=head1 LICENSE

 Copyright (c) 1999-2013 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

   http://www.ensembl.org/info/about/legal/code_licence.html

=head1 CONTACT

 Please email comments or questions to the public Ensembl
 developers list at <dev@ensembl.org>.

 Questions may also be sent to the Ensembl help desk at
 <helpdesk@ensembl.org>.

=cut

package Bio::EnsEMBL::Variation::Pipeline::InitTranscriptEffect;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Variation::Pipeline::BaseVariationProcess);

my $DEBUG = 0;

sub fetch_input {
   
    my $self = shift;

    my $include_lrg = $self->param('include_lrg');

    my $core_dba = $self->get_species_adaptor('core');
    my $var_dba = $self->get_species_adaptor('variation');
    
    my $dbc = $var_dba->dbc();

    my $ga = $core_dba->get_GeneAdaptor or die "Failed to get gene adaptor";

    my @transcript_output_ids;
    
    my $gene_count = 0;

    # fetch all the regular genes

    my @genes = @{ $ga->fetch_all };

    if ($include_lrg) {
        # fetch the LRG genes as well
        
        push @genes, @{ $ga->fetch_all_by_biotype('LRG_gene') }
    }

    for my $gene (@genes) {
        $gene_count++;
        
        for my $transcript (@{ $gene->get_all_Transcripts }) {

            push @transcript_output_ids, {
                transcript_stable_id  => $transcript->stable_id,
            };
        }            
        if ($DEBUG) {
            last if $gene_count >= 100;
        }
    }
    
    if (@transcript_output_ids) {
        
        # check we actually found some transcripts

        # truncate the table because we don't want duplicates

        $dbc->do("TRUNCATE TABLE transcript_variation");

        # disable the indexes on the table we're going to insert into as
        # this significantly speeds up the TranscriptEffect process

        $dbc->do("ALTER TABLE transcript_variation DISABLE KEYS");

        $self->param('transcript_output_ids', \@transcript_output_ids);

        $self->param(
            'rebuild_indexes', [{
                tables => ['transcript_variation'],
            }]
        );

        # we need to kick off the update_vf analysis as well, 
        # but it doesn't have any parameters we need to set here

        $self->param(
            'update_vf', [{}]
        );
    }
}

sub write_output {
    my $self = shift;
    
    if (my $transcript_output_ids = $self->param('transcript_output_ids')) {
        $self->dataflow_output_id($self->param('rebuild_indexes'), 2);
        $self->dataflow_output_id($self->param('update_vf'), 3);
        $self->dataflow_output_id($transcript_output_ids, 4);
        $self->dataflow_output_id($self->param('check_transcript_variation'), 5);
    }

    return;
}

1;