Commit 6c9f5d0f authored by Graham McVicker's avatar Graham McVicker
Browse files

POD updates

parent f3591508
#
# EnsEMBL module for Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
#
# Copyright (c) 2003 EnsEMBL
# Copyright (c) 2003 Ensembl
#
# You may distribute this module under the same terms as perl itself
=head1 NAME
Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor - An Abstract Base class for all
FeatureAdaptors
FeatureAdaptors
=head1 SYNOPSIS
......@@ -23,8 +23,7 @@ common to all feature adaptors.
=head1 CONTACT
Contact EnsEMBL development list for info: <ensembl-dev@ebi.ac.uk>
Contact Ensembl development list for info: <ensembl-dev@ebi.ac.uk>
=head1 METHODS
......@@ -259,7 +258,6 @@ sub fetch_all_by_dbID_list {
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
......@@ -989,7 +987,9 @@ sub deleteObj {
}
=head1 DEPRECATED METHODS
=cut
=head2 fetch_all_by_RawContig_constraint
......
......@@ -3,28 +3,33 @@
# Copyright EMBL-EBI 2001
#
# Author: Arne Stabenau
# based on
# based on
# Elia Stupkas Gene_Obj
#
#
# Date : 20.02.2001
#
=head1 NAME
Bio::EnsEMBL::DBSQL::ExonAdaptor - MySQL Database queries to generate and store exons (including supporting evidence)
Bio::EnsEMBL::DBSQL::ExonAdaptor - An adaptor responsible for the retrieval and
storage of exon objects
=head1 SYNOPSIS
$exon_adaptor = $database_adaptor->get_ExonAdaptor();
$exon = $exon_adaptor->fetch_by_dbID
$exon_adaptor = $database_adaptor->get_ExonAdaptor();
$exon = $exon_adaptor->fetch_by_dbID($dbID);
=head1 DESCRIPTION
The ExonAdaptor is responsible for retrieving and storing Exon objects from an
Ensembl database. Most of the ExonAdaptor functionality is inherited from the
B<Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor> class.
=head1 CONTACT
Arne Stabenau: stabenau@ebi.ac.uk
Elia Stupka : elia@ebi.ac.uk
Ewan Birney :
Post questions/comments to the Ensembl dev list: ensembl-dev@ebi.ac.uk
=head1 APPENDIX
=head1 METHODS
=cut
......@@ -285,8 +290,6 @@ sub store {
}
=head2 remove
Arg [1] : Bio::EnsEMBL::Exon $exon
......@@ -538,19 +541,16 @@ sub _objs_from_sth {
}
=head1 DEPRECATED METHODS
=cut
=head2 get_stable_entry_info
Arg [1] : Bio::EnsEMBL::Exon $exon
Example : $exon_adaptor->get_stable_entry_info($exon);
Description: gets stable info for an exon. this is not usually done at
creation time for speed purposes, and can be lazy-loaded later
if it is needed..
Returntype : none
Exceptions : none
Caller : Bio::EnsEMBL::Exon
Description: DEPRECATED. This method is no longer necessary. Exons are
always fetched with their stable identifiers (if they exist) and
no lazy loading is necessary.
=cut
......
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