BioPerl

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Bio/Assembly/Contig.pm  view on Meta::CPAN

=cut

#'
package Bio::Assembly::Contig;

use strict;

use Bio::DB::SeqFeature::Store; # isa Bio::SeqFeature::CollectionI
use Bio::Seq::PrimaryQual;      # isa Bio::Seq::QualI

use Scalar::Util qw(weaken);

use base qw(Bio::Root::Root Bio::Align::AlignI);

=head1 Object creator

=head2 new

 Title     : new
 Usage     : my $contig = Bio::Assembly::Contig->new();
 Function  : Creates a new contig object

Bio/Assembly/Contig.pm  view on Meta::CPAN

sub assembly {
    my $self = shift;
    my $assembly = shift;

    $self->throw("Using non Bio::Assembly::Scaffold object when assign contig to assembly")
    if (defined $assembly && ! $assembly->isa("Bio::Assembly::Scaffold"));
    # We create a circular reference to a Scaffold object. It is made weak
    # to prevent memory leaks.
    $self->{'_assembly'} = $assembly if (defined $assembly);
    weaken($self->{'_assembly'});

    return $self->{'_assembly'};
}

=head2 strand

 Title     : strand
 Usage     : $contig->strand($num);
 Function  : Get/Set contig orientation in a scaffold/assembly.
             Its equivalent to the strand property of sequence

Bio/SeqFeature/Gene/GeneStructure.pm  view on Meta::CPAN

# Let the code begin...


package Bio::SeqFeature::Gene::GeneStructure;
use vars qw($WeakRefs);
use strict;

BEGIN {
    eval "use Scalar::Util qw(weaken);";
    if ($@) {
	$Bio::SeqFeature::Gene::GeneStructure::WeakRefs = 0;  
    } else { $Bio::SeqFeature::Gene::GeneStructure::WeakRefs = 1; }
}


use base qw(Bio::SeqFeature::Generic Bio::SeqFeature::Gene::GeneStructureI);


sub new {

Bio/SeqFeature/Gene/GeneStructure.pm  view on Meta::CPAN

    my ($self, $fea) = @_;

    if(!$fea || ! $fea->isa('Bio::SeqFeature::Gene::TranscriptI') ) {
	$self->throw("$fea does not implement Bio::SeqFeature::Gene::TranscriptI");
    }
    unless( exists $self->{'_transcripts'}  ) {
	$self->{'_transcripts'} = [];
    }
    $self->_expand_region($fea);
    if( $Bio::SeqFeature::Gene::GeneStructure::WeakRefs ) {
	$fea->parent(weaken $self);
    } else {
	$fea->parent($self);
    }
    push(@{$self->{'_transcripts'}}, $fea);
}

=head2 flush_transcripts

 Title   : flush_transcripts()
 Usage   : $gene->flush_transcripts();

Bio/Species.pm  view on Meta::CPAN

sub new {
    my($class, @args) = @_;
    
    my $self = $class->SUPER::new(@args);
    
    # Bio::Species is now just a proxy object that just observes the NodeI
    # interface methods but delegates them to the proper classes (Bio::Taxon and
    # Bio::Tree::Tree). This will be surplanted by the much simpler
    # Bio::Taxon/Bio::DB::Taxonomy modules in the future.
    
    # Using a proxy allows proper GC w/o using weaken().  This just wraps the
    # older instances, which have no reciprocal refs (thus no circular refs).
    # This can then run proper cleanup
    
    $self->taxon(Bio::Taxon->new(@args));
    
    my ($org, $sp, $var, $classification) =
        $self->_rearrange([qw(ORGANELLE
                            SUB_SPECIES
                            VARIANT
                            CLASSIFICATION)], @args);

Bio/Species.pm  view on Meta::CPAN

sub sub_species {
    my ($self, $sub) = @_;
    
    # TODO: instead of caching the raw name, cache the actual node instance.
    if (!defined $self->{'_sub_species'}) {
        my $ss_taxon = $self->tree->find_node(-rank => 'subspecies');
        if ($ss_taxon) {
            if ($sub) {
                $ss_taxon->scientific_name($sub);
                
                # *** weakening ref to our root node in species() to solve a
                # memory leak means that we have a subspecies taxon to set
                # during the first call to species(), but it has vanished by
                # the time a user subsequently calls sub_species() to get the
                # value. So we 'cheat' and just store the subspecies name in
                # our self hash, instead of the tree. Is this a problem for
                # a Species object? Can't decide --sendu
                
                # This can now be changed to deal with this information on the
                # fly.  For now, the caching remains, but maybe we should just
                # let these things deal with mutable data as needed? -- cjfields

Changes  view on Meta::CPAN

      as part of the Google Summer of Code.  This may become BioPerl 2.0.
    * Version bump represents 'just prior to v 1.7'.  We may have point
      releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
      This code essentially is what is on the github master branch.

    [New features]

    * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
    * Bio::Tree refactor
        - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
        - removal of Scalar::Util::weaken code, which was causing odd headaches
          with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
    * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
          many others]
    * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
          [Warren Kretzschmar]
    * Bio::SeqIO::gbxml
        - bug 2515 - new contribution [Ryan Golhar, jhannah]
    * Bio::Assembly::IO
        - support for reading Maq, Sam and Bowtie files [maj]
        - support for reading 454 GS Assembler (Newbler) ACE files [fangly]

t/data/entrezgene.dat  view on Meta::CPAN

      version 0 ,
      refs {
        pmid 14517345 } ,
      create-date
        str "Jun 23 2004  4:43PM" ,
      update-date
        str "Jun 23 2004  5:16PM" } ,
    {
      type generif ,
      text "cellular generation of peroxynitrite may contribute to
 carcinogenesis and tumor progression by weakening key cellular defense
 enzymes such as arylamine N-acetyltransferase 1 (NAT1)" ,
      version 0 ,
      refs {
        pmid 14672957 } ,
      create-date
        str "Mar 24 2004 12:00AM" ,
      update-date
        str "May  9 2004  7:01AM" } ,
    {
      type generif ,