Bio::Index::Abstract(3) Abstract interface for indexing a flat file


You should not be using this module directly


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

    -dbm_package => 'DB_File'

to new (see below).


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.


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.

  [email protected]                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

[email protected]

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:

AUTHOR - Ewan Birney, James Gilbert

Email - [email protected], [email protected]


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


  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
            -dbm_package The Perl dbm module to use for the
            -verbose     Print debugging output to STDERR if


 Title   : filename
 Usage   : $value = $self->filename();
 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.


 Title   : write_flag
 Usage   : $value = $self->write_flag();
 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.


 Usage   : $value = $self->dbm_package();
 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
 Returns : The current value of dbm_package
 Args    : Value of dbm_package if setting, or none if
           getting the value.


  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


 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


  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


  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


  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


  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


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


  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
  Example : 
  Returns : 1 or exception
  Args    : none


  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()
  Example : 
  Returns : 1 or exception
  Args    :


  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


  Title   : pathtype
  Usage   : $index->pathtype($pathtype)
  Function: Set the type of the file path
            Only two values are supported, 'relative' or 'absolute'.
            If the user does not give any value, it is set to
            absolute by default. Thus it mimics the default
            behavior of Bio::Index::Abstract module.
  Example : my $index = Bio::Index::Abstract->(-pathtype => 'relative',
                                               -file     => $file.inx,
  Returns : Type of the path.
  Args    : String (relative|absolute)


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


  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 : $first_file_indexed = $index->_file_handle( 0 );
  Returns : ref to a filehandle
  Args    : INT


  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


  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


  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


  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


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


 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