Bio::EnsEMBL::IdMapping::TinyExon Class Reference

Inheritance diagram for Bio::EnsEMBL::IdMapping::TinyExon:

Public Member Functions
public Int	start ()
public Int	end ()
public Int	strand ()
public String	seq_region_name ()
public String	coord_system_name ()
public String	coord_system_version ()
public String	seq ()
public Int	phase ()
public Boolean	need_project ()
public Int	common_start ()
public Int	common_end ()
public Int	common_strand ()
public String	common_sr_name ()
public Int	length ()
Public Member Functions inherited from Bio::EnsEMBL::IdMapping::TinyFeature
public Bio::EnsEMBL::IdMapping::TinyFeature	new_fast ()
public Int	id ()
public String	stable_id ()
public Int	version ()
public String	created_date ()
public String	modified_date ()
public String	to_string ()

Detailed Description

Synopsis

# fetch an exon from the db and create a lightweight exon object
# from it
my $exon = $exon_adaptor->fetch_by_stable_id('ENSE000345437');
my $lightweight_exon = Bio::EnsEMBL::IdMapping::TinyExon->new_fast( [
    $exon->dbID,
    $exon->stable_id,
    $exon->version,
    $exon->created_date,
    $exon->modified_date,
    $exon->start,
    $exon->end,
    $exon->strand,
    $exon->slice->seq_region_name,
    $exon->slice->coord_system_name,
    $exon->slice->coord_system->version,
    $exon->slice->subseq( $exon->start, $exon->end, $exon->strand ),
    $exon->phase,
    $need_project,
] );

Description

This is a lightweight exon object for the stable Id mapping. See the
documentation in TinyFeature for general considerations about its
design.

Definition at line 37 of file TinyExon.pm.

Member Function Documentation

common_end()

public Int Bio::EnsEMBL::IdMapping::TinyExon::common_end

(

)

  Arg[1]      : (optional) Int - the exon's end in common coord_system
                coordinates
  Description : Getter/setter for the exon's end in common coord_system
                coordinates. Will return $self->end if no projection to a
                common coord_system is required.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

common_sr_name()

public String Bio::EnsEMBL::IdMapping::TinyExon::common_sr_name

(

)

  Arg[1]      : (optional) String - seq_region name of the exon's slice on the
                common coord_system
  Description : Getter/setter for the seq_region name of the exon's slice on the
                common coord_system coordinates. Will return
                $self->seq_region_name if no projection to a common coord_system
                is required.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

common_start()

public Int Bio::EnsEMBL::IdMapping::TinyExon::common_start

(

)

  Arg[1]      : (optional) Int - the exon's start in common coord_system
                coordinates
  Description : Getter/setter for the exon's start in common coord_system
                coordinates. Will return $self->start if no projection to a
                common coord_system is required.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

common_strand()

public Int Bio::EnsEMBL::IdMapping::TinyExon::common_strand

(

)

  Arg[1]      : (optional) Int - the exon's strand in common coord_system
                coordinates
  Description : Getter/setter for the exon's strand in common coord_system
                coordinates. Will return $self->strand if no projection to a
                common coord_system is required.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

coord_system_name()

public String Bio::EnsEMBL::IdMapping::TinyExon::coord_system_name

(

)

  Arg[1]      : (optional) String - coord_system name
  Description : Getter/setter for the coord_system name of the slice the exon is
                on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

coord_system_version()

public String Bio::EnsEMBL::IdMapping::TinyExon::coord_system_version

(

)

  Arg[1]      : (optional) String - coord_system version
  Description : Getter/setter for the coord_system version of the slice the
                exon is on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

end()

public Int Bio::EnsEMBL::IdMapping::TinyExon::end

(

)

  Arg[1]      : (optional) Int - the exon's end coordinate
  Description : Getter/setter for the exon's end coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

length()

public Int Bio::EnsEMBL::IdMapping::TinyExon::length

(

)

  Description : Returns the exon length (distance between start and end).
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

need_project()

public Boolean Bio::EnsEMBL::IdMapping::TinyExon::need_project

(

)

  Arg[1]      : (optional) Boolean - attribute to set
  Description : Getter/setter for the attribute determining whether an exon
                needs to be projected onto a common coord_system. You don't need
                to do so if the native coord_system is common to the source and
                target assemblies, or if no common coord_system is found (the
                Cache object has methods to determine this).
  Return type : Boolean
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

phase()

public Int Bio::EnsEMBL::IdMapping::TinyExon::phase

(

)

  Arg[1]      : (optional) Int - the exon's phase
  Description : Getter/setter for the exon's phase.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

seq()

public String Bio::EnsEMBL::IdMapping::TinyExon::seq

(

)

  Arg[1]      : (optional) String - the exon's sequence
  Description : Getter/setter for the exon's sequence.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

seq_region_name()

public String Bio::EnsEMBL::IdMapping::TinyExon::seq_region_name

(

)

  Arg[1]      : (optional) String - seq_region name
  Description : Getter/setter for the seq_region name of the slice the exon is
                on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

start()

public Int Bio::EnsEMBL::IdMapping::TinyExon::start

(

)

  Arg[1]      : (optional) Int - the exon's start coordinate
  Description : Getter/setter for the exon's start coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

strand()

public Int Bio::EnsEMBL::IdMapping::TinyExon::strand

(

)

  Arg[1]      : (optional) Int - the exon's strand
  Description : Getter/setter for the exon's strand.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/IdMapping/TinyExon.pm