NCBI C++ ToolKit
Public Types | Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
CFastaAlignmentBuilder Class Reference

Search Toolkit Book for CFastaAlignmentBuilder

Helper class to build pairwise alignments, with double gaps automatically spliced out. More...

#include "fasta_aln_builder.hpp"
(Private to src/objtools/readers.)

+ Inheritance diagram for CFastaAlignmentBuilder:
+ Collaboration diagram for CFastaAlignmentBuilder:

Public Types

enum  EConstants { kNoPos = -1, kContinued = -2 }
 special position values 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 Member Functions

 CFastaAlignmentBuilder (CRef< CSeq_id > reference_id, CRef< CSeq_id > other_id)
 
void AddData (TSeqPos alignment_pos, TSignedSeqPos reference_pos, TSignedSeqPos other_pos)
 
CRef< CSeq_alignGetCompletedAlignment (void)
 
- 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
 

Private Types

enum  EState { eDoubleGap, eReferenceOnly, eOtherOnly, eBoth }
 

Private Member Functions

void x_EnsurePos (TSignedSeqPos &pos, TSignedSeqPos last_pos, TSeqPos alignment_pos)
 
EState x_State (TSignedSeqPos reference_pos, TSignedSeqPos other_pos)
 

Private Attributes

CRef< CDense_segm_DS
 
TSeqPos m_LastAlignmentPos
 
TSignedSeqPos m_LastReferencePos
 
TSignedSeqPos m_LastOtherPos
 
EState m_LastState
 
EState m_LastNonDGState
 

Additional Inherited Members

- 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)
 
- 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 Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Helper class to build pairwise alignments, with double gaps automatically spliced out.

Definition at line 53 of file fasta_aln_builder.hpp.

Constructor & Destructor Documentation

CFastaAlignmentBuilder::CFastaAlignmentBuilder ( CRef< CSeq_id reference_id,
CRef< CSeq_id other_id 
)

Definition at line 45 of file fasta_aln_builder.cpp.

Member Function Documentation

void CFastaAlignmentBuilder::AddData ( TSeqPos  alignment_pos,
TSignedSeqPos  reference_pos,
TSignedSeqPos  other_pos 
)
CRef< CSeq_align > CFastaAlignmentBuilder::GetCompletedAlignment ( void  )
void CFastaAlignmentBuilder::x_EnsurePos ( TSignedSeqPos pos,
TSignedSeqPos  last_pos,
TSeqPos  alignment_pos 
)
inlineprivate

Definition at line 83 of file fasta_aln_builder.cpp.

References kContinued, kNoPos, and m_LastAlignmentPos.

Referenced by AddData().

CFastaAlignmentBuilder::EState CFastaAlignmentBuilder::x_State ( TSignedSeqPos  reference_pos,
TSignedSeqPos  other_pos 
)
inlineprivate

Definition at line 69 of file fasta_aln_builder.cpp.

Referenced by AddData().

Member Data Documentation

CRef<CDense_seg> CFastaAlignmentBuilder::m_DS
private

Definition at line 80 of file fasta_aln_builder.hpp.

Referenced by AddData(), and GetCompletedAlignment().

TSeqPos CFastaAlignmentBuilder::m_LastAlignmentPos
private

Definition at line 81 of file fasta_aln_builder.hpp.

Referenced by AddData(), and x_EnsurePos().

EState CFastaAlignmentBuilder::m_LastNonDGState
private

Definition at line 85 of file fasta_aln_builder.hpp.

Referenced by AddData().

TSignedSeqPos CFastaAlignmentBuilder::m_LastOtherPos
private

Definition at line 83 of file fasta_aln_builder.hpp.

Referenced by AddData().

TSignedSeqPos CFastaAlignmentBuilder::m_LastReferencePos
private

Definition at line 82 of file fasta_aln_builder.hpp.

Referenced by AddData().

EState CFastaAlignmentBuilder::m_LastState
private

Definition at line 84 of file fasta_aln_builder.hpp.

Referenced by AddData().


The documentation for this class was generated from the following files:
Modified on Mon Oct 16 16:15:50 2017 by modify_doxy.py rev. 546573