/ 
bioperl-1.5.2_005-RCb
/ Bio::Index::Abstract

NAME

Bio::Index::Abstract - Abstract interface for indexing a flat file

SYNOPSIS

You should not be using this module directly

USING DB_FILE

To use DB_File and not SDBM for this index, pass the value:

-dbm_package => 'DB_File'

to new (see below).

DESCRIPTION

This object provides the basic mechanism to associate positions in files with names. The position and filenames are stored in DBM which can then be accessed later on. It is the equivalent of flat file indexing (eg, SRS or efetch).

This object is the guts to the mechanism, which will be used by the specific objects inheriting from it.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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/

AUTHOR - Ewan Birney, James Gilbert

Email - birney@sanger.ac.uk, jgrg@sanger.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore).

new

Usage   : $index = Bio::Index::Abstract->new(
              -filename    => $dbm_file,
              -write_flag  => 0,
              -dbm_package => 'DB_File',
              -verbose     => 0);
Function: Returns a new index object.  If filename is
          specified, then open_dbm() is immediately called. 
          Bio::Index::Abstract->new() will usually be called
          directly only when opening an existing index.
Returns : A new index object
Args    : -filename    The name of the dbm index file.
          -write_flag  TRUE if write access to the dbm file is
                       needed.
          -dbm_package The Perl dbm module to use for the
                       index.
          -verbose     Print debugging output to STDERR if
                       TRUE.

filename

Title   : filename
Usage   : $value = $self->filename();
          $self->filename($value);
Function: Gets or sets the name of the dbm index file.
Returns : The current value of filename
Args    : Value of filename if setting, or none if
          getting the value.

write_flag

Title   : write_flag
Usage   : $value = $self->write_flag();
          $self->write_flag($value);
Function: Gets or sets the value of write_flag, which
          is wether the dbm file should be opened with
          write access.
Returns : The current value of write_flag (default 0)
Args    : Value of write_flag if setting, or none if
          getting the value.

dbm_package

Usage   : $value = $self->dbm_package();
          $self->dbm_package($value);

Function: Gets or sets the name of the Perl dbm module used. 
          If the value is unset, then it returns the value of
          the package variable $USE_DBM_TYPE or if that is
          unset, then it chooses the best available dbm type,
          choosing 'DB_File' in preference to 'SDBM_File'. 
          Bio::Abstract::Index may work with other dbm file
          types.

Returns : The current value of dbm_package
Args    : Value of dbm_package if setting, or none if
          getting the value.

db

Title   : db
Usage   : $index->db
Function: Returns a ref to the hash which is tied to the dbm
          file.  Used internally when adding and retrieving
          data from the database.
Example : $db = $index->db();
          $db->{ $some_key } = $data
          $data = $index->db->{ $some_key };
Returns : ref to HASH
Args    : NONE

get_stream

Title   : get_stream
Usage   : $stream = $index->get_stream( $id );
Function: Returns a file handle with the file pointer
          at the approprite place

          This provides for a way to get the actual
          file contents and not an object 

          WARNING: you must parse the record deliminter
          *yourself*. Abstract wont do this for you 
          So this code

          $fh = $index->get_stream($myid);
          while( <$fh> ) {
             # do something
          }
          will parse the entire file if you don't put in
          a last statement in, like

          while( <$fh> ) {
             /^\/\// && last; # end of record
             # do something
          }

Returns : A filehandle object
Args    : string represents the accession number
Notes   : This method should not be used without forethought

cachesize

Usage   : $index->cachesize(1000000)
Function: Sets the dbm file cache size for the index.
	    Needs to be set before the DBM file gets opened.
Example : $index->cachesize(1000000)
Returns : size of the curent cache

ffactor

Usage   : $index->ffactor(1000000)
Function: Sets the dbm file fill factor.
			Needs to be set before the DBM file gets opened.

Example : $index->ffactor(1000000)
Returns : size of the curent cache

open_dbm

Usage   : $index->open_dbm()
Function: Opens the dbm file associated with the index
          object.  Write access is only given if explicitly
          asked for by calling new(-write => 1) or having set
          the write_flag(1) on the index object.  The type of
          dbm file opened is that returned by dbm_package(). 
          The name of the file to be is opened is obtained by
          calling the filename() method.

Example : $index->_open_dbm()
Returns : 1 on success

_version

Title   : _version
Usage   : $type = $index->_version()
Function: Returns a string which identifes the version of an
          index module.  Used to permanently identify an index
          file as having been created by a particular version
          of the index module.  Must be provided by the sub class
Example : 
Returns : 
Args    : none

_code_base

Title   : _code_base
Usage   : $code = $db->_code_base();
Function:
Example :
Returns : Code package to be used with this 
Args    :

_type_and_version

Title   : _type_and_version
Usage   : Called by _initalize
Function: Checks that the index opened is made by the same index
          module and version of that module that made it.  If the
          index is empty, then it adds the information to the
          database.
Example : 
Returns : 1 or exception
Args    : none

_check_file_sizes

Title   : _check_file_sizes
Usage   : $index->_check_file_sizes()
Function: Verifies that the files listed in the database
          are the same size as when the database was built,
          or throws an exception.  Called by the new()
          function.
Example : 
Returns : 1 or exception
Args    :

make_index

Title   : make_index
Usage   : $index->make_index( FILE_LIST )
Function: Takes a list of file names, checks that they are
          all fully qualified, and then calls _filename() on
          each.  It supplies _filename() with the name of the
          file, and an integer which is stored with each record
          created by _filename().  Can be called multiple times,
          and can be used to add to an existing index file.
Example : $index->make_index( '/home/seqs1', '/home/seqs2', '/nfs/pub/big_db' );
Returns : Number of files indexed
Args    : LIST OF FILES

_filename

Title   : _filename
Usage   : $index->_filename( FILE INT )
Function: Indexes the file
Example : 
Returns : 
Args    :

_file_handle

Title   : _file_handle
Usage   : $fh = $index->_file_handle( INT )
Function: Returns an open filehandle for the file
          index INT.  On opening a new filehandle it
          caches it in the @{$index->_filehandle} array.
          If the requested filehandle is already open,
          it simply returns it from the array.
Example : $fist_file_indexed = $index->_file_handle( 0 );
Returns : ref to a filehandle
Args    : INT

_file_count

Title   : _file_count
Usage   : $index->_file_count( INT )
Function: Used by the index building sub in a sub class to
          track the number of files indexed.  Sets or gets
          the number of files indexed when called with or
          without an argument.
Example : 
Returns : INT
Args    : INT

add_record

Title   : add_record
Usage   : $index->add_record( $id, @stuff );
Function: Calls pack_record on @stuff, and adds the result
          of pack_record to the index database under key $id.
          If $id is a reference to an array, then a new entry
          is added under a key corresponding to each element
          of the array.
Example : $index->add_record( $id, $fileNumber, $begin, $end )
Returns : TRUE on success or FALSE on failure
Args    : ID LIST

pack_record

Title   : pack_record
Usage   : $packed_string = $index->pack_record( LIST )
Function: Packs an array of scalars into a single string
          joined by ASCII 034 (which is unlikely to be used
          in any of the strings), and returns it. 
Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end )
Returns : STRING or undef
Args    : LIST

unpack_record

Title   : unpack_record
Usage   : $index->unpack_record( STRING )
Function: Splits the sting provided into an array,
          splitting on ASCII 034.
Example : ( $fileNumber, $begin, $end ) = $index->unpack_record( $self->db->{$id} )
Returns : A 3 element ARRAY
Args    : STRING containing ASCII 034

count_records

Title   : count_records
Usage   : $recs = $seqdb->count_records()
Function: return count of all recs in the index 
Example :
Returns : a scalar
Args    : none

DESTROY

Title   : DESTROY
Usage   : Called automatically when index goes out of scope
Function: Closes connection to database and handles to
          sequence files
Returns : NEVER
Args    : NONE