Raw content of Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor
<![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::DBSQL::BaseAlignFeatureAdaptor - Abstract Base class for
AlignFeatureAdaptors
=head1 SYNOPSIS
Abstract class, should not be instantiated. Implementation of abstract
methods must be performed by subclasses.
=head1 DESCRIPTION
This is a base adaptor for the align feature adaptors
DnaAlignFeatureAdaptor and ProteinAlignFeatureAdaptor.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor;
use vars qw(@ISA @EXPORT);
use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
@EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}});
=head2 fetch_all_by_Slice_and_hcoverage
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice from which to obtain align features.
Arg [2] : (optional) float $hcoverage
A lower bound for the hcoverage of feats to obtain.
Arg [3] : (optional) string $logic_name
The logic name of the type of features to obtain.
Example : @feats =
$adaptor->fetch_all_by_Slice_and_hcoverage( $slice, 50.0 );
Description: Returns a listref of features created from the
database which are on the Slice $slice and with a
hcoverage greater than $hcoverage. If logic name
is defined, only features with an analysis of type
$logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
in Slice coordinates
Exceptions : none
Caller : general
Status : At Risk
=cut
sub fetch_all_by_Slice_and_hcoverage {
my ( $self, $slice, $hcoverage, $logic_name ) = @_;
my $constraint;
if ( defined($hcoverage) ) {
$constraint = "hcoverage > $hcoverage";
}
return
$self->fetch_all_by_Slice_constraint( $slice, $constraint,
$logic_name );
}
=head2 fetch_all_by_Slice_and_external_db
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice from which to obtain align features.
Arg [2] : String $external_db_name
Name of the external DB to which the align features
should be restricted.
Arg [3] : (optional) string $logic_name
The logic name of the type of features to obtain.
Example : @feats =
$adaptor->fetch_all_by_Slice_and_external_db( $slice, 'EMBL' );
Description: Returns a listref of features created from the
database which are on the Slice $slice and associated
with external DB $external_db_name. If logic name
is defined, only features with an analysis of type
$logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
in Slice coordinates
Exceptions : thrown if $external_db_name is not defined or if
the subclass does not return a table alias for the
external_db table from _tables()
Caller : general
Status : At Risk
=cut
sub fetch_all_by_Slice_and_external_db {
my ( $self, $slice, $external_db_name, $logic_name ) = @_;
if ( !defined($external_db_name) ) {
throw("Need name of external DB to restrict to");
}
my @join_tables = $self->_tables();
my $edb_alias;
foreach my $join_table (@join_tables) {
my ( $table, $table_alias ) = @{$join_table};
if ( $table eq 'external_db' ) {
$edb_alias = $table_alias;
last;
}
}
if ( !defined($edb_alias) ) {
throw("Can not find alias for external_db table");
}
my $constraint = sprintf( "%s.db_name = %s",
$edb_alias,
$self->dbc()->db_handle()
->quote( $external_db_name, SQL_VARCHAR )
);
return
$self->fetch_all_by_Slice_constraint( $slice, $constraint,
$logic_name );
} ## end sub fetch_all_by_Slice_and_external_db
=head2 fetch_all_by_Slice_and_pid
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice from which to obtain align features.
Arg [2] : (optional) float $pid
A lower bound for the percentage identity of features
to obtain.
Arg [3] : (optional) string $logic_name
The logic name of the type of features to obtain.
Example : @feats = $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 );
Description: Returns a listref of features created from the
database which are on the Slice $slice and with a
percentage identity greater than $pid. If logic name
is defined, only features with an analysis of type
$logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
in Slice coordinates
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_all_by_Slice_and_pid {
my ( $self, $slice, $pid, $logic_name ) = @_;
# #get the primary table alias
# my @tabs = $self->_tables;
# my $alias = $tabs[0]->[1];
# if(defined $pid) {
# $constraint = "${alias}.perc_ident > $pid";
# }
my $constraint;
if ( defined($pid) ) {
$constraint = sprintf( "perc_ident > %s",
$self->dbc()->db_handle()
->quote( $pid, SQL_FLOAT ) );
}
return
$self->fetch_all_by_Slice_constraint( $slice, $constraint,
$logic_name );
}
=head2 fetch_all_by_hit_name
Arg [1] : string $hit_name
The hit_name of the features to obtain
Arg [2] : (optional) string $logic_name
The analysis logic name of the type of features to
obtain.
Example : @feats =
$adaptor->fetch_all_by_hit_name( $name, $logic_name );
Description: Returns a listref of features created from the
database which correspond to the given hit_name. If
logic name is defined, only features with an analysis
of type $logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
Exceptions : thrown if hit_name is not defined
Caller : general
Status : Stable
=cut
sub fetch_all_by_hit_name {
my ( $self, $hit_name, $logic_name ) = @_;
if ( !defined($hit_name) ) {
throw("hit_name argument is required");
}
# Construct a constraint like 't1.hit_name = "123"'
my @tabs = $self->_tables();
my ( $name, $syn ) = @{ $tabs[0] };
my $constraint = sprintf( "%s.hit_name = %s",
$syn,
$self->dbc()->db_handle()->quote( $hit_name, SQL_VARCHAR ) );
if ( defined($logic_name) ) {
# Add the $logic_name constraint
$constraint =
$self->_logic_name_to_constraint( $constraint, $logic_name );
}
return $self->generic_fetch($constraint);
}
=head2 fetch_all_by_hit_name_unversioned
Arg [1] : string $hit_name
The beginning of the hit_name of the features to
obtain, e.g. AA768786 would retrieve AA768786.1,
AA768786.2 etc.
Arg [2] : (optional) string $logic_name
The analysis logic name of the type of features to
obtain.
Example : @feats =
$adaptor->fetch_all_by_hit_name( $name, $logic_name );
Description: Returns a listref of features created from the
database which start with the given hit_name. If
logic name is defined, only features with an analysis
of type $logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
Exceptions : thrown if hit_name is not defined
Caller : general
Status : At risk
=cut
sub fetch_all_by_hit_name_unversioned {
my ( $self, $hit_name, $logic_name ) = @_;
if ( !defined($hit_name) ) {
throw("hit_name argument is required");
}
#construct a constraint like 't1.hit_name = "123"'
my @tabs = $self->_tables;
my ( $name, $syn ) = @{ $tabs[0] };
my $constraint = sprintf( "%s.hit_name LIKE %s",
$syn,
$self->dbc()->db_handle()->quote( $hit_name . '.%', SQL_VARCHAR ) );
if ( defined($logic_name) ) {
# Add the $logic_name constraint
$constraint =
$self->_logic_name_to_constraint( $constraint, $logic_name );
}
return $self->generic_fetch($constraint);
}
=head2 fetch_all_by_RawContig_and_pid
Description: DEPRECATED use fetch_all_by_Slice_and_pid instead
=cut
sub fetch_all_by_RawContig_and_pid {
my($self, $contig, $pid, $logic_name) = @_;
my $constraint;
#get the primary table alias
my @tabs = $self->_tables;
my $alias = $tabs[0]->[1];
if(defined $pid) {
$constraint = "${alias}.perc_ident > $pid";
}
return $self->fetch_all_by_RawContig_constraint($contig,
$constraint,
$logic_name);
}
##implemented by subclasses:
# store
# _tables
# _columns
# _obj_from_hashref
1;
]]>