Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::DB::GFF::Adaptor::memory -- Bio::DB::GFF database adaptor for in-memory databases

SYNOPSIS

         use Bio::DB::GFF;
         my $db = Bio::DB::GFF->new(-adaptor=> 'memory',
                                    -gff    => 'my_features.gff',
                                    -fasta  => 'my_dna.fa'
                                   );

       or

         my $db = Bio::DB::GFF->new(-adaptor=>'memory');
         $db->load_gff_file('my_features.gff');
         $db->load_fasta_file('my_dna.fa');

       See Bio::DB::GFF for other methods.

DESCRIPTION

       This adaptor implements an in-memory version of Bio::DB::GFF.  It can be used to store and
       retrieve SHORT GFF files. It inherits from Bio::DB::GFF.

CONSTRUCTOR

       Use Bio::DB::GFF->new() to construct new instances of this class.  Three named arguments
       are recommended:

          Argument         Description

          -adaptor         Set to "memory" to create an instance of this class.
          -gff             Read the indicated file or directory of .gff file.
          -fasta           Read the indicated file or directory of fasta files.
          -dir             Indicates a directory containing .gff and .fa files

       If you use the -dir option and the indicated directory is writable by the current process,
       then this library will create a FASTA file index that greatly diminishes the memory usage
       of this module.

       Alternatively you may create an empty in-memory object using just the -adaptor=>'memory'
       argument and then call the load_gff_file() and load_fasta_file() methods to load GFF
       and/or sequence information. This is recommended in CGI/mod_perl/fastCGI environments
       because these methods do not modify STDIN, unlike the constructor.

METHODS

       See Bio::DB::GFF for inherited methods.

BUGS

       none ;-)

SEE ALSO

       Bio::DB::GFF, bioperl

AUTHOR

       Shuly Avraham <avraham@cshl.org>.

       Copyright (c) 2002 Cold Spring Harbor Laboratory.

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.

   _feature_by_name
        Title   : _feature_by_name
        Usage   : $db->get_features_by_name($name,$class,$callback)
        Function: get a list of features by name and class
        Returns : count of number of features retrieved
        Args    : name of feature, class of feature, and a callback
        Status  : protected

       This method is used internally.  The callback arguments are those used by make_feature().