Bio::EnsEMBL::Mapper Coordinate
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Summary
Bio::EnsEMBL::Mapper::Coordinate
Package variables
No package variables defined.
Synopsis
Description
Representation of a mapped region in a sequence; returned from Mapper.pm
when the target region maps on to valid sequence.
Methods
coord_systemDescriptionCode
endDescriptionCode
idDescriptionCode
lengthDescriptionCode
newDescriptionCode
startDescriptionCode
strandDescriptionCode
Methods description
coord_systemcode    nextTop
  Arg  1      Bio::EnsEMBL::CoordSystem
  Function    getter/setter method
  Returntype  Bio::EnsEMBL::CoordSystem
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
endcodeprevnextTop
  Arg  1      int $end
              end coordinate of object in mapped region
  Function    getter/setter method
  Returntype  int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
idcodeprevnextTop
  Arg  1      char|int $id
              id of object in mapped region
	      e.g. seq_region_id / seq_region_name
  Function    getter/setter method
  Returntype  char|int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
lengthcodeprevnextTop
  Function    getter method
  Returntype  int
  Exceptions  none
  Caller      ?
  Status      Stable
newcodeprevnextTop
  Arg [1]     char|int id of object in mapped region
  Arg [2]     int start of region   
  Arg [3]     int end of region
  Arg [4]     int strand if region
  Arg [5]     Bio::EnsEMBL::CoordSystem  coordsytem of the region
  Function    creates a new Coordinate object
  Returntype  Bio::EnsEMBL::Mapper::Coordinate
  Exceptions  none
  Status      Stable
startcodeprevnextTop
  Arg  1      int $start
              start coordinate of object in mapped region
  Function    getter/setter method
  Returntype  int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
strandcodeprevnextTop
  Arg  1      int $strand
              strand of object in mapped region
  Function    getter/setter method
  Returntype  int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable
Methods code
coord_systemdescriptionprevnextTop
sub coord_system {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'coord_system'} = $value;
  }

  return $self->{'coord_system'};
}
enddescriptionprevnextTop
sub end {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'end'} = $value;
  }

  return $self->{'end'};
}
iddescriptionprevnextTop
sub id {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'id'} = $value;
  }

  return $self->{'id'};
}
lengthdescriptionprevnextTop
sub length {
  my ($self) = @_;

  return $self->{'end'} - $self->{'start'} + 1;
}

1;
}
newdescriptionprevnextTop
sub new {
  my ( $proto, $id, $start, $end, $strand, $coord_system ) = @_;

  my $class = ref($proto) || $proto;

  return
    bless( { 'id'           => $id,
             'start'        => $start,
             'end'          => $end,
             'strand'       => $strand,
             'coord_system' => $coord_system
           },
           $class );
}
startdescriptionprevnextTop
sub start {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'start'} = $value;
  }

  return $self->{'start'};
}
stranddescriptionprevnextTop
sub strand {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'strand'} = $value;
  }

  return $self->{'strand'};
}
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>.