( void  ) const

Definition at line 418 of file blast_tabular.cpp.

References m_EValue.

Referenced by x_PartialSerialize().

◆ GetGaps()

CBlastTabular::TCoord CBlastTabular::GetGaps ( void  ) const

Definition at line 390 of file blast_tabular.cpp.

References m_Gaps.

Referenced by Modify(), and x_PartialSerialize().

◆ GetIdentity()

float CBlastTabular::GetIdentity ( void  ) const

Definition at line 445 of file blast_tabular.cpp.

References m_Identity.

Referenced by Modify(), and x_PartialSerialize().

◆ GetLength()

CBlastTabular::TCoord CBlastTabular::GetLength ( void  ) const

Definition at line 362 of file blast_tabular.cpp.

References m_Length.

Referenced by Modify(), CElementaryMatching::x_CompartPair(), and x_PartialSerialize().

◆ GetMismatches()

CBlastTabular::TCoord CBlastTabular::GetMismatches ( void  ) const

Definition at line 376 of file blast_tabular.cpp.

References m_Mismatches.

Referenced by Modify(), and x_PartialSerialize().

◆ GetRawScore()

CBlastTabular::TCoord CBlastTabular::GetRawScore ( void  ) const

Definition at line 404 of file blast_tabular.cpp.

References m_RawScore.

Referenced by Modify().

◆ GetScore()

float CBlastTabular::GetScore ( void  ) const

◆ Modify()

void CBlastTabular::Modify ( Uint1  where,
TCoord  new_pos 
)
virtual

◆ SetEValue()

void CBlastTabular::SetEValue ( double  evalue)

Definition at line 411 of file blast_tabular.cpp.

References m_EValue.

◆ SetGaps()

void CBlastTabular::SetGaps ( TCoord  gaps)

Definition at line 383 of file blast_tabular.cpp.

References m_Gaps.

Referenced by Modify().

◆ SetIdentity()

void CBlastTabular::SetIdentity ( float  identity)

Definition at line 438 of file blast_tabular.cpp.

References m_Identity.

Referenced by CBlastTabular().

◆ SetLength()

void CBlastTabular::SetLength ( TCoord  length)

Definition at line 355 of file blast_tabular.cpp.

References m_Length.

Referenced by Modify().

◆ SetMismatches()

void CBlastTabular::SetMismatches ( TCoord  mismatches)

Definition at line 369 of file blast_tabular.cpp.

References m_Mismatches.

Referenced by Modify().

◆ SetRawScore()

void CBlastTabular::SetRawScore ( TCoord  score)

Definition at line 397 of file blast_tabular.cpp.

References m_RawScore.

Referenced by Modify().

◆ SetScore()

void CBlastTabular::SetScore ( float  score)

Definition at line 425 of file blast_tabular.cpp.

References m_Score.

Referenced by Modify().

◆ sx_MineSegment()

void CBlastTabular::sx_MineSegment ( size_t  where,
const objects::CStd_seg::TLoc &  locs,
TSeqPos delta,
TSeqPos prev 
)
staticprotected

◆ x_Deserialize()

template<class F >
void CBlastTabular::x_Deserialize ( const char *  m8,
F  seq_id_extractor 
)
protected

Definition at line 320 of file blast_tabular.cpp.

References isspace(), CAlignShadow::m_Id, NCBI_THROW, and x_PartialDeserialize().

Referenced by CBlastTabular().

◆ x_PartialDeserialize()

void CBlastTabular::x_PartialDeserialize ( const char *  m8)
protectedvirtual

◆ x_PartialSerialize()

void CBlastTabular::x_PartialSerialize ( CNcbiOstream os) const
protectedvirtual

Member Data Documentation

◆ m_EValue

double CBlastTabular::m_EValue
protected

Definition at line 96 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetEValue(), SetEValue(), and x_PartialDeserialize().

◆ m_Gaps

TCoord CBlastTabular::m_Gaps
protected

Definition at line 94 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetGaps(), SetGaps(), and x_PartialDeserialize().

◆ m_Identity

float CBlastTabular::m_Identity
protected

Definition at line 97 of file blast_tabular.hpp.

Referenced by GetIdentity(), SetIdentity(), and x_PartialDeserialize().

◆ m_Length

TCoord CBlastTabular::m_Length
protected

Definition at line 92 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetLength(), SetLength(), and x_PartialDeserialize().

◆ m_Mismatches

TCoord CBlastTabular::m_Mismatches
protected

◆ m_RawScore

TCoord CBlastTabular::m_RawScore
protected

Definition at line 95 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetRawScore(), SetRawScore(), and x_PartialDeserialize().

◆ m_Score

float CBlastTabular::m_Score
protected

Definition at line 98 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetScore(), SetScore(), and x_PartialDeserialize().


The documentation for this class was generated from the following files:
Modified on Mon Mar 04 05:10:33 2024 by modify_doxy.py rev. 669887