NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Attributes | List of all members
IRepeat Class Referenceabstract

Represents ASN.1 type Repeat defined in file varrep.asn

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Minimalist pure virtual (except destructor) interface defining a read-only RepeatMasker library repeat. More...

#include <objtools/readers/rm_reader.hpp>

+ Inheritance diagram for IRepeat:

Public Types

typedef ITaxonomyResolver::TTaxId TTaxId
 

Public Member Functions

virtual ~IRepeat (void)
 Enforce virtual destructor. More...
 
virtual string GetRptName () const =0
 Gets repeat name. More...
 
virtual string GetRptFamily () const =0
 Gets repeat family, or empty string if not known. More...
 
virtual string GetRptClass () const =0
 Gets repeat class, or empty string if not known. More...
 
virtual TSeqPos GetRptLength () const =0
 Gets repeat length, or kInvalidSeqPos if not known. More...
 
virtual TTaxId GetRptSpecificity () const =0
 Gets specificity as a taxonomy ID, or 0 if not known. More...
 
virtual string GetRptSpecificityName () const =0
 Gets specificity as a name, or empty string if not known. More...
 
virtual string GetRptRepbaseId () const =0
 Gets the RepbaseID, or empty string if not known. More...
 

Static Public Attributes

static const TTaxId kInvalidTaxId = 0
 

Detailed Description

Minimalist pure virtual (except destructor) interface defining a read-only RepeatMasker library repeat.

This interface is equvalent to the semantics of a tabular RepeatMasker output file.

Note
Clients are persuaded to use IRepeatRegion, the subclass of this minimalist interface. That interface makes some accomodations for conventions of the NCBI ASN.1 data model.

Definition at line 87 of file rm_reader.hpp.

Member Typedef Documentation

◆ TTaxId

Definition at line 90 of file rm_reader.hpp.

Constructor & Destructor Documentation

◆ ~IRepeat()

virtual IRepeat::~IRepeat ( void  )
inlinevirtual

Enforce virtual destructor.

Definition at line 94 of file rm_reader.hpp.

Member Function Documentation

◆ GetRptClass()

virtual string IRepeat::GetRptClass ( ) const
pure virtual

Gets repeat class, or empty string if not known.

Implemented in SRepeatRegion, and SRepeat.

Referenced by IRawRepeatRegion::GetRptClassFamily(), and s_StandardizeNomenclature().

◆ GetRptFamily()

virtual string IRepeat::GetRptFamily ( ) const
pure virtual

Gets repeat family, or empty string if not known.

Implemented in SRepeatRegion, and SRepeat.

Referenced by IRawRepeatRegion::GetRptClassFamily(), and s_StandardizeNomenclature().

◆ GetRptLength()

virtual TSeqPos IRepeat::GetRptLength ( ) const
pure virtual

Gets repeat length, or kInvalidSeqPos if not known.

Implemented in SRepeatRegion, and SRepeat.

◆ GetRptName()

virtual string IRepeat::GetRptName ( ) const
pure virtual

Gets repeat name.

Implemented in SRepeatRegion, and SRepeat.

Referenced by CRepeatToFeat::operator()(), and s_StandardizeNomenclature().

◆ GetRptRepbaseId()

virtual string IRepeat::GetRptRepbaseId ( ) const
pure virtual

Gets the RepbaseID, or empty string if not known.

Implemented in SRepeatRegion, and SRepeat.

◆ GetRptSpecificity()

virtual TTaxId IRepeat::GetRptSpecificity ( ) const
pure virtual

Gets specificity as a taxonomy ID, or 0 if not known.

Implemented in SRepeatRegion, and SRepeat.

◆ GetRptSpecificityName()

virtual string IRepeat::GetRptSpecificityName ( ) const
pure virtual

Gets specificity as a name, or empty string if not known.

Implemented in SRepeatRegion, and SRepeat.

Member Data Documentation

◆ kInvalidTaxId

const TTaxId IRepeat::kInvalidTaxId = 0
static

Definition at line 91 of file rm_reader.hpp.


The documentation for this class was generated from the following file:
Modified on Sun Apr 14 05:25:47 2024 by modify_doxy.py rev. 669887