NAME

       Bio::Graphics::FeatureDir -- A directory of feature files and conf files

SYNOPSIS

        my $fd = Bio::Graphics::FeatureDir->new('/path/to/dir');
        $fd->add_file('tracks.conf');
        $fd->add_file('foo.gff3');
        $fd->add_file('foo.wig');
        $fd->add_fh(\*STDIN);

        my $option   = $fd->setting('EST' => 'bgcolor');
        my @features = $fd->get_features_by_name('M101');

DESCRIPTION

       This class implements most of the methods of Bio::Graphics::FeatureFile, but stores the data files and
       features in a directory indexed by the Bio::DB::SeqFeature::Store::berkeleydb adaptor. Therefore it is
       fast.

   Methods
       $fd = Bio::Graphics::FeatureDir->new('/path/to/dir');
       $fd = Bio::Graphics::FeatureDir->new(-dir => '/path/to/dir');
           Create a new FeatureDir, based in the indicated directory. In addition to the -dir directory
           argument, it takes any of the options that can be passed to Bio::Graphics::FeatureFile except for the
           -file and -text arguments;

       $db->_init_featuredb
           Internal method. Initializes the underlying feature database.

       $db->_init_conf
           Internal method -- initialize the configuration file(s)

       $created = $db->_maybe_create_dir($dir)
           Create $dir and its parents if it doesn't exist. Return true if the directory was created. Throws an
           exception on filesystem errors.

       $dir = $db->dir
           Returns the base directory.

       $conf = $db->conf
           Returns the underlying Bio::Graphics::FeatureFile object

       $db = $db->db
           Returns the underlying Bio::DB::SeqFeature::Store object

       $db->add_file($file)
           Add the file to the directory. Can add files of type .fa, .gff, .gff3, .conf and .ff.

       $db->add_fh(\*FILEHANDLE [,'name'])
           Add the contents of the indicated filehandle to repository.  Name is optional; if provided it will be
           used as the base for all files created.

SEE ALSO

       Bio::Graphics::Feature, Bio::Graphics::FeatureFile

AUTHOR

       Lincoln Stein <lincoln.stein@gmail.com>.

       Copyright (c) 2009 Ontario Institute for Cancer Research

       This package and its accompanying libraries is free software; you can redistribute it and/or modify it
       under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic
       License 2.0.  Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for
       disclaimers of warranty.

POD ERRORS

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       Around line 160:
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       Around line 272:
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       Around line 274:
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