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appears.

=head2 Feature Tags

Tags can be added to features by adding a fourth column consisting of
"tag=value" pairs:

 Gene  B0511.1  Chr1:516..619,3185..3294 Note="Putative primase"

Tags and their values take any form you want, and multiple tags can be
separated by semicolons. You can also repeat tags multiple times:

 Gene  B0511.1  Chr1:516..619,3185..3294 GO_Term=GO:100;GO_Term=GO:2087

Several tags have special meanings:

 Tag     Meaning
 ---     -------

 Type    The primary tag for a subfeature.
 Score   The score of a feature or subfeature.
 Phase   The phase of a feature or subfeature.
 URL     A URL to link to (via the Bio::Graphics library).
 Note    A note to attach to the feature for display by the Bio::Graphics library.

For example, in the common case of an mRNA, you can use the "Type" tag
to distinguish the parts of the mRNA into UTR and CDS:

 mRNA B0511.1 Chr1:1..100 Type=UTR
 mRNA B0511.1 Chr1:101..200,300..400,500..800 Type=CDS
 mRNA B0511.1 Chr1:801..1000 Type=UTR

The top level feature's primary tag will be "mRNA", and its subparts
will have types UTR and CDS as indicated. Additional tags that are
placed in the first line of the feature will be applied to the top
level. In this example, the note "Putative primase" will be applied to
the mRNA at the top level of the feature:

 mRNA B0511.1 Chr1:1..100 Type=UTR;Note="Putative primase"
 mRNA B0511.1 Chr1:101..200,300..400,500..800 Type=CDS
 mRNA B0511.1 Chr1:801..1000 Type=UTR

=head2 Feature Groups

Features can be grouped so that they are rendered by the "group"
glyph.  To start a group, create a two-column feature entry showing
the group type and a name for the group.  Follow this with a list of
feature entries with a blank type.  For example:

 EST	yk53c10
 	yk53c10.3	15000-15500,15700-15800
 	yk53c10.5	18892-19154

This example is declaring that the ESTs named yk53c10.3 and yk53c10.5
belong to the same group named yk53c10.

=head2 Comments and the #include Directive

Lines that begin with the # sign are treated as comments and
ignored. When a # sign appears within a line, everything to the right
of the symbol is also ignored, unless it looks like an HTML fragment or
an HTML color, e.g.:

 # this is ignored
 [Example]
 glyph   = generic   # this comment is ignored
 bgcolor = #FF0000
 link    = http://www.google.com/search?q=$name#results

Be careful, because the processing of # signs uses a regexp heuristic. To be safe, 
always put a space after the # sign to make sure it is treated as a comment.

The special comment "#include 'filename'" acts like the C preprocessor
directive and will insert the comments of a named file into the
position at which it occurs. Relative paths will be treated relative
to the file in which the #include occurs. Nested #include directives
are allowed:

 #include "/usr/local/share/my_directives.txt"
 #include 'my_directives.txt'
 #include chromosome3_features.gff3

You can enclose the file path in single or double quotes as shown
above. If there are no spaces in the filename the quotes are optional.

Include file processing is not very smart. Avoid creating circular
#include references. You have been warned!

=head2 Caveats

Note that this loader always creates denormalized features such that
subfeatures and their parents are stored as one big database
object. The GFF3 format and its loader is usually preferred for both
space and execution efficiency.

=head1 METHODS

=cut


use strict;
use Carp 'croak';
use File::Spec;
use Text::ParseWords 'shellwords','quotewords';

use base 'Bio::DB::SeqFeature::Store::Loader';

=head2 new

 Title   : new
 Usage   : $loader = Bio::DB::SeqFeature::Store::FeatureFileLoader->new(@options)
 Function: create a new parser
 Returns : a Bio::DB::SeqFeature::Store::FeatureFileLoader parser and loader
 Args    : several - see below
 Status  : public

This method creates a new FeatureFile loader and establishes its connection
with a Bio::DB::SeqFeature::Store database. Arguments are -name=E<gt>$value
pairs as described in this table:

 Name               Value