Raw content of Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Prodom # Author: Gary Williams (gw3@sanger.ac.uk) # Copyright (c) Marc Sohrmann, 2001 # You may distribute this code under the same terms as perl itself # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =pod =head1 NAME Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Prodom =head1 SYNOPSIS my $seg = Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Prodom->new ( -db => $db, -input_id => $input_id, -analysis => $analysis, ); $seg->fetch_input; # gets sequence from DB $seg->run; $seg->output; $seg->write_output; # writes features to to DB =head1 DESCRIPTION This object wraps Bio::EnsEMBL::Analysis::Runnable::Prodom to add functionality to read and write to databases. A Bio::EnsEMBL::Analysis::DBSQL::DBAdaptor is required for database access (db). The query sequence is provided through the input_id. The appropriate Bio::EnsEMBL::Analysis object must be passed for extraction of parameters. =head1 CONTACT Gary Williams =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. =cut package Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Prodom; use strict; use vars qw(@ISA); use Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation; use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Prodom; @ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation); # runnable method sub fetch_input { my ($self,@args)=@_; $self->SUPER::fetch_input(@args); my $run = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Prodom->new( -query => $self->query, -analysis => $self->analysis); $self->runnable($run) } 1;