NCBI C++ ToolKit
Public Types | Public Member Functions | Public Attributes | List of all members
SRepeatRegion Class Reference

Search Toolkit Book for SRepeatRegion

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_locGetLocation (void) const
 Gets the location of this repeat. More...
 
CConstRef< CFeat_idGetId () 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_locquery_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

Definition at line 354 of file rm_reader.hpp.

◆ 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:
Modified on Mon Apr 22 04:04:55 2024 by modify_doxy.py rev. 669887