Search Toolkit Book for CSparse_seg_Base
========================================================================== More...
#include <objects/seqalign/Sparse_seg_.hpp>
Inheritance diagram for CSparse_seg_Base:
Collaboration diagram for CSparse_seg_Base:
Public Types | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_master_id , e_rows , e_row_scores , e_ext } |
| typedef CSeq_id | TMaster_id |
| typedef vector< CRef< CSparse_align > > | TRows |
| typedef vector< CRef< CScore > > | TRow_scores |
| typedef vector< CRef< CSparse_seg_ext > > | TExt |
| typedef Tparent::CMemberIndex< E_memberIndex, 5 > | TmemberIndex |
| 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 | |
| CSparse_seg_Base (void) | |
| virtual | ~CSparse_seg_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetMaster_id (void) const |
| Check if a value has been assigned to Master_id data member. More... | |
| bool | CanGetMaster_id (void) const |
| Check if it is safe to call GetMaster_id method. More... | |
| void | ResetMaster_id (void) |
| Reset Master_id data member. More... | |
| const TMaster_id & | GetMaster_id (void) const |
| Get the Master_id member data. More... | |
| void | SetMaster_id (TMaster_id &value) |
| Assign a value to Master_id data member. More... | |
| TMaster_id & | SetMaster_id (void) |
| Assign a value to Master_id data member. More... | |
| bool | IsSetRows (void) const |
| pairwise alignments constituting this multiple alignment Check if a value has been assigned to Rows data member. More... | |
| bool | CanGetRows (void) const |
| Check if it is safe to call GetRows method. More... | |
| void | ResetRows (void) |
| Reset Rows data member. More... | |
| const TRows & | GetRows (void) const |
| Get the Rows member data. More... | |
| TRows & | SetRows (void) |
| Assign a value to Rows data member. More... | |
| bool | IsSetRow_scores (void) const |
| per-row scores Check if a value has been assigned to Row_scores data member. More... | |
| bool | CanGetRow_scores (void) const |
| Check if it is safe to call GetRow_scores method. More... | |
| void | ResetRow_scores (void) |
| Reset Row_scores data member. More... | |
| const TRow_scores & | GetRow_scores (void) const |
| Get the Row_scores member data. More... | |
| TRow_scores & | SetRow_scores (void) |
| Assign a value to Row_scores data member. More... | |
| bool | IsSetExt (void) const |
| index of extra items Check if a value has been assigned to Ext data member. More... | |
| bool | CanGetExt (void) const |
| Check if it is safe to call GetExt method. More... | |
| void | ResetExt (void) |
| Reset Ext data member. More... | |
| const TExt & | GetExt (void) const |
| Get the Ext member data. More... | |
| TExt & | SetExt (void) |
| Assign a value to Ext data member. More... | |
| virtual void | Reset (void) |
| Reset the whole object. More... | |
| Public Member Functions inherited from CSerialObject | |
| CSerialObject (void) | |
| virtual | ~CSerialObject (void) |
| virtual const CTypeInfo * | GetThisTypeInfo (void) const =0 |
| virtual void | Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) |
| Set object to copy of another one. More... | |
| virtual bool | Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const |
| Check if both objects contain the same values. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| void | ThrowUnassigned (TMemberIndex index) const |
| void | ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const |
| bool | HasNamespaceName (void) const |
| Check if object data type has namespace name. More... | |
| const string & | GetNamespaceName (void) const |
| Get namespace name. More... | |
| bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More... | |
| const string & | GetNamespacePrefix (void) const |
| Get namespace prefix. 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... | |
| 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 CSerialObject | Tparent |
Private Member Functions | |
| CSparse_seg_Base (const CSparse_seg_Base &) | |
| CSparse_seg_Base & | operator= (const CSparse_seg_Base &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| CRef< TMaster_id > | m_Master_id |
| vector< CRef< CSparse_align > > | m_Rows |
| vector< CRef< CScore > > | m_Row_scores |
| vector< CRef< CSparse_seg_ext > > | m_Ext |
Additional Inherited Members | |
| Static Public Member Functions inherited from CSerialObject | |
| static void | SetVerifyDataThread (ESerialVerifyData verify) |
| static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
| static string | UnassignedString (void) |
| static CStringUTF8 | UnassignedStringUTF8 (void) |
| static char | UnassignedByte (void) |
| 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 CSerialObject | |
| static const char * | ms_UnassignedStr = "<*unassigned*>" |
| static const char | ms_UnassignedByte = char(0xcd) |
| 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
==========================================================================
Sparse-seg follows the semantics of dense-seg and is more optimal for representing sparse multiple alignments
==========================================================================
Definition at line 85 of file Sparse_seg_.hpp.
The documentation for this class was generated from the following files:
- include/objects/seqalign/Sparse_seg_.hpp
- src/objects/seqalign/Sparse_seg_.cpp
