Search Toolkit Book for CStd_seg
#include <objects/seqalign/Std_seg.hpp>
Inheritance diagram for CStd_seg:
Collaboration diagram for CStd_seg:
Public Member Functions | |
| CStd_seg (void) | |
| ~CStd_seg (void) | |
| TDim | CheckNumRows (void) const |
| void | Validate (bool full_test=false) const |
| TSignedSeqPos | GetSeqStart (TDim row) const |
| TSignedSeqPos | GetSeqStop (TDim row) const |
| CRange< TSignedSeqPos > | GetSeqRange (TDim row) const |
| void | SwapRows (TDim row1, TDim row2) |
| Swap two rows (changing *order*, not content) More... | |
| void | OffsetRow (TDim row, TSignedSeqPos offset) |
| Offset row's coords. More... | |
| void | RemapToLoc (TDim row, const CSeq_loc &dst_loc, bool ignore_strand=false) |
| CRef< CSeq_loc > | CreateRowSeq_loc (TDim row) const |
| Public Member Functions inherited from CStd_seg_Base | |
| CStd_seg_Base (void) | |
| virtual | ~CStd_seg_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetDim (void) const |
| dimensionality Check if a value has been assigned to Dim data member. More... | |
| bool | CanGetDim (void) const |
| Check if it is safe to call GetDim method. More... | |
| void | ResetDim (void) |
| Reset Dim data member. More... | |
| void | SetDefaultDim (void) |
| Assign default value to Dim data member. More... | |
| TDim | GetDim (void) const |
| Get the Dim member data. More... | |
| void | SetDim (TDim value) |
| Assign a value to Dim data member. More... | |
| TDim & | SetDim (void) |
| Assign a value to Dim data member. More... | |
| bool | IsSetIds (void) const |
| Check if a value has been assigned to Ids data member. More... | |
| bool | CanGetIds (void) const |
| Check if it is safe to call GetIds method. More... | |
| void | ResetIds (void) |
| Reset Ids data member. More... | |
| const TIds & | GetIds (void) const |
| Get the Ids member data. More... | |
| TIds & | SetIds (void) |
| Assign a value to Ids data member. More... | |
| bool | IsSetLoc (void) const |
| Check if a value has been assigned to Loc data member. More... | |
| bool | CanGetLoc (void) const |
| Check if it is safe to call GetLoc method. More... | |
| void | ResetLoc (void) |
| Reset Loc data member. More... | |
| const TLoc & | GetLoc (void) const |
| Get the Loc member data. More... | |
| TLoc & | SetLoc (void) |
| Assign a value to Loc data member. More... | |
| bool | IsSetScores (void) const |
| Check if a value has been assigned to Scores data member. More... | |
| bool | CanGetScores (void) const |
| Check if it is safe to call GetScores method. More... | |
| void | ResetScores (void) |
| Reset Scores data member. More... | |
| const TScores & | GetScores (void) const |
| Get the Scores member data. More... | |
| TScores & | SetScores (void) |
| Assign a value to 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 CStd_seg_Base | Tparent |
Private Member Functions | |
| CStd_seg (const CStd_seg &value) | |
| CStd_seg & | operator= (const CStd_seg &value) |
Additional Inherited Members | |
| Public Types inherited from CStd_seg_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_dim , e_ids , e_loc , e_scores } |
| typedef int | TDim |
| typedef vector< CRef< CSeq_id > > | TIds |
| typedef vector< CRef< CSeq_loc > > | TLoc |
| typedef vector< CRef< CScore > > | TScores |
| 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... | |
| 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 53 of file Std_seg.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 55 of file Std_seg.hpp.
Constructor & Destructor Documentation
◆ CStd_seg() [1/2]
|
inline |
Definition at line 98 of file Std_seg.hpp.
◆ ~CStd_seg()
| CStd_seg::~CStd_seg | ( | void | ) |
Definition at line 53 of file Std_seg.cpp.
◆ CStd_seg() [2/2]
Member Function Documentation
◆ CheckNumRows()
| CStd_seg::TDim CStd_seg::CheckNumRows | ( | void | ) | const |
Definition at line 58 of file Std_seg.cpp.
References _ASSERT, CStd_seg_Base::GetDim(), CStd_seg_Base::GetIds(), CStd_seg_Base::GetLoc(), CStd_seg_Base::IsSetIds(), kMax_Int, NCBI_THROW, and ncbi::grid::netcache::search::fields::size.
Referenced by Validate().
◆ CreateRowSeq_loc()
Definition at line 293 of file Std_seg.cpp.
References CSeq_loc::Assign(), CStd_seg_Base::GetDim(), CStd_seg_Base::GetLoc(), NStr::IntToString(), NCBI_THROW, and row.
◆ GetSeqRange()
| CRange< TSignedSeqPos > CStd_seg::GetSeqRange | ( | TDim | row | ) | const |
Definition at line 145 of file Std_seg.cpp.
References CStd_seg_Base::GetDim(), CSeq_interval_Base::GetFrom(), CStd_seg_Base::GetLoc(), CSeq_interval_Base::GetTo(), i, ITERATE, NCBI_THROW, and row.
Referenced by CStdSegHit::CStdSegHit().
◆ GetSeqStart()
| TSignedSeqPos CStd_seg::GetSeqStart | ( | TDim | row | ) | const |
Definition at line 76 of file Std_seg.cpp.
References CStd_seg_Base::GetDim(), CStd_seg_Base::GetLoc(), i, ITERATE, NCBI_THROW, and row.
Referenced by CHitMatrixDataSource::GetStdSegRange().
◆ GetSeqStop()
| TSignedSeqPos CStd_seg::GetSeqStop | ( | TDim | row | ) | const |
Definition at line 99 of file Std_seg.cpp.
References CStd_seg_Base::GetDim(), CStd_seg_Base::GetLoc(), i, ITERATE, NCBI_THROW, and row.
Referenced by CHitMatrixDataSource::GetStdSegRange().
◆ OffsetRow()
| void CStd_seg::OffsetRow | ( | TDim | row, |
| TSignedSeqPos | offset | ||
| ) |
Offset row's coords.
Definition at line 170 of file Std_seg.cpp.
References _ASSERT, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Pnt, CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), NCBI_THROW, offset, row, CSeq_loc::SetInt(), CStd_seg_Base::SetLoc(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().
◆ operator=()
◆ RemapToLoc()
Definition at line 210 of file Std_seg.cpp.
References _ASSERT, CSeq_loc::CheckId(), CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, eExtreme_Positional, CSerialObject::Equals(), CStd_seg_Base::GetDim(), CSeq_interval_Base::GetFrom(), CStd_seg_Base::GetIds(), CSeq_loc_Base::GetInt(), CSeq_loc::GetStop(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), NStr::IntToString(), CStd_seg_Base::IsSetIds(), kInvalidSeqPos, NCBI_THROW, row, CSeq_loc::SetInt(), CStd_seg_Base::SetLoc(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().
◆ SwapRows()
Swap two rows (changing *order*, not content)
Definition at line 128 of file Std_seg.cpp.
References _ASSERT, CStd_seg_Base::GetLoc(), CStd_seg_Base::IsSetIds(), NCBI_THROW, CStd_seg_Base::SetIds(), CStd_seg_Base::SetLoc(), ncbi::grid::netcache::search::fields::size, and swap().
◆ Validate()
Definition at line 122 of file Std_seg.cpp.
References CheckNumRows().
The documentation for this class was generated from the following files:
- include/objects/seqalign/Std_seg.hpp
- src/objects/seqalign/Std_seg.cpp
