Bio::EnsEMBL::IdMapping TinyExon
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Summary
Bio::EnsEMBL::IdMapping::TinyExon - lightweight exon object
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::IdMapping::TinyFeature
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::IdMapping::TinyFeature
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.
Methods
common_endDescriptionCode
common_sr_nameDescriptionCode
common_startDescriptionCode
common_strandDescriptionCode
coord_system_nameDescriptionCode
coord_system_versionDescriptionCode
endDescriptionCode
is_knownDescriptionCode
lengthDescriptionCode
need_projectDescriptionCode
phaseDescriptionCode
seqDescriptionCode
seq_region_nameDescriptionCode
startDescriptionCode
strandDescriptionCode
Methods description
common_endcode    nextTop
  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
common_sr_namecodeprevnextTop
  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
common_startcodeprevnextTop
  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
common_strandcodeprevnextTop
  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
coord_system_namecodeprevnextTop
  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
coord_system_versioncodeprevnextTop
  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
endcodeprevnextTop
  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
is_knowncodeprevnextTop
  Description : Determine whether an exon is known. In the context of stable Id
                mapping, this is true for all exons.
  Return type : Boolean
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
lengthcodeprevnextTop
  Description : Returns the exon length (distance between start and end).
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
need_projectcodeprevnextTop
  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
phasecodeprevnextTop
  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
seqcodeprevnextTop
  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
seq_region_namecodeprevnextTop
  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
startcodeprevnextTop
  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
strandcodeprevnextTop
  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
Methods code
common_enddescriptionprevnextTop
sub common_end {
  my $self = shift;

  # when used as a setter, always set a value
  $self->[15] = shift if (@_);

  # when used as a getter
  if (scalar(@$self) > 14) {
    # return value for common coord_system if available (but avoid
    # autovivification gotcha!)
    return $self->[15];
  } elsif ($self->need_project) {
    # return undef if common value expected but not there (e.g. no projection
    # found
    return undef;
  } else {
    # return native value
    return $self->end;
  }
}
common_sr_namedescriptionprevnextTop
sub common_sr_name {
  my $self = shift;

  # when used as a setter, always set a value
  $self->[17] = shift if (@_);

  # when used as a getter
  if (scalar(@$self) > 14) {
    # return value for common coord_system if available (but avoid
    # autovivification gotcha!)
    return $self->[17];
  } elsif ($self->need_project) {
    # return undef if common value expected but not there (e.g. no projection
    # found
    return undef;
  } else {
    # return native value
    return $self->seq_region_name;
  }
}
common_startdescriptionprevnextTop
sub common_start {
  my $self = shift;

  # when used as a setter, always set a value
  $self->[14] = shift if (@_);

  # when used as a getter
  if (scalar(@$self) > 14) {
    # return value for common coord_system if available (but avoid
    # autovivification gotcha!)
    return $self->[14];
  } elsif ($self->need_project) {
    # return undef if common value expected but not there (e.g. no projection
    # found
    return undef;
  } else {
    # return native value
    return $self->start;
  }
}
common_stranddescriptionprevnextTop
sub common_strand {
  my $self = shift;

  # when used as a setter, always set a value
  $self->[16] = shift if (@_);

  # when used as a getter
  if (scalar(@$self) > 14) {
    # return value for common coord_system if available (but avoid
    # autovivification gotcha!)
    return $self->[16];
  } elsif ($self->need_project) {
    # return undef if common value expected but not there (e.g. no projection
    # found
    return undef;
  } else {
    # return native value
    return $self->strand;
  }
}
coord_system_namedescriptionprevnextTop
sub coord_system_name {
  my $self = shift;
  $self->[9] = shift if (@_);
  return $self->[9];
}
coord_system_versiondescriptionprevnextTop
sub coord_system_version {
  my $self = shift;
  $self->[10] = shift if (@_);
  return $self->[10];
}
enddescriptionprevnextTop
sub end {
  my $self = shift;
  $self->[6] = shift if (@_);
  return $self->[6];
}
is_knowndescriptionprevnextTop
sub is_known {
  return 1;
}


1;
}
lengthdescriptionprevnextTop
sub length {
  my $self = shift;
  return ($self->end - $self->start + 1);
}
need_projectdescriptionprevnextTop
sub need_project {
  my $self = shift;
  $self->[13] = shift if (@_);
  return $self->[13];
}
phasedescriptionprevnextTop
sub phase {
  my $self = shift;
  $self->[12] = shift if (@_);
  return $self->[12];
}
seqdescriptionprevnextTop
sub seq {
  my $self = shift;
  $self->[11] = shift if (@_);
  return $self->[11];
}
seq_region_namedescriptionprevnextTop
sub seq_region_name {
  my $self = shift;
  $self->[8] = shift if (@_);
  return $self->[8];
}
startdescriptionprevnextTop
sub start {
  my $self = shift;
  $self->[5] = shift if (@_);
  return $self->[5];
}
stranddescriptionprevnextTop
sub strand {
  my $self = shift;
  $self->[7] = shift if (@_);
  return $self->[7];
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.