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.\" ========================================================================
.\"
.IX Title "Bio::Graphics::FeatureDir 3pm"
.TH Bio::Graphics::FeatureDir 3pm "2019-11-25" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Graphics::FeatureDir \-\- A directory of feature files and conf files
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 5
\& my $fd = Bio::Graphics::FeatureDir\->new(\*(Aq/path/to/dir\*(Aq);
\& $fd\->add_file(\*(Aqtracks.conf\*(Aq);
\& $fd\->add_file(\*(Aqfoo.gff3\*(Aq);
\& $fd\->add_file(\*(Aqfoo.wig\*(Aq);
\& $fd\->add_fh(\e*STDIN);
\& 
\& my $option   = $fd\->setting(\*(AqEST\*(Aq => \*(Aqbgcolor\*(Aq);
\& my @features = $fd\->get_features_by_name(\*(AqM101\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This class implements most of the methods of
Bio::Graphics::FeatureFile, but stores the data files and features in
a directory indexed by the Bio::DB::SeqFeature::Store::berkeleydb
adaptor. Therefore it is fast.
.SS "Methods"
.IX Subsection "Methods"
.ie n .IP "$fd = Bio::Graphics::FeatureDir\->new('/path/to/dir');" 4
.el .IP "\f(CW$fd\fR = Bio::Graphics::FeatureDir\->new('/path/to/dir');" 4
.IX Item "$fd = Bio::Graphics::FeatureDir->new('/path/to/dir');"
.PD 0
.ie n .IP "$fd = Bio::Graphics::FeatureDir\->new(\-dir => '/path/to/dir');" 4
.el .IP "\f(CW$fd\fR = Bio::Graphics::FeatureDir\->new(\-dir => '/path/to/dir');" 4
.IX Item "$fd = Bio::Graphics::FeatureDir->new(-dir => '/path/to/dir');"
.PD
Create a new FeatureDir, based in the indicated directory. In addition
to the \-dir directory argument, it takes any of the options that can
be passed to Bio::Graphics::FeatureFile except for the \-file and \-text
arguments;
.ie n .IP "$db\->_init_featuredb" 4
.el .IP "\f(CW$db\fR\->_init_featuredb" 4
.IX Item "$db->_init_featuredb"
Internal method. Initializes the underlying feature database.
.ie n .IP "$db\->_init_conf" 4
.el .IP "\f(CW$db\fR\->_init_conf" 4
.IX Item "$db->_init_conf"
Internal method \*(-- initialize the configuration file(s)
.ie n .IP "$created = $db\->_maybe_create_dir($dir)" 4
.el .IP "\f(CW$created\fR = \f(CW$db\fR\->_maybe_create_dir($dir)" 4
.IX Item "$created = $db->_maybe_create_dir($dir)"
Create \f(CW$dir\fR and its parents if it doesn't exist. Return true if the directory
was created. Throws an exception on filesystem errors.
.ie n .IP "$dir = $db\->dir" 4
.el .IP "\f(CW$dir\fR = \f(CW$db\fR\->dir" 4
.IX Item "$dir = $db->dir"
Returns the base directory.
.ie n .IP "$conf = $db\->conf" 4
.el .IP "\f(CW$conf\fR = \f(CW$db\fR\->conf" 4
.IX Item "$conf = $db->conf"
Returns the underlying Bio::Graphics::FeatureFile object
.ie n .IP "$db = $db\->db" 4
.el .IP "\f(CW$db\fR = \f(CW$db\fR\->db" 4
.IX Item "$db = $db->db"
Returns the underlying Bio::DB::SeqFeature::Store object
.ie n .IP "$db\->add_file($file)" 4
.el .IP "\f(CW$db\fR\->add_file($file)" 4
.IX Item "$db->add_file($file)"
Add the file to the directory. Can add files of type .fa, .gff, .gff3,
\&.conf and .ff.
.ie n .IP "$db\->add_fh(\e*FILEHANDLE [,'name'])" 4
.el .IP "\f(CW$db\fR\->add_fh(\e*FILEHANDLE [,'name'])" 4
.IX Item "$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.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Graphics::Feature,
Bio::Graphics::FeatureFile
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lincoln.stein@gmail.com>.
.PP
Copyright (c) 2009 Ontario Institute for Cancer Research
.PP
This package and its accompanying libraries is free software; you can
redistribute it and/or modify it under the terms of the \s-1GPL\s0 (either
version 1, or at your option, any later version) or the Artistic
License 2.0.  Refer to \s-1LICENSE\s0 for the full license text. In addition,
please see \s-1DISCLAIMER\s0.txt for disclaimers of warranty.
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 160:" 4
.IX Item "Around line 160:"
\&'=item' outside of any '=over'
.IP "Around line 272:" 4
.IX Item "Around line 272:"
=cut found outside a pod block.  Skipping to next block.
.IP "Around line 274:" 4
.IX Item "Around line 274:"
You forgot a '=back' before '=head1'