Raw content of Bio::EnsEMBL::ProjectionSegment
<![CDATA[=head1 LICENSE
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
=head1 CONTACT
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>.
=cut
=head1 NAME
Bio::EnsEMBL::ProjectionSegment - part of the list that is returned from
project function calls
=head1 SYNOPSIS
$slice =
$sa->fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );
my $projection = $slice->project("clone");
foreach my $projection_segment (@$projection) {
print( " from_start ", $projection_segment->from_start(), "\n" );
print( " from_end ", $projection_segment->from_end(), "\n" );
print( " to_Slice ",
$projection_segment->to_Slice()->name(), "\n" );
}
=head1 DESCRIPTION
The ProjectionSegment is a helper object to make the arrays returned by
project more accessible. Instead of writing $segment->[0], $segment->[1]
or $segment->[2] its possible to use the more descriptive notation of
$segment->from_start(), $segement->from_end(), $segment->to_Slice().
=head1 METHODS
=cut
package Bio::EnsEMBL::ProjectionSegment;
#
# WARNING: THIS CLASS IS REPRESENTED BY A BLESSED ARRAY REFERENCE
# NOT A HASH REFERENCE
#
=head2 from_start
Args : none
Example : $coord_in_fetaure_start = $segment->from_start()
Description: First element in projects returned segment lists
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub from_start {
my $self = shift;
return $self->[0];
}
=head2 from_end
Args : none
Example : $coord_in_feature_end = $segment->from_end()
Description: Second element in projects returned segment lists
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub from_end {
my $self = shift;
return $self->[1];
}
=head2 to_Slice
Args : none
Example : $target_slice = $segment->to_Slice()
Description: Third element in projects returned segment lists
Returntype : Bio::EnsEMBL::Slice
Exceptions : none
Caller : general
Status : Stable
=cut
sub to_Slice {
my $self = shift;
return $self->[2];
}
1;
]]>