Bio::EnsEMBL
RepeatFeature
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Summary
Bio::EnsEMBL::RepeatFeature - A feature representing a repeat on a piece of
sequence.
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
my $rf = new Bio::EnsEMBL::Feature(
-start => 100,
-end => 220,
-strand => -1,
-slice => $slice,
-analysis => $analysis,
-repeat_consensus => $rc,
-hstart => 10,
-hend => 100,
-hstrand => 1,
-score => 83.2
);
my $hstart = $feat->hstart;
my $hend = $feat->hend;
# move the feature to the chromosomal coordinate system
$feature = $feature->transform('chromosome');
# move the feature to a different slice
# (possibly on another coord system)
$feature = $feature->transfer($new_slice);
# project the feature onto another coordinate system possibly across
# boundaries:
@projection = @{ $feature->project('contig') };
# change the start, end, and strand of the feature in place
$feature->move( $new_start, $new_end, $new_strand );
Description
This a feature representing a repeat region on a sequence
Methods
Methods description
Arg [1] : none
Example : print $rf->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For repeat_features this is the
name of the repeat consensus if it is available otherwise it is
an empty string.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable |
Arg [1] : (optional) int $hend
Example : $hit_end = $repeat->hend;
Description: Getter/Setter for the end bp of this repeat match on the
consensus sequence.
Returntype : int
Exceptions : none
Caller : general
Status : Stable |
Arg [1] : (optional) int $hstart
Example : $hit_start = $repeat->hstart;
Description: Getter/Setter for the start bp of this repeat match on the
consensus sequence.
Returntype : int
Exceptions : none
Caller : general
Status : Stable |
Arg [1] : none
Example : none
Description: always returns 1. method exists for consistancy with other
features.
Returntype : int
Exceptions : none
Caller : general
Status : Stable |
Arg [REPEAT_CONSENSUS] : Bio::EnsEMBL::RepeatConsensus (optional)
The repeat consensus for this repeat feature
Arg [HSTART] : int (optional)
The hit start on the consensus sequence
Arg [HEND] : int (optional)
The hit end on the consensus sequence
Arg [SCORE] : float (optional)
The score
Arg [...] : Named arguments to superclass constructor
(see Bio::EnsEMBL::Feaure)
Example : $rf = Bio::EnsEMBL::RepeatFeature->new(-REPEAT_CONSENSUS => $rc,
-HSTART => 10,
-HEND => 100,
-SCORE => 58.0,
-START => 1_000_100,
-END => 1_000_190,
-STRAND => 1,
-ANALYSIS => $an,
-SLICE => $chr_slice);
Description: Creates a new Bio::EnsEMBL::RepeatFeature object
Returntype : Bio::EnsEMBL::RepeatFeature
Exceptions : none
Caller : RepeatFeatureAdaptors
Status : Stable |
Arg [1] : hash reference $hashref
Example : none
Description: This is an ultra fast constructor which requires knowledge of
the objects internals to be used. It is only used by
RepeatFeatureAdaptors (when thousands of repeats need to be
quickly created). The constructor 'new' should be used in
most instances.
Returntype : Bio::EnsEMBL::RepeatFeature
Exceptions : none
Caller : RepeatFeatureAdaptors |
Arg [1] : (optional) Bio::EnsEMBL::RepeatConsensus
Example : $repeat_consensus = $repeat->repeat_consensus;
Description: Getter/Setter for the repeat consensus of this repeat
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general
Status : Stable |
Arg [1] : (optional) float $score
Example : $score = $repeat->score();
Description: Getter/Setter for the score of this repeat feature
Returntype : int
Exceptions : none
Caller : general
Status : Stable |
Methods code
sub display_id
{ my $self = shift;
my $id = '';
my $rc = $self->{'repeat_consensus'};
if($rc) {
$id = $rc->name();
}
return $id;
}
1;
__END__} | sub hend
{ my $self = shift;
$self->{'hend'} = shift if(@_);
return $self->{'hend'};} | sub hstart
{ my $self = shift;
$self->{'hstart'} = shift if(@_);
return $self->{'hstart'};} | sub new
{ my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($repeat_consensus, $hstart, $hend, $score) =
rearrange(['REPEAT_CONSENSUS','HSTART','HEND','SCORE'], @_);
$self->repeat_consensus($repeat_consensus);
$self->{'hstart'} = $hstart;
$self->{'hend'} = $hend;
$self->{'score'} = $score;
return $self;} | sub new_fast
{ my ($class, $hashref) = @_;
return bless $hashref, $class; } | sub repeat_consensus
{ my $self = shift;
if(@_) {
my $rc = shift;
if(defined($rc)) {
if(!ref($rc) || !$rc->isa('Bio::EnsEMBL::RepeatConsensus')) {
throw('RepeatConsensus arg must be a Bio::EnsEMBL::RepeatConsensus');
}
}
$self->{'repeat_consensus'} = $rc;
}
return $self->{'repeat_consensus'};} | sub score
{ my $self = shift;
$self->{'score'} = shift if(@_);
return $self->{'score'};} | General documentation
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
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