bio::graphics::featuredir(3pm) [debian man page]

Bio::Graphics::FeatureDir(3pm)				User Contributed Perl Documentation			    Bio::Graphics::FeatureDir(3pm)

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

       Hey! The above document had some coding errors, which are explained below:

       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'

perl v5.14.2							    2012-02-20					    Bio::Graphics::FeatureDir(3pm)