Raw content of Bio::EnsEMBL::Compara::SitewiseOmega
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#
# Ensembl module for Bio::EnsEMBL::Compara::SitewiseOmega
#
# Cared for by Albert Vilella <avilella@ebi.ac.uk>
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Compara::SitewiseOmega - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 AUTHOR - Albert Vilella
This modules is part of the Ensembl project
Email avilella@ebi.ac.uk
Describe contact details here
=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::Compara::SitewiseOmega;
use strict;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(warning deprecate throw);
=head2 new_fast
Arg [1] : hash reference $hashref
Example : none
Description: This is an ultra fast constructor which requires knowledge of
the objects internals to be used.
Returntype :
Exceptions : none
Caller :
=cut
sub new_fast {
my ($class, $hashref) = @_;
return bless $hashref, $class;
}
=head2 member_position
Arg [1] : Bio::EnsEMBL::Member $member
Arg [2] : Bio::SimpleAlign $aln
Example : $sitewise_omega->member_position($member,$aln);
Description: Obtain the member position for a given sitewise_omega value
Returntype : integer
Exceptions : return undef if member not in the alignment or aln_position not in member
Caller : general
Status : At risk
=cut
sub member_position {
my ($self, $member, $aln) = @_;
throw("$member is not a Bio::EnsEMBL::Compara::Member object")
unless ($member->isa("Bio::EnsEMBL::Compara::Member"));
throw("$aln is not a Bio::SimpleAlign object")
unless ($aln->isa("Bio::SimpleAlign"));
my @seqs = $aln->each_seq_with_id($member->stable_id);
my $seq = $seqs[0];
my $seq_location;
eval { $seq_location = $seq->location_from_column($self->aln_position);};
return undef if ($@);
my $location_type;
eval { $location_type = $seq_location->location_type;};
return undef if ($@);
if ($seq_location->location_type eq 'EXACT') {
my $member_position = $seq_location->start;
return $member_position;
}
return undef;
}
=head2 adaptor
Arg [1] : Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor $adaptor
Example : $sitewise_omega->adaptor($adaptor);
Description: Getter/Setter for the adaptor this object used for database
interaction
Returntype : Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor object
Exceptions : thrown if the argument is not a
Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor object
Caller : general
Status : At risk
=cut
sub adaptor {
my ( $self, $adaptor ) = @_;
if (defined($adaptor)) {
throw("$adaptor is not a Bio::EnsEMBL::Compara::DBSQL::SitewiseOmegaAdaptor object")
unless ($adaptor->isa("Bio::EnsEMBL::Compara::DBSQL::SitewiseOmegaAdaptor"));
$self->{'adaptor'} = $adaptor;
}
return $self->{'adaptor'};
}
=head2 aln_position
Arg [1] : (opt) integer
Example : $sitewise_dnds->aln_position(1);
Description: Getter/Setter for the alignment position
Returntype : integer. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk
=cut
sub aln_position {
my ($self, $aln_position) = @_;
if(defined $aln_position) {
$self->{'aln_position'} = $aln_position;
}
$self->{'aln_position'}= undef unless(defined($self->{'aln_position'}));
return $self->{'aln_position'};
}
=head2 omega
Arg [1] : (opt) integer
Example : $sitewise_dnds->omega(1);
Description: Getter/Setter for the omega value
Returntype : integer. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk
=cut
sub omega {
my ($self, $omega) = @_;
if(defined $omega) {
$self->{'omega'} = $omega;
}
$self->{'omega'}= undef unless(defined($self->{'omega'}));
return $self->{'omega'};
}
=head2 omega_lower
Arg [1] : (opt) float
Example : $sitewise_dnds->omega_lower(1);
Description: Getter/Setter for the omega_lower value
Returntype : float. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk
=cut
sub omega_lower {
my ($self, $omega_lower) = @_;
if(defined $omega_lower) {
$self->{'omega_lower'} = $omega_lower;
}
$self->{'omega_lower'}= undef unless(defined($self->{'omega_lower'}));
return $self->{'omega_lower'};
}
=head2 omega_upper
Arg [1] : (opt) float
Example : $sitewise_dnds->omega_upper(1);
Description: Getter/Setter for the omega_upper value
Returntype : float. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk
=cut
sub omega_upper {
my ($self, $omega_upper) = @_;
if(defined $omega_upper) {
$self->{'omega_upper'} = $omega_upper;
}
$self->{'omega_upper'}= undef unless(defined($self->{'omega_upper'}));
return $self->{'omega_upper'};
}
=head2 optimal
Arg [1] : (opt) float
Example : $sitewise_dnds->optimal(1);
Description: Getter/Setter for the optimal value
Returntype : float. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk
=cut
sub optimal {
my ($self, $optimal) = @_;
if(defined $optimal) {
$self->{'optimal'} = $optimal;
}
$self->{'optimal'}= undef unless(defined($self->{'optimal'}));
return $self->{'optimal'};
}
=head2 threshold_on_branch_ds
Arg [1] : (opt) float
Example : $sitewise_dnds->threshold_on_branch_ds(1);
Description: Getter/Setter for the threshold_on_branch_ds value
Returntype : float. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk
=cut
sub threshold_on_branch_ds {
my ($self, $threshold_on_branch_ds) = @_;
if(defined $threshold_on_branch_ds) {
$self->{'threshold_on_branch_ds'} = $threshold_on_branch_ds;
}
$self->{'threshold_on_branch_ds'}= undef unless(defined($self->{'threshold_on_branch_ds'}));
return $self->{'threshold_on_branch_ds'};
}
=head2 type
Arg [1] : (opt) integer
Example : $sitewise_dnds->type(1);
Description: Getter/Setter for the type value
Returntype : integer. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk
=cut
sub type {
my ($self, $type) = @_;
if(defined $type) {
$self->{'type'} = $type;
}
$self->{'type'}= undef unless(defined($self->{'type'}));
return $self->{'type'};
}
=head2 node_id
Arg [1] : (opt) integer
Example : $sitewise_dnds->node_id(1);
Description: Getter/Setter for the node_id value
Returnnode_id : integer. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk
=cut
sub node_id {
my ($self, $node_id) = @_;
if(defined $node_id) {
$self->{'node_id'} = $node_id;
}
$self->{'node_id'}= undef unless(defined($self->{'node_id'}));
return $self->{'node_id'};
}
=head2 tree_node_id
Arg [1] : (opt) integer
Example : $sitewise_dnds->tree_node_id(1);
Description: Getter/Setter for the tree_node_id value
Returntree_node_id : integer. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk
=cut
sub tree_node_id {
my ($self, $tree_node_id) = @_;
if(defined $tree_node_id) {
$self->{'tree_node_id'} = $tree_node_id;
}
$self->{'tree_node_id'}= undef unless(defined($self->{'tree_node_id'}));
return $self->{'tree_node_id'};
}
sub dbID {
my ($self, $dbID) = @_;
if(defined $dbID) {
$self->{'_dbID'} = $dbID;
}
$self->{'_dbID'}= undef unless(defined($self->{'_dbID'}));
return $self->{'_dbID'};
}
1;
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