Search Toolkit Book for CAlignStrandSorter
CAlignStrandSorter is a sorter used to sort alignments based on alignment strand. More...
#include <gui/widgets/seq_graphic/alignment_sorter.hpp>
Inheritance diagram for CAlignStrandSorter:
Collaboration diagram for CAlignStrandSorter:
Public Types | |
| enum | EGroup { eInvalid = -1 , eForward = 0 , eReverse } |
| 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 | |
| CAlignStrandSorter (const string &sort_str) | |
| virtual string | GroupIdxToName (int idx) const |
| Convert group index into group name. More... | |
| virtual int | GetGroupIdx (const objects::CSeq_align &align) 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 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... | |
Detailed Description
CAlignStrandSorter is a sorter used to sort alignments based on alignment strand.
There are two categories:
- forward
- backward
Definition at line 45 of file alignment_sorter.hpp.
Member Enumeration Documentation
◆ EGroup
| Enumerator | |
|---|---|
| eInvalid | maybe it is valid, but not considered |
| eForward | |
| eReverse | |
Definition at line 50 of file alignment_sorter.hpp.
Constructor & Destructor Documentation
◆ CAlignStrandSorter()
Definition at line 62 of file alignment_sorter.cpp.
References eForward, set< Key, Compare >::empty(), NStr::EqualNocase(), eReverse, i, set< Key, Compare >::insert(), m_SortGroups, CTrackUtils::TokenizeWithEscape(), and NStr::TruncateSpaces().
Member Function Documentation
◆ GetGroupIdx()
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 IAlignSorter.
Definition at line 90 of file alignment_sorter.cpp.
References eForward, eInvalid, eReverse, and m_SortGroups.
◆ GetID()
Definition at line 119 of file alignment_sorter.cpp.
Referenced by CAlignSorterFactory::CreateAlignSorter(), GetSorterDescr(), CAlignmentTrack::OnToggleContent(), and CAlignmentTrack::x_OnContentIconClicked().
◆ GetSorterDescr()
|
static |
Definition at line 126 of file alignment_sorter.cpp.
References GetID().
Referenced by GetThisDescr(), and CAlignSorterFactory::SetTrackSetting().
◆ GetThisDescr()
|
virtual |
Return a name for the sorter.
Implements IObjectSorter.
Definition at line 113 of file alignment_sorter.cpp.
References GetSorterDescr().
◆ GroupIdxToName()
Convert group index into group name.
Implements IObjectSorter.
Definition at line 84 of file alignment_sorter.cpp.
References s_GroupIdxToName().
Member Data Documentation
◆ m_SortGroups
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 71 of file alignment_sorter.hpp.
Referenced by CAlignStrandSorter(), and GetGroupIdx().
The documentation for this class was generated from the following files:
- include/gui/widgets/seq_graphic/alignment_sorter.hpp
- src/gui/widgets/seq_graphic/alignment_sorter.cpp
