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IRawRepeatRegion Class Referenceabstract

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

#include <objtools/readers/rm_reader.hpp>

+ Inheritance diagram for IRawRepeatRegion:
+ Collaboration diagram for IRawRepeatRegion:

Public Types

typedef ENa_strand TStrand
 
typedef unsigned int TRptId
 
typedef unsigned long TScore
 
typedef double TPercent
 
- Public Types inherited from IRepeat
typedef ITaxonomyResolver::TTaxId TTaxId
 

Public Member Functions

virtual ~IRawRepeatRegion (void)
 Enforce virtual destructor. More...
 
virtual TRptId GetRptId () const =0
 
virtual TScore GetSwScore () const =0
 
virtual TPercent GetPercDiv () const =0
 
virtual TPercent GetPercDel () const =0
 
virtual TPercent GetPercIns () const =0
 
virtual TSeqPos GetRptPosBegin () const =0
 
virtual TSeqPos GetRptPosEnd () const =0
 
virtual TSeqPos GetRptLeft () const =0
 
virtual TSeqPos GetSeqLeft () const =0
 
virtual bool IsOverlapped () const =0
 Flag that there is a higher-scoring match whose domain partly (<80%) includes the domain of this match. More...
 
virtual string GetSeqIdString () const =0
 
virtual TSeqPos GetSeqPosBegin () const =0
 
virtual TSeqPos GetSeqPosEnd () const =0
 
virtual bool IsReverseStrand () const =0
 
string GetRptClassFamily () const
 Covenience function to get the class and family as one value, the way that RepeatMasker emits them. More...
 
- Public Member Functions inherited from IRepeat
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 unsigned int kInvalidRptId = kMax_UInt
 
- Static Public Attributes inherited from IRepeat
static const TTaxId kInvalidTaxId = 0
 

Detailed Description

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

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.
Warning
This interface subclasses IRepeat. It is an abuse of the inheritance relationship, better modeled via a containment relationship, e.g. HAS-A, by adding a GetRepeat() member to get an object exposing IRepeat. However: (i) RepeatMasker *.out format is denormalized (in the database sense that the same repeat, placed multiply, will have its attributes copied redundantly to multiple lines of output), and further, (ii) attributes which should be constant for a given repeat despite placement, are in fact modifed per placement (e.g. a given specific repeat has a "length", but it can vary, e.g. depending on copy number). Due to the above, it was considered reasonable to pretend that a repeat region IS-A repeat, rather than point to one.

Definition at line 172 of file rm_reader.hpp.

Member Typedef Documentation

◆ TPercent

Definition at line 178 of file rm_reader.hpp.

◆ TRptId

typedef unsigned int IRawRepeatRegion::TRptId

Definition at line 176 of file rm_reader.hpp.

◆ TScore

typedef unsigned long IRawRepeatRegion::TScore

Definition at line 177 of file rm_reader.hpp.

◆ TStrand

Definition at line 175 of file rm_reader.hpp.

Constructor & Destructor Documentation

◆ ~IRawRepeatRegion()

virtual IRawRepeatRegion::~IRawRepeatRegion ( void  )
inlinevirtual

Enforce virtual destructor.

Definition at line 183 of file rm_reader.hpp.

Member Function Documentation

◆ GetPercDel()

virtual TPercent IRawRepeatRegion::GetPercDel ( ) const
pure virtual

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ GetPercDiv()

virtual TPercent IRawRepeatRegion::GetPercDiv ( ) const
pure virtual

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ GetPercIns()

virtual TPercent IRawRepeatRegion::GetPercIns ( ) const
pure virtual

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ GetRptClassFamily()

string IRawRepeatRegion::GetRptClassFamily ( ) const

Covenience function to get the class and family as one value, the way that RepeatMasker emits them.

The two are separated by a slash '/' character.

Definition at line 103 of file rm_reader.cpp.

References IRepeat::GetRptClass(), and IRepeat::GetRptFamily().

Referenced by CRepeatToFeat::operator()().

◆ GetRptId()

virtual TRptId IRawRepeatRegion::GetRptId ( ) const
pure virtual

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ GetRptLeft()

virtual TSeqPos IRawRepeatRegion::GetRptLeft ( ) const
pure virtual

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ GetRptPosBegin()

virtual TSeqPos IRawRepeatRegion::GetRptPosBegin ( ) const
pure virtual

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ GetRptPosEnd()

virtual TSeqPos IRawRepeatRegion::GetRptPosEnd ( ) const
pure virtual

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ GetSeqIdString()

virtual string IRawRepeatRegion::GetSeqIdString ( ) const
pure virtual

Implemented in SRepeatRegion, and IRepeatRegion.

◆ GetSeqLeft()

virtual TSeqPos IRawRepeatRegion::GetSeqLeft ( ) const
pure virtual

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ GetSeqPosBegin()

virtual TSeqPos IRawRepeatRegion::GetSeqPosBegin ( ) const
pure virtual

Implemented in IRepeatRegion.

◆ GetSeqPosEnd()

virtual TSeqPos IRawRepeatRegion::GetSeqPosEnd ( ) const
pure virtual

Implemented in IRepeatRegion.

◆ GetSwScore()

virtual TScore IRawRepeatRegion::GetSwScore ( ) const
pure virtual

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ IsOverlapped()

virtual bool IRawRepeatRegion::IsOverlapped ( ) const
pure virtual

Flag that there is a higher-scoring match whose domain partly (<80%) includes the domain of this match.

Implemented in SRepeatRegion.

Referenced by CRepeatToFeat::operator()().

◆ IsReverseStrand()

virtual bool IRawRepeatRegion::IsReverseStrand ( ) const
pure virtual

Implemented in IRepeatRegion.

Member Data Documentation

◆ kInvalidRptId

const unsigned int IRawRepeatRegion::kInvalidRptId = kMax_UInt
static

Definition at line 180 of file rm_reader.hpp.


The documentation for this class was generated from the following files:
Modified on Mon Apr 22 04:04:07 2024 by modify_doxy.py rev. 669887