NCBI C++ ToolKit
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Search Toolkit Book for CDbvarValidationSorter
CDbvarValidationSorter is a feature sorter used to sort variant features based on variant quality. More...
#include <gui/widgets/seq_graphic/dbvar_feature_sorter.hpp>
Public Types | |
enum | EGroup { eInvalid = -1 , eSameSample_DiffPlatform = 0 , eDiffSample_DiffPlatform , eDiffSample_SamePlatform , eSeenInPlubic , eNovel , eNotAssessed , 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 atomic< Uint8 > | TCounter |
Counter type is CAtomiCounter. More... | |
typedef Uint8 | TCount |
Alias for value type of counter. More... | |
Public Member Functions | |
CDbvarValidationSorter (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... | |
CObject & | operator= (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 |
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 string & | GetID () |
static SSorterDescriptor | GetSorterDescr () |
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) |
Private Attributes | |
set< EGroup > | m_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... | |
CDbvarValidationSorter is a feature sorter used to sort variant features based on variant quality.
There are two categories:
Definition at line 209 of file dbvar_feature_sorter.hpp.
Enumerator | |
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eInvalid | maybe it is valid, but not considered |
eSameSample_DiffPlatform | |
eDiffSample_DiffPlatform | |
eDiffSample_SamePlatform | |
eSeenInPlubic | |
eNovel | |
eNotAssessed | |
eOther |
Definition at line 214 of file dbvar_feature_sorter.hpp.
Definition at line 562 of file dbvar_feature_sorter.cpp.
References set< Key, Compare >::empty(), eOther, NStr::EqualNocase(), eSameSample_DiffPlatform, i, set< Key, Compare >::insert(), m_SortGroups, s_ValidationTypeIdxToName(), CTrackUtils::TokenizeWithEscape(), and NStr::TruncateSpaces().
Get the sorted group index for a given feature.
@ret any index >=0 will be considered as a valid index. Otherwise, it is an invalid index.
Implements IFeatSorter.
Definition at line 593 of file dbvar_feature_sorter.cpp.
References eInvalid, eOther, NStr::EqualNocase(), eSameSample_DiffPlatform, i, ITERATE, m_SortGroups, and s_ValidationTypeIdxToName().
Definition at line 636 of file dbvar_feature_sorter.cpp.
Referenced by GetSorterDescr(), and CSGFeatureJob::SetSortBy().
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Definition at line 644 of file dbvar_feature_sorter.cpp.
References GetID().
Referenced by GetThisDescr(), and CVarTrackFactory::x_GetSettings().
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Return a name for the sorter.
Implements IObjectSorter.
Definition at line 630 of file dbvar_feature_sorter.cpp.
References GetSorterDescr().
Convert group index into group name.
Implements IObjectSorter.
Definition at line 587 of file dbvar_feature_sorter.cpp.
References s_ValidationTypeIdxToName().
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 240 of file dbvar_feature_sorter.hpp.
Referenced by CDbvarValidationSorter(), and GetGroupIdx().