Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Index::Stockholm - Interface for indexing Stockholm files


           use strict;
           use Bio::Index::Stockholm;
           my ($indexfile,$file1,$file2,$query);
           my $index = Bio::Index::Stockholm->new(-filename => $indexfile,
                                                                 -write_flag => 1);

           # get raw data stream starting at alignment position
           my $fh = $index->get_stream($query);

           # fetch individual alignment
           my $align = $index->fetch_aln($query); # alias for fetch_report
           my $align = $index->fetch_report($query); # same as above
           print "query is ", $align->display_id, "\n";


       Indexes Stockholm format alignments such as those from Pfam and Rfam.  Returns raw stream
       data using the ID or a Bio::SimpleAlign object (via Bio::AlignIO).

       This module also allows for ID parsing using a callback:

          # make the index

          # here is where the retrieval key is specified
          sub get_id {
             my $line = shift;
             $line =~ /^>.+gi\|(\d+)/;

       The indexer is capable of indexing based on multiple IDs passed back from the callback;
       this is assuming of course all IDs are unique.  The default is to use the alignment ID
       provided for Rfam/Pfam output.

       Note: for best results 'use strict'.


       - allow using an alternative regex for indexing (for instance, the ID instead of AC)


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AUTHOR - Chris Fields

       Email cjfields-at-bioperl-dot-org


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

         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

   Bio::Index::Stockholm implemented methods
        Title   : fetch_report
        Usage   : my $align = $idx->fetch_report($id);
        Function: Returns a Bio::SimpleAlign object
                  for a specific alignment
        Returns : Bio::SimpleAlign
        Args    : valid id

        Title   : fetch_aln
        Usage   : my $align = $idx->fetch_aln($id);
        Function: Returns a Bio::SimpleAlign object
                  for a specific alignment
        Returns : Bio::SimpleAlign
        Args    : valid id
        Note    : alias for fetch_report

   Require methods from Bio::Index::Abstract
         Title   : _index_file
         Usage   : $index->_index_file( $file_name, $i )
         Function: Specialist function to index report file(s).
                   Is provided with a filename and an integer
                   by make_index in its SUPER class.
         Example :
         Returns :
         Args    :

         Title   : id_parser
         Usage   : $index->id_parser( CODE )
         Function: Stores or returns the code used by record_id to
                   parse the ID for record from a string.
                   Returns \&default_id_parser (see below) if not
                   set. An entry will be added to
                   the index for each string in the list returned.
         Example : $index->id_parser( \&my_id_parser )
         Returns : reference to CODE if called without arguments
         Args    : CODE

         Title   : default_id_parser
         Usage   : $id = default_id_parser($line)
         Function: The default parser for
         Returns : Array of specified ids
         Args    : a line string

   Bio::Index::Abstract methods
        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 whether 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   : 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 won't do this for you
                  So this code

                  $fh = $index->get_stream($myid);
                  while( <$fh> ) {
                     # do something
                  will parse the entire file if you do not 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->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   : _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 : $fist_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   : DESTROY
        Usage   : Called automatically when index goes out of scope
        Function: Closes connection to database and handles to
                  sequence files
        Returns : NEVER
        Args    : NONE