NCBI C++ ToolKit
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CDisplaySeqalign::SAlnInfo Struct Reference

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store alnvec and score info More...

#include <objtools/align_format/showalign.hpp>

+ Inheritance diagram for CDisplaySeqalign::SAlnInfo:
+ Collaboration diagram for CDisplaySeqalign::SAlnInfo:

Public Attributes

CRef< objects::CAlnVec > alnvec
 
int score
 
double bits
 
double evalue
 
list< stringuse_this_seqid
 
int comp_adj_method
 
int sum_n
 
string id_label
 
SAlnRowInfoalnRowInfo
 
vector< objects::SFeatInfo * > feat_list
 
CRange< TSeqPosactual_range
 
TGi subject_gi
 
objects::SFeatInfo * feat5
 
objects::SFeatInfo * feat3
 
int match
 
int positive
 
int gap
 
int identity
 

Additional Inherited Members

- 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 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 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

store alnvec and score info

Definition at line 569 of file showalign.hpp.

Member Data Documentation

◆ actual_range

CRange<TSeqPos> CDisplaySeqalign::SAlnInfo::actual_range

Definition at line 583 of file showalign.hpp.

◆ alnRowInfo

SAlnRowInfo* CDisplaySeqalign::SAlnInfo::alnRowInfo

◆ alnvec

CRef< objects::CAlnVec > CDisplaySeqalign::SAlnInfo::alnvec

Definition at line 570 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplayAlnvecInfo().

◆ bits

double CDisplaySeqalign::SAlnInfo::bits

Definition at line 572 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplayAlignInfo().

◆ comp_adj_method

int CDisplaySeqalign::SAlnInfo::comp_adj_method

Definition at line 575 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplayAlignInfo().

◆ evalue

double CDisplaySeqalign::SAlnInfo::evalue

Definition at line 573 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplayAlignInfo().

◆ feat3

objects::SFeatInfo* CDisplaySeqalign::SAlnInfo::feat3

Definition at line 586 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplaySingleAlignParams().

◆ feat5

objects::SFeatInfo* CDisplaySeqalign::SAlnInfo::feat5

Definition at line 585 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplaySingleAlignParams().

◆ feat_list

vector<objects::SFeatInfo*> CDisplaySeqalign::SAlnInfo::feat_list

Definition at line 582 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplaySingleAlignParams().

◆ gap

int CDisplaySeqalign::SAlnInfo::gap

◆ id_label

string CDisplaySeqalign::SAlnInfo::id_label

Definition at line 577 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplaySingleAlignParams().

◆ identity

int CDisplaySeqalign::SAlnInfo::identity

◆ match

int CDisplaySeqalign::SAlnInfo::match

◆ positive

int CDisplaySeqalign::SAlnInfo::positive

◆ score

int CDisplaySeqalign::SAlnInfo::score

Definition at line 571 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplayAlignInfo().

◆ subject_gi

TGi CDisplaySeqalign::SAlnInfo::subject_gi

Definition at line 584 of file showalign.hpp.

◆ sum_n

int CDisplaySeqalign::SAlnInfo::sum_n

Definition at line 576 of file showalign.hpp.

Referenced by CDisplaySeqalign::x_DisplayAlignInfo().

◆ use_this_seqid

list<string> CDisplaySeqalign::SAlnInfo::use_this_seqid

Definition at line 574 of file showalign.hpp.


The documentation for this struct was generated from the following file:
Modified on Mon Jun 24 05:23:40 2024 by modify_doxy.py rev. 669887