Search Toolkit Book for CDense_diag
#include <objects/seqalign/Dense_diag.hpp>
Inheritance diagram for CDense_diag:
Collaboration diagram for CDense_diag:
Public Member Functions | |
| CDense_diag (void) | |
| ~CDense_diag (void) | |
| TDim | CheckNumRows (void) const |
| Validators. More... | |
| void | Validate () const |
| CRange< TSeqPos > | GetSeqRange (TDim row) const |
| GetSeqRange. More... | |
| TSeqPos | GetSeqStart (TDim row) const |
| TSeqPos | GetSeqStop (TDim row) const |
| ENa_strand | GetSeqStrand (TDim row) const |
| void | OffsetRow (TDim row, TSignedSeqPos offset) |
| Offset row's coords. More... | |
| CRef< CSeq_interval > | CreateRowSeq_interval (TDim row) const |
| Public Member Functions inherited from CDense_diag_Base | |
| CDense_diag_Base (void) | |
| virtual | ~CDense_diag_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 |
| sequences in order 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 | IsSetStarts (void) const |
| start OFFSETS in ids order Check if a value has been assigned to Starts data member. More... | |
| bool | CanGetStarts (void) const |
| Check if it is safe to call GetStarts method. More... | |
| void | ResetStarts (void) |
| Reset Starts data member. More... | |
| const TStarts & | GetStarts (void) const |
| Get the Starts member data. More... | |
| TStarts & | SetStarts (void) |
| Assign a value to Starts data member. More... | |
| bool | IsSetLen (void) const |
| len of aligned segments Check if a value has been assigned to Len data member. More... | |
| bool | CanGetLen (void) const |
| Check if it is safe to call GetLen method. More... | |
| void | ResetLen (void) |
| Reset Len data member. More... | |
| TLen | GetLen (void) const |
| Get the Len member data. More... | |
| void | SetLen (TLen value) |
| Assign a value to Len data member. More... | |
| TLen & | SetLen (void) |
| Assign a value to Len data member. More... | |
| bool | IsSetStrands (void) const |
| Check if a value has been assigned to Strands data member. More... | |
| bool | CanGetStrands (void) const |
| Check if it is safe to call GetStrands method. More... | |
| void | ResetStrands (void) |
| Reset Strands data member. More... | |
| const TStrands & | GetStrands (void) const |
| Get the Strands member data. More... | |
| TStrands & | SetStrands (void) |
| Assign a value to Strands 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 CDense_diag_Base | Tparent |
Private Member Functions | |
| CDense_diag (const CDense_diag &value) | |
| CDense_diag & | operator= (const CDense_diag &value) |
Additional Inherited Members | |
| Public Types inherited from CDense_diag_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_dim , e_ids , e_starts , e_len , e_strands , e_scores } |
| typedef int | TDim |
| typedef vector< CRef< CSeq_id > > | TIds |
| typedef vector< TSeqPos > | TStarts |
| typedef TSeqPos | TLen |
| typedef vector< ENa_strand > | TStrands |
| typedef vector< CRef< CScore > > | TScores |
| typedef Tparent::CMemberIndex< E_memberIndex, 7 > | 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 58 of file Dense_diag.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 60 of file Dense_diag.hpp.
Constructor & Destructor Documentation
◆ CDense_diag() [1/2]
|
inline |
Definition at line 93 of file Dense_diag.hpp.
◆ ~CDense_diag()
| CDense_diag::~CDense_diag | ( | void | ) |
Definition at line 53 of file Dense_diag.cpp.
◆ CDense_diag() [2/2]
|
private |
Member Function Documentation
◆ CheckNumRows()
|
inline |
Validators.
Definition at line 125 of file Dense_diag.hpp.
References CDense_diag_Base::GetDim(), CDense_diag_Base::GetIds(), CDense_diag_Base::GetStarts(), NCBI_THROW, and ncbi::grid::netcache::search::fields::size.
Referenced by OffsetRow(), and Validate().
◆ CreateRowSeq_interval()
| CRef< CSeq_interval > CDense_diag::CreateRowSeq_interval | ( | TDim | row | ) | const |
Definition at line 111 of file Dense_diag.cpp.
References CDense_diag_Base::GetDim(), CDense_diag_Base::GetIds(), CDense_diag_Base::GetLen(), CDense_diag_Base::GetStarts(), CDense_diag_Base::GetStrands(), NStr::IntToString(), CDense_diag_Base::IsSetStrands(), NCBI_THROW, row, CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().
◆ GetSeqRange()
GetSeqRange.
Definition at line 118 of file Dense_diag.hpp.
References GetSeqStart(), GetSeqStop(), and row.
◆ GetSeqStart()
Definition at line 99 of file Dense_diag.hpp.
References CDense_diag_Base::GetDim(), CDense_diag_Base::GetStarts(), NCBI_THROW, and row.
Referenced by GetSeqRange(), and GetSeqStop().
◆ GetSeqStop()
Definition at line 111 of file Dense_diag.hpp.
References CDense_diag_Base::GetLen(), GetSeqStart(), and row.
Referenced by GetSeqRange().
◆ GetSeqStrand()
| ENa_strand CDense_diag::GetSeqStrand | ( | TDim | row | ) | const |
Definition at line 93 of file Dense_diag.cpp.
References CDense_diag_Base::CanGetStrands(), CDense_diag_Base::GetDim(), CDense_diag_Base::GetStrands(), NCBI_THROW, row, and ncbi::grid::netcache::search::fields::size.
◆ OffsetRow()
| void CDense_diag::OffsetRow | ( | TDim | row, |
| TSignedSeqPos | offset | ||
| ) |
Offset row's coords.
Definition at line 72 of file Dense_diag.cpp.
References _ASSERT, CheckNumRows(), CDense_diag_Base::GetDim(), CDense_diag_Base::GetStarts(), NCBI_THROW, offset, row, and CDense_diag_Base::SetStarts().
◆ operator=()
|
private |
◆ Validate()
| void CDense_diag::Validate | ( | void | ) | const |
Definition at line 58 of file Dense_diag.cpp.
References CheckNumRows(), CDense_diag_Base::GetStrands(), and NCBI_THROW.
Referenced by CreateDense_diagFromAnchoredAln().
The documentation for this class was generated from the following files:
- include/objects/seqalign/Dense_diag.hpp
- src/objects/seqalign/Dense_diag.cpp
