view release on metacpan or  search on metacpan

lib/Bio/EnsEMBL/Utils/Converter/bio_ens.pm  view on Meta::CPAN

distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut


=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

=head1 AUTHOR

Juguang Xiao <juguang@fugu-sg.org>

=cut

=head1 NAME

Bio::EnsEMBL::Utils::Converter::bio_ens

=head1 SYNOPISIS

You should not use this module directly. Please check out the
Bio::EnsEMBL::Utils::Converter module.

=head1 DESCRIPTION

=head1 METHODS

=cut

package Bio::EnsEMBL::Utils::Converter::bio_ens;
$Bio::EnsEMBL::Utils::Converter::bio_ens::VERSION = '114.0.0';
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Analysis;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Converter;
use Scalar::Util qw(weaken);
@ISA = qw(Bio::EnsEMBL::Utils::Converter);

=head2 new

Please see Bio::EnsEMBL::Utils::Converter::new

=cut

sub new {
    my ($caller, @args) = @_;
    my $class = ref($caller) || $caller;

    if($class eq 'Bio::EnsEMBL::Utils::Converter::bio_ens'){
        my %params = @args;
        @params{map{lc $_} keys %params} = values %params;
        my $module = $class->_guess_module($params{-in}, $params{-out});
        return undef unless ($class->_load_module($module));
        return "$module"->new(@args);
    }else{
        my $self = $class->SUPER::new(@args);
#        $self->_initialize(@args);
        return $self;
    }
}

sub _initialize {
    my ($self, @args) = @_;
    $self->SUPER::_initialize(@args);
    
    my ($dbadaptor, 
        $dbdriver, $dbhost, $dbport, $dbuser, $dbpass, $dbname,
        $analysis, $analysis_dbid, $analysis_logic_name, 
        $contig, $contig_dbid, $contig_name, 
        $translation_id) =
        
        $self->_rearrange([qw(DBADAPTOR 
            DBDRIVER DBHOST DBPORT DBUSER DBPASS DBNAME
            ANALYSIS ANALYSIS_DBID ANALYSIS_LOGIC_NAME 
            CONTIG CONTIG_DBID CONTIG_NAME
            TRANSLATION_ID)], @args);

    
    if(defined $dbadaptor){
        $self->dbadaptor($dbadaptor);
    }elsif(defined $dbname){
        $self->ensembl_db(@args);
    }else{
        # No db information.
    }
    
    if(defined $analysis){
        $self->analysis($analysis);
        # then ignore the analysis_dbid and analysis_logic_name
    }elsif(defined $analysis_dbid){
        $self->analysis_dbID($analysis_dbid);
    }elsif(defined $analysis_logic_name){
        $self->analysis_logic_name($analysis_logic_name);
    }else{
        # No analysis information offered
    }
    
    if(defined $contig){
        ($contig) = ref($contig) eq 'ARRAY' ? @{$contig} : $contig;
        $self->contig($contig);
    }elsif(defined $contig_dbid){
        $self->contig_dbID($contig_dbid);
    }elsif(defined $contig_name){
        $self->contig_name($contig_name);
    }else{
        # No contig information
    }

    if(defined $translation_id){
        $self->translation_id($translation_id);
    }
}


sub _guess_module {
    my ($self, $in, $out) = @_;
    my $tail;
    if($in eq 'Bio::Search::HSP::GenericHSP'){
        $tail = 'bio_ens_hsp';
    }elsif($in eq 'Bio::SeqFeature::Generic'){
        $tail = 'bio_ens_seqFeature';
    }elsif($in eq 'Bio::SeqFeature::FeaturePair'){
        $tail = 'bio_ens_featurePair';
    }elsif($in eq 'Bio::Pipeline::Analysis'){
        $tail = 'bio_ens_analysis';
    }elsif($in eq 'Bio::Tools::Prediction::Gene'){
        $tail = 'bio_ens_predictionGene';
    }elsif($in eq 'Bio::Tools::Prediction::Exon'){
        $tail = 'bio_ens_predictionExon';
    }elsif($in eq 'Bio::SeqFeature::Gene::GeneStructure'){
        $tail = 'bio_ens_gene';
    }elsif($in eq 'Bio::SeqFeature::Gene::Transcript'){
        $tail = 'bio_ens_transcript';
    }elsif($in eq 'Bio::SeqFeature::Gene::Exon'){
        $tail = 'bio_ens_exon';
    }else{
        $self->throw("[$in] to [$out], not supported");
    }
    return "Bio::EnsEMBL::Utils::Converter::$tail";
}


=head2 analysis

  Title   : analysis
  Usage   : $self->analysis
  Function: get and set for analysis
  Return  : L<Bio::EnsEMBL::Analysis>
  Args    : L<Bio::EnsEMBL::Analysis>   

=cut

sub analysis {
    my ($self, $arg) = @_;
    if(defined($arg)){
        # convert the analysis, if it's not Bio::Pipeline::Analysis
        if($arg->isa('Bio::Pipeline::Analysis')){
            my $converter_for_analysis = new Bio::EnsEMBL::Utils::Converter(
                -in => 'Bio::Pipeline::Analysis',
                -out => 'Bio::EnsEMBL::Analysis'
            );
            ($arg) = @{ $converter_for_analysis->convert([$arg]) };
        }

        $self->throws("A Bio::EnsEMBL::Analysis object expected.") 
            unless($arg->isa('Bio::EnsEMBL::Analysis'));
        $self->{_analysis} = $arg;
        $self->{_analysis_dbid} = $arg->dbID;
        $self->{_analysis_logic_name} = $arg->logic_name;
    }
    return $self->{_analysis};
}


=head2 contig