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Summary

Bio::DB::FileCache - In file cache for BioSeq objects

Package variables

Included modules

Inherit

Bio::DB::SeqI Bio::Root::Root

Synopsis

  $cachedb = Bio::DB::FileCache->new($real_db);

  #
  # $real_db is a Bio::DB::RandomAccessI database
  #

  $seq = $cachedb->get_Seq_by_id('ROA1_HUMAN');

  #
  # $seq is a Bio::Seq object
  #

  # more control provided with named-parameter form

  $cachedb = Bio::DB::FileCache->new( -seqdb => $real_db,
				      -file  => $path,
				      -keep  => $flag,
				    );

Description

This is a disk cache system which saves the objects returned by
Bio::DB::RandomAccessI on disk. The disk cache grows without limit,
while the process is running, but is automatically unlinked at process
termination unless the -keep flag is set.
This module requires DB_File and Storable.

Methods

Methods description

 Title   : new
 Usage   : $db = Bio::DB::FileCache->new(
                 -seqdb => $db,   # Bio::DB::RandomAccessI database
                 -file  => $path, # path to index file
                 -keep  => $flag, # don't unlink index file
          )
 Function: creates a new on-disk cache
 Returns : a Bio::DB::RandomAccessI database
 Args    : as above
 Throws  : "Must be a randomaccess database" exception
           "Could not open primary index file" exception

 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

 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

 Title   : seqdb
 Usage   : $seqdb = $db->seqdb([$seqdb])
 Function: gets/sets the Bio::DB::RandomAccessI database
 Returns : a Bio::DB::RandomAccessI database
 Args    : new sequence database (optional)
 Throws  : nothing

 Title   : file_name
 Usage   : $path = $db->file_name([$file_name])
 Function: gets/sets the name of the cache file
 Returns : a path
 Args    : new cache file name (optional)
 Throws  : nothing

 Title   : keep
 Usage   : $keep = $db->keep([$flag])
 Function: gets/sets the value of the "keep" flag
 Returns : current value
 Args    : new value (optional)
 Throws  : nothing

 Title   : db
 Usage   : $db->db
 Function: returns tied hash to index database
 Returns : a Berkeley DB tied hashref
 Args    : none
 Throws  : nothing

 Title   : flush
 Usage   : $db->flush
 Function: flushes the cache
 Returns : nothing
 Args    : none
 Throws  : nothing

 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

sub new {

    my ($class,@args) = @_;

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

    my ($seqdb,$file_name,$keep) = $self->_rearrange([qw(SEQDB FILE
							 KEEP)],@args);

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

    $self->seqdb($seqdb);
    $file_name ||= tmpnam();
    $self->file_name($file_name);
    $self->keep($keep);

    $self->_open_database($file_name);
    return $self;

}

sub get_Seq_by_id {

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

   # look in the cache first
   my $obj = $self->_get('id' => $id);
   return $obj if defined $obj;

   # get object from seqdb
   $obj = $self->seqdb->get_Seq_by_id($id);
   $self->_store('id' => $id, $obj);

   return $obj;

}

sub get_Seq_by_acc {

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

   # look in the cache first
   my $obj = $self->_get('acc' => $acc);
   return $obj if defined $obj;

   # get object from seqdb
   $obj = $self->seqdb->get_Seq_by_acc($acc);
   $self->_store('acc' => $acc, $obj);

   return $obj;

}

sub seqdb {

    my ($self, $seqdb) = @_;
    if ($seqdb) {
        $self->{'seqdb'} = $seqdb;
    } else {
        return $self->{'seqdb'};
    }

}

sub file_name {

  my $self = shift;
  my $d = $self->{file_name};
  $self->{file_name} = shift if @_;
  $d;

}

sub keep {

  my $self = shift;
  my $d = $self->{keep};
  $self->{keep} = shift if @_;
  $d;

}

sub db {

 shift->{db}

}

sub flush {

  my $db = shift->db or return;
  %{$db} = ();

}

sub _get {

  my $self = shift;
  my ($type,$id) = @_;
  my $serialized = $self->db->{"${type}_${id}"};
  my $obj = thaw($serialized);
  $obj;

}

sub _store {

  my $self = shift;
  my ($type,$id,$obj) = @_;
  if( ! defined $obj ) {
      # bug #1628
      $self->debug("tried to store an undefined value for $id, skipping");
      return;
  }
  my $serialized = freeze($obj);
  $self->db->{"${type}_${id}"} = $serialized;

}

sub get_Seq_by_version {

   my ($self,@args) = @_;
   $self->throw("Not implemented it");

}

sub DESTROY {

  my $self = shift;
  unlink $self->file_name unless $self->keep;

}

sub _open_database {

  my $self = shift;
  my $file = shift;
  my $flags = O_CREAT|O_RDWR;
  my %db;
  tie(%db,'DB_File',$file,$flags,0666,$DB_BTREE)
    or $self->throw("Could not open primary index file");
  $self->{db} =\% db;
  unlink $file unless $self->keep;
}

## End of Package

1;

}

General documentation

Lincoln Stein <lstein@cshl.org>

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.

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/

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _