bio_ens.pm

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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;
 
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
 
  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   : 
  Function: 
  Return  :
  Args    :
 
=cut
 
sub analysis_logic_name {
    my ($self, $arg) = @_;
    
    return $self->{_analysis_logic_name} unless(defined $arg);
    my $analysis;
    eval{
        $analysis = 
            $self->dbadaptor->get_AnalysisAdaptor->fetch_by_logic_name($arg);
    };
    $self->throw("Not found analysis with logic name as \[$arg\]\n$@") if($@);
 
    $self->analysis($analysis);
    return $self->{_analysis_logic_name};
}
 
=head2 contig_dbID
 
  Title   : contig_dbID
  Usage   : $self->contig_dbID
  Function: get and set for contig_dbID
  Return  : 
  Args    :    
 
=cut
 
sub contig_dbID {
    my ($self, $arg) = @_;
    if(defined($arg)){
        my $contig;
        eval{
            $contig = 
                $self->dbadaptor->get_RawContigAdaptor->fetch_by_dbID($arg);
        };
        $self->throw("Failed during fetching contig by dbID\n$@") if($@);
        $self->contig($contig);
    }
    return $self->{_contig_dbid};
}
 
=head2 contig_name
  Title   : contig_name
  Usage   : $self->contig_name
  Function: get and set for contig_name
  Return  : 
  Args    :    
=cut
 
sub contig_name {
    my ($self, $arg) = @_;
    if(defined($arg)){
        my $contig;
        eval{
            $contig = 
                $self->dbadaptor->get_RawContigAdaptor->fetch_by_name($arg);
        };
        $self->throw("Failed during fetching contig by dbID\n$@") if($@);
        $self->contig($contig);
    }
    return $self->{_contig_name};
}
 
=head2 slice_dbID
  Title   : slice
  Usage   : $self->slice
  Function: get and set for slice
  Return  : L<Bio::EnsEMBL::Slice>
  Args    : L<Bio::EnsEMBL::Slice>   
=cut
 
sub slice_dbID {
    my ($self, $arg) = @_;
    if(defined($arg)){
        my $slice;
        $self->throw("undefined dbadpator") unless defined $self->dbadpaotr;
 
        eval{
            my $sliceAdaptor = $self->dbadaptor->get_SliceAdaptor;
            $slice = $sliceAdaptor->fetch_by_dbID($arg);
        };
            
        $self->throw("Failed to fetch slice by dbID\n$@") if($@);
        $self->contig($slice);
    }
}
 
=head2 slice_chr_start_end
  Title   : slice_chr_start_end
  Usage   : my $slice = $self->slice_chr_start_end($chr, $start, $end);
  Function: get and set for slice_chr_start_end
  Return  : 
  Args    :    
=cut
 
sub slice_chr_start_end {
    my ($self, $chr, $start, $end) = @_;
    if(defined($chr) && defined($start) && defined($end)){
        my $slice;
        eval{
            my $sliceAdaptor = $self->dbadaptor->get_SliceAdaptor;
            $slice = $sliceAdaptor->fetch_by_chr_start_end($chr, $start, $end);
        };
        $self->throw("Failed to fetch slice by chr start end\n$@") if($@);
        $self->contig($slice);
    }
}
 
sub translation_id {
    my ($self, $arg) = @_;
    return $self->{_translation_id} = $arg if(defined($arg));
    return $self->{_translation_id};
}
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