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CSpliced_seg Class Reference

Represents ASN.1 type Spliced-seg defined in file seqalign.asn

Search Toolkit Book for CSpliced_seg

#include <objects/seqalign/Spliced_seg.hpp>

+ Inheritance diagram for CSpliced_seg:
+ Collaboration diagram for CSpliced_seg:

Public Types

typedef int TDim
 types More...
 
- Public Types inherited from CSpliced_seg_Base
enum  EProduct_type { eProduct_type_transcript = 0 , eProduct_type_protein = 1 }
 
enum class  E_memberIndex {
  e__allMandatory = 0 , e_product_id , e_genomic_id , e_product_strand ,
  e_genomic_strand , e_product_type , e_exons , e_poly_a ,
  e_product_length , e_modifiers
}
 
typedef CSeq_id TProduct_id
 
typedef CSeq_id TGenomic_id
 
typedef ENa_strand TProduct_strand
 
typedef ENa_strand TGenomic_strand
 
typedef EProduct_type TProduct_type
 
typedef list< CRef< CSpliced_exon > > TExons
 
typedef TSeqPos TPoly_a
 
typedef TSeqPos TProduct_length
 
typedef list< CRef< CSpliced_seg_modifier > > TModifiers
 
typedef Tparent::CMemberIndex< E_memberIndex, 10 > 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CSpliced_seg (void)
 
 ~CSpliced_seg (void)
 
void Validate (bool full_test=false) const
 Validators. More...
 
TDim CheckNumRows (void) const
 
bool IsConsistentBiologicalOrder (void) const
 
CRange< TSeqPosGetSeqRange (TDim row) const
 GetSeqRange NB: In case the product-type is protein, these only return the amin part of Prot-pos. More...
 
TSeqPos GetSeqStart (TDim row) const
 
TSeqPos GetSeqStop (TDim row) const
 
ENa_strand GetSeqStrand (TDim row) const
 Get strand (the first one if segments have different strands). More...
 
CRef< CSeq_alignAsDiscSeg () const
 Convert this alignment to a discontinuous segment. More...
 
- Public Member Functions inherited from CSpliced_seg_Base
 CSpliced_seg_Base (void)
 
virtual ~CSpliced_seg_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetProduct_id (void) const
 product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member. More...
 
bool CanGetProduct_id (void) const
 Check if it is safe to call GetProduct_id method. More...
 
void ResetProduct_id (void)
 Reset Product_id data member. More...
 
const TProduct_idGetProduct_id (void) const
 Get the Product_id member data. More...
 
void SetProduct_id (TProduct_id &value)
 Assign a value to Product_id data member. More...
 
TProduct_idSetProduct_id (void)
 Assign a value to Product_id data member. More...
 
bool IsSetGenomic_id (void) const
 Check if a value has been assigned to Genomic_id data member. More...
 
bool CanGetGenomic_id (void) const
 Check if it is safe to call GetGenomic_id method. More...
 
void ResetGenomic_id (void)
 Reset Genomic_id data member. More...
 
const TGenomic_idGetGenomic_id (void) const
 Get the Genomic_id member data. More...
 
void SetGenomic_id (TGenomic_id &value)
 Assign a value to Genomic_id data member. More...
 
TGenomic_idSetGenomic_id (void)
 Assign a value to Genomic_id data member. More...
 
bool IsSetProduct_strand (void) const
 should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member. More...
 
bool CanGetProduct_strand (void) const
 Check if it is safe to call GetProduct_strand method. More...
 
void ResetProduct_strand (void)
 Reset Product_strand data member. More...
 
TProduct_strand GetProduct_strand (void) const
 Get the Product_strand member data. More...
 
void SetProduct_strand (TProduct_strand value)
 Assign a value to Product_strand data member. More...
 
TProduct_strandSetProduct_strand (void)
 Assign a value to Product_strand data member. More...
 
bool IsSetGenomic_strand (void) const
 Check if a value has been assigned to Genomic_strand data member. More...
 
bool CanGetGenomic_strand (void) const
 Check if it is safe to call GetGenomic_strand method. More...
 
void ResetGenomic_strand (void)
 Reset Genomic_strand data member. More...
 
TGenomic_strand GetGenomic_strand (void) const
 Get the Genomic_strand member data. More...
 
void SetGenomic_strand (TGenomic_strand value)
 Assign a value to Genomic_strand data member. More...
 
TGenomic_strandSetGenomic_strand (void)
 Assign a value to Genomic_strand data member. More...
 
bool IsSetProduct_type (void) const
 Check if a value has been assigned to Product_type data member. More...
 
bool CanGetProduct_type (void) const
 Check if it is safe to call GetProduct_type method. More...
 
void ResetProduct_type (void)
 Reset Product_type data member. More...
 
TProduct_type GetProduct_type (void) const
 Get the Product_type member data. More...
 
void SetProduct_type (TProduct_type value)
 Assign a value to Product_type data member. More...
 
TProduct_typeSetProduct_type (void)
 Assign a value to Product_type data member. More...
 
bool IsSetExons (void) const
 set of segments involved each segment corresponds to one exon exons are always in biological order Check if a value has been assigned to Exons data member. More...
 
bool CanGetExons (void) const
 Check if it is safe to call GetExons method. More...
 
void ResetExons (void)
 Reset Exons data member. More...
 
const TExonsGetExons (void) const
 Get the Exons member data. More...
 
TExonsSetExons (void)
 Assign a value to Exons data member. More...
 
bool IsSetPoly_a (void) const
 start of poly(A) tail on the transcript For sense transcripts: aligned product positions < poly-a <= product-length poly-a == product-length indicates inferred poly(A) tail at transcript's end For antisense transcripts: -1 <= poly-a < aligned product positions poly-a == -1 indicates inferred poly(A) tail at transcript's start Check if a value has been assigned to Poly_a data member. More...
 
bool CanGetPoly_a (void) const
 Check if it is safe to call GetPoly_a method. More...
 
void ResetPoly_a (void)
 Reset Poly_a data member. More...
 
TPoly_a GetPoly_a (void) const
 Get the Poly_a member data. More...
 
void SetPoly_a (TPoly_a value)
 Assign a value to Poly_a data member. More...
 
TPoly_aSetPoly_a (void)
 Assign a value to Poly_a data member. More...
 
bool IsSetProduct_length (void) const
 length of the product, in bases/residues from this (or from poly-a if present), a 3' unaligned length can be extracted Check if a value has been assigned to Product_length data member. More...
 
bool CanGetProduct_length (void) const
 Check if it is safe to call GetProduct_length method. More...
 
void ResetProduct_length (void)
 Reset Product_length data member. More...
 
TProduct_length GetProduct_length (void) const
 Get the Product_length member data. More...
 
void SetProduct_length (TProduct_length value)
 Assign a value to Product_length data member. More...
 
TProduct_lengthSetProduct_length (void)
 Assign a value to Product_length data member. More...
 
bool IsSetModifiers (void) const
 alignment descriptors / modifiers this provides us a set for extension Check if a value has been assigned to Modifiers data member. More...
 
bool CanGetModifiers (void) const
 Check if it is safe to call GetModifiers method. More...
 
void ResetModifiers (void)
 Reset Modifiers data member. More...
 
const TModifiersGetModifiers (void) const
 Get the Modifiers member data. More...
 
TModifiersSetModifiers (void)
 Assign a value to Modifiers 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 CTypeInfoGetThisTypeInfo (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 stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (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...
 
CObjectoperator= (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 CSpliced_seg_Base Tparent
 

Private Member Functions

 CSpliced_seg (const CSpliced_seg &value)
 
CSpliced_segoperator= (const CSpliced_seg &value)
 

Additional Inherited Members

- Static Public Member Functions inherited from CSpliced_seg_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EProduct_type (void)
 Access to EProduct_type's attributes (values, names) as defined in spec. 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 56 of file Spliced_seg.hpp.

Member Typedef Documentation

◆ TDim

types

Definition at line 66 of file Spliced_seg.hpp.

◆ Tparent

Definition at line 58 of file Spliced_seg.hpp.

Constructor & Destructor Documentation

◆ CSpliced_seg() [1/2]

CSpliced_seg::CSpliced_seg ( void  )
inline

Definition at line 99 of file Spliced_seg.hpp.

◆ ~CSpliced_seg()

CSpliced_seg::~CSpliced_seg ( void  )

Definition at line 50 of file Spliced_seg.cpp.

◆ CSpliced_seg() [2/2]

CSpliced_seg::CSpliced_seg ( const CSpliced_seg value)
private

Member Function Documentation

◆ AsDiscSeg()

CRef< CSeq_align > CSpliced_seg::AsDiscSeg ( ) const

◆ CheckNumRows()

TDim CSpliced_seg::CheckNumRows ( void  ) const
inline

Definition at line 70 of file Spliced_seg.hpp.

Referenced by CAlnSpanVertModel::x_Init().

◆ GetSeqRange()

CRange< TSeqPos > CSpliced_seg::GetSeqRange ( TDim  row) const

GetSeqRange NB: In case the product-type is protein, these only return the amin part of Prot-pos.

The frame is ignored.

Definition at line 299 of file Spliced_seg.cpp.

References ctll::empty(), CSpliced_seg_Base::eProduct_type_protein, CSpliced_seg_Base::eProduct_type_transcript, CSpliced_seg_Base::GetExons(), CSpliced_seg_Base::GetProduct_type(), ITERATE, NCBI_THROW, result, and row.

Referenced by CSeq_align::GetSeqRange().

◆ GetSeqStart()

TSeqPos CSpliced_seg::GetSeqStart ( TDim  row) const

◆ GetSeqStop()

TSeqPos CSpliced_seg::GetSeqStop ( TDim  row) const

◆ GetSeqStrand()

ENa_strand CSpliced_seg::GetSeqStrand ( TDim  row) const

◆ IsConsistentBiologicalOrder()

bool CSpliced_seg::IsConsistentBiologicalOrder ( void  ) const

◆ operator=()

CSpliced_seg& CSpliced_seg::operator= ( const CSpliced_seg value)
private

◆ Validate()

void CSpliced_seg::Validate ( bool  full_test = false) const

Validators.

Definition at line 159 of file Spliced_seg.cpp.

References CProduct_pos::AsSeqPos(), CSpliced_exon_Base::CanGetProduct_strand(), CSpliced_seg_Base::CanGetProduct_strand(), CSpliced_exon_chunk_Base::e_Diag, CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, ctll::empty(), eNa_strand_minus, CSpliced_seg_Base::eProduct_type_protein, CSpliced_exon_chunk_Base::GetDiag(), CSpliced_seg_Base::GetExons(), CRange_Base::GetFrom(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_chunk_Base::GetGenomic_ins(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_exon_chunk_Base::GetMatch(), CSpliced_exon_chunk_Base::GetMismatch(), CSpliced_exon_Base::GetParts(), CSpliced_seg_Base::GetPoly_a(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_chunk_Base::GetProduct_ins(), CSpliced_seg_Base::GetProduct_length(), CSpliced_exon_Base::GetProduct_start(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_type(), CRange_Base::GetTo(), COpenRange< TSeqPos >::GetWhole(), CSpliced_exon_Base::IsSetGenomic_id(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_exon_Base::IsSetParts(), CSpliced_seg_Base::IsSetPoly_a(), CSpliced_exon_Base::IsSetProduct_id(), CSpliced_seg_Base::IsSetProduct_id(), CSpliced_seg_Base::IsSetProduct_length(), CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_seg_Base::IsSetProduct_strand(), ITERATE, NCBI_THROW, prot, CRange_Base::SetFrom(), CRange_Base::SetTo(), and CSpliced_exon_chunk_Base::Which().

Referenced by InitSplicedsegFromPairwiseAln(), MakeSplicedSeg(), and CSeq_align::Validate().


The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:09:58 2024 by modify_doxy.py rev. 669887