Bio::Graphics::FeatureDir -- A directory of feature files and conf files
my $fd = Bio::Graphics::FeatureDir->new('/path/to/dir');
my $option = $fd->setting('EST' => 'bgcolor');
my @features = $fd->get_features_by_name('M101');
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.
- $fd =
- $fd = Bio::Graphics::FeatureDir->new(-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
- Internal method. Initializes the underlying feature
- Internal method -- initialize the configuration
- $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
- $dir = $db->dir
- Returns the base directory.
- $conf = $db->conf
- Returns the underlying Bio::Graphics::FeatureFile
- $db = $db->db
- Returns the underlying Bio::DB::SeqFeature::Store
- 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
Lincoln Stein <email@example.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.
Hey! The above document had some coding errors, which are explained
- Around line 160:
- '=item' outside of any '=over'
- Around line 272:
- =cut found outside a pod block. Skipping to next
- Around line 274:
- You forgot a '=back' before '=head1'