Raw content of Bio::EnsEMBL::ExternalData::Haplotype::Pattern
<![CDATA[#
# BioPerl module for Bio::EnsEMBL::ExternalData::Haplotype::Pattern
#
# Cared for by Tony Cox <avc@sanger.ac.uk>
#
# Copyright EnsEMBL
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Pattern - DESCRIPTION of Object
This object represents a database of haplotype patterns.
=head1 SYNOPSIS
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::ExternalData::Haplotype::HaplotypeAdaptor;
use Bio::EnsEMBL::ExternalData::Haplotype::Haplotype;
use Bio::EnsEMBL::ExternalData::Haplotype::Pattern;
$hapdb = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-user => 'ensro',
-dbname => 'haplotype_5_28',
-host => 'ecs3d',
-driver => 'mysql',
);
my $hap_adtor = Bio::EnsEMBL::ExternalData::Haplotype::HaplotypeAdaptor->new($hapdb);
$hap = $hap_adtor->get_Haplotype_by_id('B10045'); # Haplotype id
### You can add the HaplotypeAdaptor as an 'external adaptor' to the 'main'
### Ensembl database object, then use it as:
$ensdb = Bio::EnsEMBL::DBSQL::DBAdaptor->new( ... );
$ensdb->add_ExternalAdaptor('haplotype', $hap_adtor);
# then later on, elsewhere:
$hap_adtor = $ensdb->get_ExternalAdaptor('haplotype');
# also available:
$ensdb->list_ExternalAdaptors();
$ensdb->remove_ExternalAdaptor('haplotype');
=head1 DESCRIPTION
This module is an entry point into a database of haplotypes,
The objects can only be read from the database, not written. (They are
loaded ussing a separate perl script).
For more info, see Haplotype.pm
=head1 CONTACT
Tony Cox <Lavc@sanger.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...;
package Bio::EnsEMBL::ExternalData::Haplotype::Pattern;
use vars qw(@ISA);
use strict;
# Object preamble - inheriets from Bio::Root::Object
use Bio::Root::Object;
@ISA = qw(Bio::Root::Object);
=head2 new
Title : new
Usage : not intended for general use.
Function:
Example :
Returns : a haplotype pattern - caller may also fill using methods
Args :
=cut
sub new {
my ($class, $adaptor, $pattern_id, $count, $pattern, $pattern_frequency) = @_;
my $self = {};
bless $self,$class;
$self->{'_adaptor'} = $adaptor;
$self->{'pattern_id'} = $pattern_id;
$self->{'count'} = $count;
$self->{'pattern'} = uc($pattern);
$self->{'pattern_frequency'} = $pattern_frequency;
return($self);
}
=head2 id
Title : id
Usage :
Function: get/set the display id of the pattern
Example :
Returns :
Args :
=cut
sub id {
my ($self,$value) = @_;
if( defined $value) {
$self->pattern_id($value);
}
return $self->pattern_id();
}
=head2 pattern_id
Title : pattern_id
Usage :
Function: get/set the display id of the pattern
Example :
Returns :
Args :
=cut
sub pattern_id {
my ($self,$value) = @_;
if( defined $value) {
$self->{'pattern_id'} = $value;
}
return $self->{'pattern_id'};
}
=head2 block_id
Title : block_id
Usage :
Function: get/set the block id of the Haplotype
Example :
Returns :
Args :
=cut
sub block_id {
my ($self,$value) = @_;
if( defined $value) {
$self->{'block_id'} = $value;
}
return $self->{'block_id'};
}
=head2 count
Title : count
Usage :
Function: get/set the count for the pattern
: this is number of chromosomes that were observed to be consistent
: with this pattern
Example :
Returns :
Args :
=cut
sub count {
my ($self,$value) = @_;
if( defined $value) {
$self->{'count'} = $value;
}
return $self->{'count'};
}
=head2 pattern_length
Title : pattern_length
Usage : read only
Function: get the length for the pattern
Example :
Returns :
Args :
=cut
sub pattern_length {
my ($self) = @_;
return (length($self->{'pattern'}));
}
=head2 pattern
Title : pattern
Usage :
Function: get/set the consensus pattern of bases for this pattern
Example :
Returns :
Args :
=cut
sub pattern {
my ($self,$value) = @_;
if( defined $value) {
$self->{'pattern'} = $value;
}
return $self->{'pattern'};
}
=head2 pattern_frequency
Title : pattern_frequency
Usage :
Function: get/set the consensus pattern frequency for this pattern
Example :
Returns :
Args :
=cut
sub pattern_frequency {
my ($self,$value) = @_;
if( defined $value) {
$self->{'pattern_frequency'} = $value;
}
return $self->{'pattern_frequency'};
}
=head2 samples
Title : samples
Usage :
Function: store a ref to a hash of sample data
Example :
Returns :
Args : ref to a hash of sample=>patterns
=cut
sub samples {
my ($self,$value) = @_;
if( defined $value) {
$self->{'samples'} = $value;
}
return $self->{'samples'};
}
=head2 unclassified_samples
Title : unclassified_samples
Usage :
Function: store a ref to a hash of unclassified sample data
Example :
Returns :
Args :
=cut
sub unclassified_samples {
my ($self,$value) = @_;
if( defined $value) {
$self->{'unclassified_samples'} = $value;
}
return $self->{'unclassified_samples'};
}
=head2 ref_base
Title : ref_base
Usage :
Function: get/set the reference sequence base for the pattern
Example :
Returns :
Args :
=cut
sub ref_base {
my ($self,$value) = @_;
if( defined $value) {
$self->{'ref_base'} = $value;
}
return $self->{'ref_base'};
}
=head2 alt_base
Title : alt_base
Usage :
Function: get/set the alternative sequence base for the pattern
Example :
Returns :
Args :
=cut
sub alt_base {
my ($self,$value) = @_;
if( defined $value) {
$self->{'alt_base'} = $value;
}
return $self->{'alt_base'};
}
=head2 ref_calls
Title : ref_calls
Usage :
Function: get/set the no calls of reference sequence base for the pattern
Example :
Returns :
Args :
=cut
sub ref_calls {
my ($self,$value) = @_;
if( defined $value) {
$self->{'ref_calls'} = $value;
}
return $self->{'ref_calls'};
}
=head2 alt_calls
Title : alt_base
Usage :
Function: get/set the no calls of the alternative sequence base for the pattern
Example :
Returns :
Args :
=cut
sub alt_calls {
my ($self,$value) = @_;
if( defined $value) {
$self->{'alt_calls'} = $value;
}
return $self->{'alt_calls'};
}
1;
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