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 = 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
- Internal method. Initializes the underlying feature database.
- 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
- 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 block.
- Around line 274:
- You forgot a '=back' before '=head1'