Structure implementing the IRepeatRegion API as a simple store of data memebers. More...

#include <objtools/readers/rm_reader.hpp>

Inheritance diagram for SRepeatRegion:

Collaboration diagram for SRepeatRegion:

Public Types
typedef SRepeatRegion	TThisType

typedef IRepeatRegion	TParent

Public Types inherited from IRawRepeatRegion
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
CConstRef< CSeq_loc >	GetLocation (void) const
	Gets the location of this repeat. More...

CConstRef< CFeat_id >	GetId () const
	Gets the more general feature ID for this repeat, which identifies a single repeat, which may be multi-segement, and allows linking the segments together. More...

string	GetRptName () const
	Gets repeat name. More...

string	GetRptFamily () const
	Gets repeat family, or empty string if not known. More...

string	GetRptClass () const
	Gets repeat class, or empty string if not known. More...

TSeqPos	GetRptLength () const
	Gets repeat length, or kInvalidSeqPos if not known. More...

TTaxId	GetRptSpecificity () const
	Returns 0, not known. More...

string	GetRptSpecificityName () const
	Returns an empty string, not known. More...

string	GetRptRepbaseId () const
	Returns an empty string, not known. More...

TRptId	GetRptId () const

TScore	GetSwScore () const

TPercent	GetPercDiv () const

TPercent	GetPercDel () const

TPercent	GetPercIns () const

TSeqPos	GetRptPosBegin () const

TSeqPos	GetRptPosEnd () const

TSeqPos	GetRptLeft () const

TSeqPos	GetSeqLeft () const

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

string	GetSeqIdString () const
	Overridden version returns the orginal unparsed sequence identifier, if it was set (non-empty). More...

Public Member Functions inherited from IRepeatRegion
virtual void	GetLocation (CSeq_loc &result) const
	Gets a copy of the location into the Seq-loc instance provided by the caller. More...

virtual TSeqPos	GetSeqPosBegin () const
	Convenience function that gets the position start on the sequence, without dealing with a Seq-loc. More...

virtual TSeqPos	GetSeqPosEnd () const
	Convenience functions that gets the position end on the sequence, without dealing with a Seq-loc. More...

virtual bool	IsReverseStrand () const
	Convenience functions that gets the strand on the sequence, without dealing with a Seq-loc. More...

Public Member Functions inherited from IRawRepeatRegion
virtual	~IRawRepeatRegion (void)
	Enforce virtual destructor. More...

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...

Public Attributes
CRef< CSeq_loc >	query_location

TScore	sw_score

TSeqPos	query_left

TPercent	perc_div

TPercent	perc_del

TPercent	perc_ins

string	query_sequence

string	strand

string	matching_repeat

string	rpt_class

string	rpt_family

TSeqPos	rpt_pos_begin

TSeqPos	rpt_pos_end

TSeqPos	rpt_left

TRptId	rpt_id

bool	overlapped

Additional Inherited Members
Static Public Attributes inherited from IRawRepeatRegion
static const unsigned int	kInvalidRptId = kMax_UInt

Static Public Attributes inherited from IRepeat
static const TTaxId	kInvalidTaxId = 0

Detailed Description

Structure implementing the IRepeatRegion API as a simple store of data memebers.

The requirements for this class include that it be lossless with regard to the content from tabular RepeatMasker output. If this class doesn't represent some attribute, then as far as all consumers of RepeatMasker data are concerned, that attribute doesn't exist. As an example of data loss, even standardization of the sequence identifier, from string name to Seq-id, is potentially lossy. Thus, this class overrides the default implementation of GetSeqIdString().

There are several clients in need of a lightweight and minimalist representation of a repeat match. This structure provides that storage. This representation is very raw, and closely mirrors one line of tabular RepeatMasker output.

By contrast, the NCBI data model provides a Seq-feat representation of repeats, but that representation is burdened with INSDC and NCBI standards.

Note: This class only implements the columns present in the RepeatMasker *.out file format. Several attributes of IRepeat are not present in this format, and are thus not available.

Definition at line 350 of file rm_reader.hpp.

Member Typedef Documentation

◆ TParent

typedef IRepeatRegion SRepeatRegion::TParent

Definition at line 354 of file rm_reader.hpp.

◆ TThisType

typedef SRepeatRegion SRepeatRegion::TThisType

Definition at line 353 of file rm_reader.hpp.

Member Function Documentation

◆ GetId()

CConstRef< CFeat_id > SRepeatRegion::GetId ( ) const

virtual

Gets the more general feature ID for this repeat, which identifies a single repeat, which may be multi-segement, and allows linking the segments together.

The feature ID can be either a CFeat_id as in ASN.1, or a RepeatMasker feature ID encoded as such a CFeat_id using a local integer ID.

Implements IRepeatRegion.

Definition at line 160 of file rm_reader.cpp.

References GetRptId(), and result.

◆ GetLocation()

CConstRef< CSeq_loc > SRepeatRegion::GetLocation ( void ) const

virtual

Gets the location of this repeat.

Warning: Repeat features may be multi-interval. RepeatMasker can identify repeats that have been split by other intervening repeats, and while RepeatMasker output will emit these as multiple lines, tied together by repeat ID, in the NCBI ASN.1 data model this may be normalized into a single multi-interval feature.

Implements IRepeatRegion.

Definition at line 155 of file rm_reader.cpp.

References query_location.

◆ GetPercDel()

SRepeatRegion::TPercent SRepeatRegion::GetPercDel ( ) const

virtual

Implements IRawRepeatRegion.

Definition at line 227 of file rm_reader.cpp.

References perc_del.

◆ GetPercDiv()

SRepeatRegion::TPercent SRepeatRegion::GetPercDiv ( ) const

virtual

Implements IRawRepeatRegion.

Definition at line 222 of file rm_reader.cpp.

References perc_div.

◆ GetPercIns()

SRepeatRegion::TPercent SRepeatRegion::GetPercIns ( ) const

virtual

Implements IRawRepeatRegion.

Definition at line 232 of file rm_reader.cpp.

References perc_ins.

◆ GetRptClass()

string SRepeatRegion::GetRptClass ( ) const

virtual

Gets repeat class, or empty string if not known.

Implements IRepeat.

Definition at line 189 of file rm_reader.cpp.

References rpt_class.

◆ GetRptFamily()

string SRepeatRegion::GetRptFamily ( ) const

virtual

Gets repeat family, or empty string if not known.

Implements IRepeat.

Definition at line 184 of file rm_reader.cpp.

References rpt_family.

◆ GetRptId()

SRepeatRegion::TRptId SRepeatRegion::GetRptId ( ) const

virtual

Implements IRawRepeatRegion.

Definition at line 212 of file rm_reader.cpp.

References rpt_id.

Referenced by GetId().

◆ GetRptLeft()

TSeqPos SRepeatRegion::GetRptLeft ( ) const

virtual

Implements IRawRepeatRegion.

Definition at line 247 of file rm_reader.cpp.

References rpt_left.

Referenced by GetRptLength().

◆ GetRptLength()

TSeqPos SRepeatRegion::GetRptLength ( ) const

virtual

Gets repeat length, or kInvalidSeqPos if not known.

Implements IRepeat.

Definition at line 198 of file rm_reader.cpp.

References GetRptLeft(), GetRptPosEnd(), and kInvalidSeqPos.

◆ GetRptName()

string SRepeatRegion::GetRptName ( ) const

virtual

Gets repeat name.

Implements IRepeat.

Definition at line 179 of file rm_reader.cpp.

References matching_repeat.

◆ GetRptPosBegin()

TSeqPos SRepeatRegion::GetRptPosBegin ( ) const

virtual

Implements IRawRepeatRegion.

Definition at line 237 of file rm_reader.cpp.

References rpt_pos_begin.

◆ GetRptPosEnd()

TSeqPos SRepeatRegion::GetRptPosEnd ( ) const

virtual

Implements IRawRepeatRegion.

Definition at line 242 of file rm_reader.cpp.

References rpt_pos_end.

Referenced by GetRptLength().

◆ GetRptRepbaseId()

string SRepeatRegion::GetRptRepbaseId ( ) const

virtual

Returns an empty string, not known.

The Repbase ID is not present in RepeatMasker output.

Implements IRepeat.

Definition at line 208 of file rm_reader.cpp.

References kEmptyStr.

◆ GetRptSpecificity()

SRepeatRegion::TTaxId SRepeatRegion::GetRptSpecificity ( ) const

virtual

Returns 0, not known.

The specificity is not present in RepeatMasker output.

Implements IRepeat.

Definition at line 194 of file rm_reader.cpp.

◆ GetRptSpecificityName()

string SRepeatRegion::GetRptSpecificityName ( ) const

virtual

Returns an empty string, not known.

The specificity is not present in RepeatMasker output.

Implements IRepeat.

Definition at line 204 of file rm_reader.cpp.

References kEmptyStr.

◆ GetSeqIdString()

string SRepeatRegion::GetSeqIdString ( ) const

virtual

Overridden version returns the orginal unparsed sequence identifier, if it was set (non-empty).

Reimplemented from IRepeatRegion.

Definition at line 170 of file rm_reader.cpp.

References IRepeatRegion::GetSeqIdString(), and query_sequence.

◆ GetSeqLeft()

TSeqPos SRepeatRegion::GetSeqLeft ( ) const

virtual

Implements IRawRepeatRegion.

Definition at line 252 of file rm_reader.cpp.

References query_left.

◆ GetSwScore()

SRepeatRegion::TScore SRepeatRegion::GetSwScore ( ) const

virtual

Implements IRawRepeatRegion.

Definition at line 217 of file rm_reader.cpp.

References sw_score.

◆ IsOverlapped()

bool SRepeatRegion::IsOverlapped ( ) const

virtual

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

Implements IRawRepeatRegion.

Definition at line 257 of file rm_reader.cpp.

References overlapped.

Member Data Documentation

◆ matching_repeat

string SRepeatRegion::matching_repeat

Definition at line 407 of file rm_reader.hpp.

Referenced by GetRptName(), and CRepeatMaskerReader::ParseRecord().

◆ overlapped

bool SRepeatRegion::overlapped

Definition at line 414 of file rm_reader.hpp.

Referenced by IsOverlapped(), and CRepeatMaskerReader::ParseRecord().

◆ perc_del

TPercent SRepeatRegion::perc_del

Definition at line 403 of file rm_reader.hpp.

Referenced by GetPercDel(), and CRepeatMaskerReader::ParseRecord().

◆ perc_div

TPercent SRepeatRegion::perc_div

Definition at line 402 of file rm_reader.hpp.

Referenced by GetPercDiv(), and CRepeatMaskerReader::ParseRecord().

◆ perc_ins

TPercent SRepeatRegion::perc_ins

Definition at line 404 of file rm_reader.hpp.

Referenced by GetPercIns(), and CRepeatMaskerReader::ParseRecord().

◆ query_left

TSeqPos SRepeatRegion::query_left

Definition at line 401 of file rm_reader.hpp.

Referenced by GetSeqLeft(), and CRepeatMaskerReader::ParseRecord().

◆ query_location

CRef<CSeq_loc> SRepeatRegion::query_location

Definition at line 399 of file rm_reader.hpp.

Referenced by GetLocation(), and CRepeatMaskerReader::ParseRecord().

◆ query_sequence

string SRepeatRegion::query_sequence

Definition at line 405 of file rm_reader.hpp.

Referenced by GetSeqIdString(), and CRepeatMaskerReader::ParseRecord().

◆ rpt_class

string SRepeatRegion::rpt_class

Definition at line 408 of file rm_reader.hpp.

Referenced by GetRptClass(), and CRepeatMaskerReader::ParseRecord().

◆ rpt_family

string SRepeatRegion::rpt_family

Definition at line 409 of file rm_reader.hpp.

Referenced by GetRptFamily(), and CRepeatMaskerReader::ParseRecord().

◆ rpt_id

TRptId SRepeatRegion::rpt_id

Definition at line 413 of file rm_reader.hpp.

Referenced by GetRptId(), and CRepeatMaskerReader::ParseRecord().

◆ rpt_left

TSeqPos SRepeatRegion::rpt_left

Definition at line 412 of file rm_reader.hpp.

Referenced by GetRptLeft(), and CRepeatMaskerReader::ParseRecord().

◆ rpt_pos_begin

TSeqPos SRepeatRegion::rpt_pos_begin

Definition at line 410 of file rm_reader.hpp.

Referenced by GetRptPosBegin(), and CRepeatMaskerReader::ParseRecord().

◆ rpt_pos_end

TSeqPos SRepeatRegion::rpt_pos_end

Definition at line 411 of file rm_reader.hpp.

Referenced by GetRptPosEnd(), and CRepeatMaskerReader::ParseRecord().

◆ strand

string SRepeatRegion::strand

Definition at line 406 of file rm_reader.hpp.

◆ sw_score

TScore SRepeatRegion::sw_score

Definition at line 400 of file rm_reader.hpp.

Referenced by GetSwScore(), and CRepeatMaskerReader::ParseRecord().

The documentation for this class was generated from the following files:

include/objtools/readers/rm_reader.hpp
src/objtools/readers/rm_reader.cpp

Public Types

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TParent

◆ TThisType

Member Function Documentation

◆ GetId()

◆ GetLocation()

◆ GetPercDel()

◆ GetPercDiv()

◆ GetPercIns()

◆ GetRptClass()

◆ GetRptFamily()

◆ GetRptId()

◆ GetRptLeft()

◆ GetRptLength()

◆ GetRptName()

◆ GetRptPosBegin()

◆ GetRptPosEnd()

◆ GetRptRepbaseId()

◆ GetRptSpecificity()

◆ GetRptSpecificityName()

◆ GetSeqIdString()

◆ GetSeqLeft()

◆ GetSwScore()

◆ IsOverlapped()

Member Data Documentation

◆ matching_repeat

◆ overlapped

◆ perc_del

◆ perc_div

◆ perc_ins

◆ query_left

◆ query_location

◆ query_sequence

◆ rpt_class

◆ rpt_family

◆ rpt_id

◆ rpt_left

◆ rpt_pos_begin

◆ rpt_pos_end

◆ strand

◆ sw_score