Bio::DB InMemoryCache
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Summary
Bio::DB::InMemoryCache - Abstract interface for a sequence database
Package variables
No package variables defined.
Included modules
Bio::Seq
Inherit
Bio::DB::SeqI Bio::Root::Root
Synopsis
  $cachedb = Bio::DB::InMemoryCache->new( -seqdb => $real_db,
-number => 1000);
#
# get a database object somehow using a concrete class
#
$seq = $cachedb->get_Seq_by_id('ROA1_HUMAN'); # # $seq is a Bio::Seq object #
Description
This is a memory cache system which saves the objects returned by
Bio::DB::RandomAccessI in memory to a hard limit of sequences.
Methods
new
No description
Code
get_Seq_by_idDescriptionCode
get_Seq_by_accDescriptionCode
number
No description
Code
seqdb
No description
Code
agr
No description
Code
_load_Seq
No description
Code
_number_free
No description
Code
get_Seq_by_versionDescriptionCode
Methods description
get_Seq_by_idcode    nextTop
 Title   : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "id does not exist" exception
get_Seq_by_acccodeprevnextTop
 Title   : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
get_Seq_by_versioncodeprevnextTop
 Title   : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by sequence version
Returns : A Bio::Seq object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
Methods code
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;

    my $self = Bio::Root::Root->new();
    bless $self,$class;

    my ($seqdb,$number,$agr) =
		$self->_rearrange([qw(SEQDB NUMBER AGRESSION)],@args);

    if( !defined $seqdb || !ref $seqdb ||
		  !$seqdb->isa('Bio::DB::RandomAccessI') ) {
       $self->throw("Must be a RandomAccess database not a [$seqdb]");
    }

    if( !defined $number ) {
        $number = 1000;
    }

    $self->seqdb($seqdb);
    $self->number($number);
    $self->agr($agr);

    # we consider acc as the primary id here
$self->{'_cache_number_hash'} = {}; $self->{'_cache_id_hash'} = {}; $self->{'_cache_acc_hash'} = {}; $self->{'_cache_number'} = 1; return $self;
}
get_Seq_by_iddescriptionprevnextTop
sub get_Seq_by_id {
   my ($self,$id) = @_;

   if( defined $self->{'_cache_id_hash'}->{$id} ) {
		my $acc = $self->{'_cache_id_hash'}->{$id};
		my $seq = $self->{'_cache_acc_hash'}->{$acc};
		$self->{'_cache_number_hash'}->{$seq->accession} =
		  $self->{'_cache_number'}++;
		return $seq;
   } else {
		return $self->_load_Seq('id',$id);
   }
}
get_Seq_by_accdescriptionprevnextTop
sub get_Seq_by_acc {
   my ($self,$acc) = @_;

   #print STDERR "In cache get for $acc\n";
if( defined $self->{'_cache_acc_hash'}->{$acc} ) { #print STDERR "Returning cached $acc\n";
my $seq = $self->{'_cache_acc_hash'}->{$acc}; $self->{'_cache_number_hash'}->{$seq->accession} = $self->{'_cache_number'}++; return $seq; } else { return $self->_load_Seq('acc',$acc); }
}
numberdescriptionprevnextTop
sub number {
    my ($self, $number) = @_;
    if ($number) {
        $self->{'number'} = $number;
    } else {
        return $self->{'number'};
    }
}
seqdbdescriptionprevnextTop
sub seqdb {
    my ($self, $seqdb) = @_;
    if ($seqdb) {
        $self->{'seqdb'} = $seqdb;
    } else {
        return $self->{'seqdb'};
    }
}
agrdescriptionprevnextTop
sub agr {
    my ($self, $agr) = @_;
    if ($agr) {
        $self->{'agr'} = $agr;
    } else {
        return $self->{'agr'};
    }
}
_load_SeqdescriptionprevnextTop
sub _load_Seq {
  my ($self,$type,$id) = @_;

  my $seq;

  if( $type eq 'id') {
    $seq = $self->seqdb->get_Seq_by_id($id);
  }elsif ( $type eq 'acc' ) {
    $seq = $self->seqdb->get_Seq_by_acc($id);
  } else {
    $self->throw("Bad internal error. Don't understand $type");
  }
  if( ! $seq ) {
      # warding off bug #1628
$self->debug("could not find seq $id in seqdb\n"); return; } if( $self->agr() ) { #print STDERR "Pulling out into memory\n";
my $newseq = Bio::Seq->new( -display_id => $seq->display_id, -accession_number => $seq->accession, -seq => $seq->seq, -desc => $seq->desc, ); if( $self->agr() == 1 ) { foreach my $sf ( $seq->top_SeqFeatures() ) { $newseq->add_SeqFeature($sf); } $newseq->annotation($seq->annotation); } $seq = $newseq; } if( $self->_number_free < 1 ) { # remove the latest thing from the hash
my @accs = sort { $self->{'_cache_number_hash'}->{$a} <=> $self->{'_cache_number_hash'}->{$b} } keys %{$self->{'_cache_number_hash'}}; my $acc = shift @accs; # remove this guy
my $seq = $self->{'_cache_acc_hash'}->{$acc}; delete $self->{'_cache_number_hash'}->{$acc}; delete $self->{'_cache_id_hash'}->{$seq->id}; delete $self->{'_cache_acc_hash'}->{$acc}; } # up the number, register this sequence into the hash.
$self->{'_cache_id_hash'}->{$seq->id} = $seq->accession; $self->{'_cache_acc_hash'}->{$seq->accession} = $seq; $self->{'_cache_number_hash'}->{$seq->accession} = $self->{'_cache_number'}++; return $seq;
}
_number_freedescriptionprevnextTop
sub _number_free {
  my $self = shift;

  return $self->number - scalar(keys %{$self->{'_cache_number_hash'}});
}
get_Seq_by_versiondescriptionprevnextTop
sub get_Seq_by_version {
   my ($self,@args) = @_;
   $self->throw("Not implemented it");
}

## End of Package
1;
}
General documentation
CONTACTTop
Ewan Birney <birney@ebi.ac.uk>
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _