NCBI C++ ToolKit
Classes | Public Types | Public Member Functions | Private Types | Private Member Functions | Static Private Member Functions | Private Attributes | Friends | List of all members
CAlnMixSequences Class Reference

Search Toolkit Book for CAlnMixSequences

#include <objtools/alnmgr/alnseq.hpp>

+ Inheritance diagram for CAlnMixSequences:
+ Collaboration diagram for CAlnMixSequences:

Classes

struct  SSeqIds
 

Public Types

enum  EAddFlags { fCalcScore = 0x01 , fForceTranslation = 0x02 , fPreserveRows = 0x04 }
 
typedef vector< CRef< CAlnMixSeq > > TSeqs
 
typedef int TAddFlags
 
- 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

 CAlnMixSequences (void)
 
 CAlnMixSequences (CScope &scope)
 
const TSeqsGet () const
 
TSeqsSet ()
 
void Add (const CDense_seg &ds, TAddFlags flags=0)
 
void SortByScore ()
 
void SortByChainScore ()
 
void BuildRows ()
 
void InitRowsStartIts ()
 
void InitExtraRowsStartIts ()
 
void RowsStartItsContsistencyCheck (size_t match_idx)
 
- 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

typedef map< CBioseq_Handle, CRef< CAlnMixSeq > > TBioseqHandleMap
 
typedef map< CRef< CSeq_id >, CRef< CAlnMixSeq >, SSeqIdsTSeqIdMap
 

Private Member Functions

void x_IdentifyAlnMixSeq (CRef< CAlnMixSeq > &aln_seq, const CSeq_id &seq_id)
 

Static Private Member Functions

static bool x_CompareScores (const CRef< CAlnMixSeq > &seq1, const CRef< CAlnMixSeq > &seq2)
 
static bool x_CompareChainScores (const CRef< CAlnMixSeq > &seq1, const CRef< CAlnMixSeq > &seq2)
 

Private Attributes

size_t m_DsCnt
 
map< const CDense_seg *, vector< CRef< CAlnMixSeq > > > m_DsSeq
 
CRef< CScopem_Scope
 
TSeqs m_Seqs
 
TSeqIdMap m_SeqIds
 
TBioseqHandleMap m_BioseqHandles
 
bool m_ContainsAA
 
bool m_ContainsNA
 
vector< CRef< CAlnMixSeq > > m_Rows
 
list< CRef< CAlnMixSeq > > m_ExtraRows
 

Friends

class CAlnMix
 
class CAlnMixMatches
 
class CAlnMixSegments
 
class CAlnMixMerger
 

Additional Inherited Members

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

Detailed Description

Definition at line 57 of file alnseq.hpp.

Member Typedef Documentation

◆ TAddFlags

Definition at line 83 of file alnseq.hpp.

◆ TBioseqHandleMap

Definition at line 105 of file alnseq.hpp.

◆ TSeqIdMap

Definition at line 114 of file alnseq.hpp.

◆ TSeqs

Definition at line 65 of file alnseq.hpp.

Member Enumeration Documentation

◆ EAddFlags

Enumerator
fCalcScore 
fForceTranslation 
fPreserveRows 

Definition at line 70 of file alnseq.hpp.

Constructor & Destructor Documentation

◆ CAlnMixSequences() [1/2]

CAlnMixSequences::CAlnMixSequences ( void  )

Definition at line 52 of file alnseq.cpp.

◆ CAlnMixSequences() [2/2]

CAlnMixSequences::CAlnMixSequences ( CScope scope)

Definition at line 60 of file alnseq.cpp.

Member Function Documentation

◆ Add()

void CAlnMixSequences::Add ( const CDense_seg ds,
TAddFlags  flags = 0 
)

◆ BuildRows()

void CAlnMixSequences::BuildRows ( )

◆ Get()

const TSeqs& CAlnMixSequences::Get ( void  ) const
inline

Definition at line 67 of file alnseq.hpp.

References m_Seqs.

◆ InitExtraRowsStartIts()

void CAlnMixSequences::InitExtraRowsStartIts ( )

◆ InitRowsStartIts()

void CAlnMixSequences::InitRowsStartIts ( )

◆ RowsStartItsContsistencyCheck()

void CAlnMixSequences::RowsStartItsContsistencyCheck ( size_t  match_idx)

Definition at line 344 of file alnseq.cpp.

References ITERATE, m_Rows, and NON_CONST_ITERATE.

Referenced by CAlnMixSegments::Build().

◆ Set()

TSeqs& CAlnMixSequences::Set ( void  )
inline

Definition at line 68 of file alnseq.hpp.

References m_Seqs.

◆ SortByChainScore()

void CAlnMixSequences::SortByChainScore ( )

Definition at line 98 of file alnseq.cpp.

References m_Seqs, and x_CompareChainScores().

Referenced by CAlnMix::Merge().

◆ SortByScore()

void CAlnMixSequences::SortByScore ( )

Definition at line 91 of file alnseq.cpp.

References m_Seqs, and x_CompareScores().

Referenced by CAlnMix::Merge().

◆ x_CompareChainScores()

bool CAlnMixSequences::x_CompareChainScores ( const CRef< CAlnMixSeq > &  seq1,
const CRef< CAlnMixSeq > &  seq2 
)
inlinestaticprivate

Definition at line 80 of file alnseq.cpp.

References CAlnMixSeq::m_ChainScore, and CAlnMixSeq::m_Score.

Referenced by SortByChainScore().

◆ x_CompareScores()

bool CAlnMixSequences::x_CompareScores ( const CRef< CAlnMixSeq > &  seq1,
const CRef< CAlnMixSeq > &  seq2 
)
inlinestaticprivate

Definition at line 71 of file alnseq.cpp.

References CAlnMixSeq::m_Score.

Referenced by SortByScore().

◆ x_IdentifyAlnMixSeq()

void CAlnMixSequences::x_IdentifyAlnMixSeq ( CRef< CAlnMixSeq > &  aln_seq,
const CSeq_id seq_id 
)
private

Friends And Related Function Documentation

◆ CAlnMix

friend class CAlnMix
friend

Definition at line 100 of file alnseq.hpp.

◆ CAlnMixMatches

friend class CAlnMixMatches
friend

Definition at line 101 of file alnseq.hpp.

◆ CAlnMixMerger

friend class CAlnMixMerger
friend

Definition at line 103 of file alnseq.hpp.

◆ CAlnMixSegments

friend class CAlnMixSegments
friend

Definition at line 102 of file alnseq.hpp.

Member Data Documentation

◆ m_BioseqHandles

TBioseqHandleMap CAlnMixSequences::m_BioseqHandles
private

Definition at line 130 of file alnseq.hpp.

Referenced by x_IdentifyAlnMixSeq().

◆ m_ContainsAA

bool CAlnMixSequences::m_ContainsAA
private

Definition at line 131 of file alnseq.hpp.

Referenced by Add(), and x_IdentifyAlnMixSeq().

◆ m_ContainsNA

bool CAlnMixSequences::m_ContainsNA
private

Definition at line 132 of file alnseq.hpp.

Referenced by Add(), and x_IdentifyAlnMixSeq().

◆ m_DsCnt

size_t CAlnMixSequences::m_DsCnt
private

Definition at line 124 of file alnseq.hpp.

Referenced by Add().

◆ m_DsSeq

map<const CDense_seg*, vector<CRef<CAlnMixSeq> > > CAlnMixSequences::m_DsSeq
private

Definition at line 126 of file alnseq.hpp.

Referenced by CAlnMixMatches::Add(), and Add().

◆ m_ExtraRows

list<CRef<CAlnMixSeq> > CAlnMixSequences::m_ExtraRows
private

Definition at line 134 of file alnseq.hpp.

Referenced by InitExtraRowsStartIts().

◆ m_Rows

vector<CRef<CAlnMixSeq> > CAlnMixSequences::m_Rows
private

Definition at line 133 of file alnseq.hpp.

Referenced by BuildRows(), InitRowsStartIts(), and RowsStartItsContsistencyCheck().

◆ m_Scope

CRef<CScope> CAlnMixSequences::m_Scope
private

Definition at line 127 of file alnseq.hpp.

Referenced by Add(), and x_IdentifyAlnMixSeq().

◆ m_SeqIds

TSeqIdMap CAlnMixSequences::m_SeqIds
private

Definition at line 129 of file alnseq.hpp.

Referenced by Add().

◆ m_Seqs

TSeqs CAlnMixSequences::m_Seqs
private

Definition at line 128 of file alnseq.hpp.

Referenced by Add(), BuildRows(), Get(), Set(), SortByChainScore(), SortByScore(), and x_IdentifyAlnMixSeq().


The documentation for this class was generated from the following files:
Modified on Tue Nov 28 02:21:12 2023 by modify_doxy.py rev. 669887