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=head1 LICENSE

See the NOTICE file distributed with this work for additional information
regarding copyright ownership.

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
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
    }

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

            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

  Title   : contig
  Usage   : $self->contig
  Function: get and set for contig
  Return  : 
  Args    :    

=cut

sub contig {
    my ($self, $arg) = @_;
    if(defined($arg)){
        if($arg->isa('Bio::EnsEMBL::RawContig')){
            $self->{_contig_dbid} = $arg->dbID;
            $self->{_contig_name} = $arg->name;
        }elsif($arg->isa('Bio::EnsEMBL::Slice')){
                $self->{_slice_dbid} = $arg->dbID;
        }elsif($arg->isa('Bio::PrimarySeqI')){
            ;
        }else{
            $self->throw("a Bio::EnsEMBL::RawContig needed");
        }
        $self->{_contig} = $arg;
        
    }
    return $self->{_contig};
}
    
=head2 dbadaptor

  Title   : dbadaptor
  Usage   : $self->dbadaptor
  Function: get and set for dbadaptor
  Return  : L<Bio::EnsEMBL::DBSQL::DBAdaptor>
  Args    : L<Bio::EnsEMBL::DBSQL::DBAdaptor>   

=cut

sub dbadaptor {
    my ($self, $arg) = @_;
    if(defined($arg)){
        $self->throws("A Bio::EnsEMBL::DBSQL::DBAdaptor object expected.") unless(defined $arg);
        weaken($self->{_dbadaptor} = $arg);
    }
    return $self->{_dbadaptor};
}

=head2 ensembl_db

  Title   : ensembl_db
  Usage   : 
  Function: 
  Return  :
  Args    :

=cut

sub ensembl_db {
    my ($self, @args) = @_;
    
    my ($dbdriver, $dbhost, $dbport, $dbuser, $dbpass, $dbname) = $self->_rearrange(
        [qw(DBDRIVER DBHOST DBPORT DBUSER DBPASS DBNAME)], @args);

    my $dbadaptor = new Bio::EnsEMBL::DBSQL::DBAdaptor(
        -driver => $dbdriver,
        -host => $dbhost,
        -port => $dbport,
        -user => $dbuser,
        -pass => $dbpass,
        -dbname => $dbname
    );
    $self->dbadaptor($dbadaptor);
}

=head2 analysis_dbID

  Title   : analysis_dbID
  Usage   : 
  Function: 
  Return  :
  Args    :

=cut

sub analysis_dbID {
    my ($self, $arg) = @_;

    if(defined $arg){
        my $analysis;
        eval{
            $analysis = $self->dbadaptor->get_AnalysisAdaptor->fetch_by_dbID($arg);
        };
        $self->throw("Failed during fetching analysis by dbID\n$@") if($@);
        $self->analysis($analysis);
    }
    $self->{_analysis_dbid};    
}


=head2 analysis_logic_name

  Title   : analysis_logic_name
  Usage   :