Raw content of Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Seg =pod =head1 NAME Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Seg =head1 SYNOPSIS my $seg = Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Seg->new ( -db => $db, -input_id => $input_id, -analysis => $analysis, ); $seg->fetch_input; # gets sequence from DB $seg->run; $seg->output; $seg->write_output; # writes features to to DB NB: The input_id can either be a peptide id or the location for a protein file. =head1 DESCRIPTION This object wraps Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg to add functionality to read and write to databases. The query sequence is provided through the input_id. The appropriate Bio::EnsEMBL::Analysis object must be passed for extraction of parameters. =head1 CONTACT Marc Sohrmann: ms2@sanger.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. =cut package Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Seg; use strict; use vars qw(@ISA); use Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation; use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg; @ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation); sub fetch_input { my ($self, @args) = @_; $self->SUPER::fetch_input(@args); my $run = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg->new(-query => $self->query, -analysis => $self->analysis); $self->runnable($run); } 1;