NCBI C++ ToolKit
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CDbvarClinicalAsstSorter Class Reference

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CDbvarClinicalAsstSorter is a feature sorter used to sort variant features based on variant quality. More...

#include <gui/widgets/seq_graphic/dbvar_feature_sorter.hpp>

+ Inheritance diagram for CDbvarClinicalAsstSorter:
+ Collaboration diagram for CDbvarClinicalAsstSorter:

Public Types

enum  EGroup {
  eInvalid = -1, eBenign = 0, ePathogenic, eLikelyPathogenic,
  eLikelyBenign, eLikelyUnknown, eNotTested, eOther
}
 
- 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

 CDbvarClinicalAsstSorter (const string &sort_str)
 
virtual string GroupIdxToName (int idx) const
 Convert group index into group name. More...
 
virtual int GetGroupIdx (const objects::CMappedFeat &feat) const
 Get the sorted group index for a given feature. More...
 
virtual SSorterDescriptor GetThisDescr () const
 Return a name for the sorter. 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
 
- Public Member Functions inherited from IFeatSorter
virtual bool ChildFeatureFirst () const
 Priority on sorting parent or child features. More...
 
- Public Member Functions inherited from IObjectSorter
virtual ~IObjectSorter ()
 

Static Public Member Functions

static const stringGetID ()
 
static SSorterDescriptor GetSorterDescr ()
 
- 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)
 

Private Attributes

set< EGroupm_SortGroups
 Curently intended sorting groups. More...
 

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

Detailed Description

CDbvarClinicalAsstSorter is a feature sorter used to sort variant features based on variant quality.

There are two categories:

Definition at line 129 of file dbvar_feature_sorter.hpp.

Member Enumeration Documentation

Enumerator
eInvalid 

maybe it is valid, but not considered

eBenign 
ePathogenic 
eLikelyPathogenic 
eLikelyBenign 
eLikelyUnknown 
eNotTested 
eOther 

Definition at line 134 of file dbvar_feature_sorter.hpp.

Constructor & Destructor Documentation

CDbvarClinicalAsstSorter::CDbvarClinicalAsstSorter ( const string sort_str)

Member Function Documentation

int CDbvarClinicalAsstSorter::GetGroupIdx ( const objects::CMappedFeat &  feat) const
virtual

Get the sorted group index for a given feature.

any index >=0 will be considered as a valid index. Otherwise, it is an invalid index.

Implements IFeatSorter.

Definition at line 348 of file dbvar_feature_sorter.cpp.

References data, eBenign, eInvalid, eLikelyBenign, eLikelyPathogenic, eLikelyUnknown, eNotTested, eOther, ePathogenic, CUser_object_Base::GetData(), ITERATE, and m_SortGroups.

const string & CDbvarClinicalAsstSorter::GetID ( void  )
static

Definition at line 405 of file dbvar_feature_sorter.cpp.

Referenced by GetSorterDescr(), and CSGFeatureJob::SetSortBy().

IObjectSorter::SSorterDescriptor CDbvarClinicalAsstSorter::GetSorterDescr ( )
static

Definition at line 413 of file dbvar_feature_sorter.cpp.

References GetID().

Referenced by CVarTrackFactory::GetSettings(), and GetThisDescr().

IObjectSorter::SSorterDescriptor CDbvarClinicalAsstSorter::GetThisDescr ( ) const
virtual

Return a name for the sorter.

Implements IObjectSorter.

Definition at line 399 of file dbvar_feature_sorter.cpp.

References GetSorterDescr().

string CDbvarClinicalAsstSorter::GroupIdxToName ( int  idx) const
virtual

Convert group index into group name.

Implements IObjectSorter.

Definition at line 342 of file dbvar_feature_sorter.cpp.

References s_ClinGroupIdxToName().

Member Data Documentation

set<EGroup> CDbvarClinicalAsstSorter::m_SortGroups
private

Curently intended sorting groups.

Any feature that doesn't belong to any of the listed groups, an invalid group index will be assigned.

Definition at line 160 of file dbvar_feature_sorter.hpp.

Referenced by CDbvarClinicalAsstSorter(), and GetGroupIdx().


The documentation for this class was generated from the following files:
Modified on Mon Aug 03 11:39:05 2015 by modify_doxy.py rev. 426318