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Bio::DB::FileCache(3) User Contributed Perl DocumentationBio::DB::FileCache(3)

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

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,
					   );
       =head1 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.

CONTACT
       Lincoln Stein <lstein@cshl.org>

   Support
       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 Bugs
       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:

	 http://bugzilla.open-bio.org/

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

   new
	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

       If no index file is specified, will create a temporary file in your
       system's temporary file directory.  The name of this temporary file can
       be retrieved using file_name().

   get_Seq_by_id
	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_acc
	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

   seqdb
	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

   file_name
	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

       It probably isn't useful to set the cache file name after you've opened
       it.

   keep
	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

       The keep flag will cause the index file to be unlinked when the process
       exits.  Since on some operating systems (Unix, OS/2) the unlinking
       occurs during the new() call immediately after opening the file, it
       probably isn't safe to change this value.

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

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

   get_Seq_by_version
	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

perl v5.14.1			  2011-07-22		 Bio::DB::FileCache(3)
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