Search Toolkit Book for CSparse_align
#include <objects/seqalign/Sparse_align.hpp>
Inheritance diagram for CSparse_align:
Collaboration diagram for CSparse_align:
Public Types | |
| typedef int | TDim |
| types More... | |
| Public Types inherited from CSparse_align_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_first_id , e_second_id , e_numseg , e_first_starts , e_second_starts , e_lens , e_second_strands , e_seg_scores } |
| typedef CSeq_id | TFirst_id |
| typedef CSeq_id | TSecond_id |
| typedef int | TNumseg |
| typedef vector< int > | TFirst_starts |
| typedef vector< int > | TSecond_starts |
| typedef vector< TSeqPos > | TLens |
| typedef vector< ENa_strand > | TSecond_strands |
| typedef vector< CRef< CScore > > | TSeg_scores |
| typedef Tparent::CMemberIndex< E_memberIndex, 9 > | 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_align (void) | |
| ~CSparse_align (void) | |
| void | Validate (bool full_test=false) const |
| Validators. More... | |
| TDim | CheckNumRows (void) const |
| TNumseg | CheckNumSegs (void) const |
| Public Member Functions inherited from CSparse_align_Base | |
| CSparse_align_Base (void) | |
| virtual | ~CSparse_align_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetFirst_id (void) const |
| Check if a value has been assigned to First_id data member. More... | |
| bool | CanGetFirst_id (void) const |
| Check if it is safe to call GetFirst_id method. More... | |
| void | ResetFirst_id (void) |
| Reset First_id data member. More... | |
| const TFirst_id & | GetFirst_id (void) const |
| Get the First_id member data. More... | |
| void | SetFirst_id (TFirst_id &value) |
| Assign a value to First_id data member. More... | |
| TFirst_id & | SetFirst_id (void) |
| Assign a value to First_id data member. More... | |
| bool | IsSetSecond_id (void) const |
| Check if a value has been assigned to Second_id data member. More... | |
| bool | CanGetSecond_id (void) const |
| Check if it is safe to call GetSecond_id method. More... | |
| void | ResetSecond_id (void) |
| Reset Second_id data member. More... | |
| const TSecond_id & | GetSecond_id (void) const |
| Get the Second_id member data. More... | |
| void | SetSecond_id (TSecond_id &value) |
| Assign a value to Second_id data member. More... | |
| TSecond_id & | SetSecond_id (void) |
| Assign a value to Second_id data member. More... | |
| bool | IsSetNumseg (void) const |
| number of segments Check if a value has been assigned to Numseg data member. More... | |
| bool | CanGetNumseg (void) const |
| Check if it is safe to call GetNumseg method. More... | |
| void | ResetNumseg (void) |
| Reset Numseg data member. More... | |
| TNumseg | GetNumseg (void) const |
| Get the Numseg member data. More... | |
| void | SetNumseg (TNumseg value) |
| Assign a value to Numseg data member. More... | |
| TNumseg & | SetNumseg (void) |
| Assign a value to Numseg data member. More... | |
| bool | IsSetFirst_starts (void) const |
| starts on the first sequence [numseg] Check if a value has been assigned to First_starts data member. More... | |
| bool | CanGetFirst_starts (void) const |
| Check if it is safe to call GetFirst_starts method. More... | |
| void | ResetFirst_starts (void) |
| Reset First_starts data member. More... | |
| const TFirst_starts & | GetFirst_starts (void) const |
| Get the First_starts member data. More... | |
| TFirst_starts & | SetFirst_starts (void) |
| Assign a value to First_starts data member. More... | |
| bool | IsSetSecond_starts (void) const |
| starts on the second sequence [numseg] Check if a value has been assigned to Second_starts data member. More... | |
| bool | CanGetSecond_starts (void) const |
| Check if it is safe to call GetSecond_starts method. More... | |
| void | ResetSecond_starts (void) |
| Reset Second_starts data member. More... | |
| const TSecond_starts & | GetSecond_starts (void) const |
| Get the Second_starts member data. More... | |
| TSecond_starts & | SetSecond_starts (void) |
| Assign a value to Second_starts data member. More... | |
| bool | IsSetLens (void) const |
| lengths of segments [numseg] Check if a value has been assigned to Lens data member. More... | |
| bool | CanGetLens (void) const |
| Check if it is safe to call GetLens method. More... | |
| void | ResetLens (void) |
| Reset Lens data member. More... | |
| const TLens & | GetLens (void) const |
| Get the Lens member data. More... | |
| TLens & | SetLens (void) |
| Assign a value to Lens data member. More... | |
| bool | IsSetSecond_strands (void) const |
| Check if a value has been assigned to Second_strands data member. More... | |
| bool | CanGetSecond_strands (void) const |
| Check if it is safe to call GetSecond_strands method. More... | |
| void | ResetSecond_strands (void) |
| Reset Second_strands data member. More... | |
| const TSecond_strands & | GetSecond_strands (void) const |
| Get the Second_strands member data. More... | |
| TSecond_strands & | SetSecond_strands (void) |
| Assign a value to Second_strands data member. More... | |
| bool | IsSetSeg_scores (void) const |
| per-segment scores Check if a value has been assigned to Seg_scores data member. More... | |
| bool | CanGetSeg_scores (void) const |
| Check if it is safe to call GetSeg_scores method. More... | |
| void | ResetSeg_scores (void) |
| Reset Seg_scores data member. More... | |
| const TSeg_scores & | GetSeg_scores (void) const |
| Get the Seg_scores member data. More... | |
| TSeg_scores & | SetSeg_scores (void) |
| Assign a value to Seg_scores 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 CSparse_align_Base | Tparent |
Private Member Functions | |
| CSparse_align (const CSparse_align &value) | |
| CSparse_align & | operator= (const CSparse_align &value) |
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
Definition at line 58 of file Sparse_align.hpp.
Member Typedef Documentation
◆ TDim
| typedef int CSparse_align::TDim |
types
Definition at line 68 of file Sparse_align.hpp.
◆ Tparent
|
private |
Definition at line 60 of file Sparse_align.hpp.
Constructor & Destructor Documentation
◆ CSparse_align() [1/2]
|
inline |
Definition at line 88 of file Sparse_align.hpp.
◆ ~CSparse_align()
| CSparse_align::~CSparse_align | ( | void | ) |
Definition at line 49 of file Sparse_align.cpp.
◆ CSparse_align() [2/2]
|
private |
Member Function Documentation
◆ CheckNumRows()
|
inline |
Definition at line 72 of file Sparse_align.hpp.
Referenced by Validate().
◆ CheckNumSegs()
| CSparse_align::TNumseg CSparse_align::CheckNumSegs | ( | void | ) | const |
Definition at line 61 of file Sparse_align.cpp.
References _SEQALIGN_ASSERT, CSparse_align_Base::GetFirst_starts(), CSparse_align_Base::GetLens(), CSparse_align_Base::GetNumseg(), CSparse_align_Base::GetSecond_starts(), CSparse_align_Base::GetSecond_strands(), CSparse_align_Base::GetSeg_scores(), CSparse_align_Base::IsSetSecond_strands(), CSparse_align_Base::IsSetSeg_scores(), kMax_Int, and ncbi::grid::netcache::search::fields::size.
Referenced by Validate().
◆ operator=()
|
private |
◆ Validate()
Validators.
Definition at line 54 of file Sparse_align.cpp.
References CheckNumRows(), and CheckNumSegs().
The documentation for this class was generated from the following files:
- include/objects/seqalign/Sparse_align.hpp
- src/objects/seqalign/Sparse_align.cpp
