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Bio::DB::GFF::Adaptor::memory.3pm

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().