now add this to trunk

svn path=/Bio-FeatureIO/trunk/; revision=16799

Build.PL

@@ -0,0 +1,30 @@
+#!/usr/bin/perl -w
+
+# This is a Module::Build script for BioPerl-Run installation.
+# See http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm
+
+use strict;
+use warnings;
+use Module::Build;
+
+my $build = Module::Build->new(
+    dist_name           => 'Bio::FeatureIO',
+    dist_version        => '0.01',
+    module_name         => 'Bio::FeatureIO',
+    dist_author         => 'BioPerl Team <bioperl-l@bioperl.org>',
+    dist_abstract       => 'Bio::FeatureIO - feature parsers',
+    license             => 'perl',
+    recursive_test_files => 1,
+    requires            => {
+                            'perl'               => '5.6.1',
+                            'Bio::Root::Version' => '1.006900',
+                            'URI::Escape'        => '0',    # dealing with web resources/Bio::FeatureIO::gff,Bio::FeatureIO::interpro,Bio::DB::Biblio::eutils,Bio::DB::EUtilParameters,Bio::DB::Query::GenBank,Bio::DB::NCBIHelper,Bio::SeqFeature::Annotated',
+                            'XML::DOM::XPath'    => '0.13', # parsing interpro features/Bio::FeatureIO::interpro',
+                           },
+    dynamic_config      => 1,
+);
+
+# Create the build script and exit
+$build->create_build_script;
+
+exit;

Changes

@@ -0,0 +1,5 @@
+Revision history for Perl extension Bio::FeatureIO.
+
+0.01  Sun Jan 31 14:49:01 2010
+	- initial split off from BioPerl core 
+

README

@@ -0,0 +1,30 @@
+Bio-FeatureIO version 0.01
+==========================
+
+Bio::FeatureIO is a BioPerl-based parser for feature data from common biological
+sequence formats, such as GFF3, GTF, and BED.
+
+INSTALLATION
+
+To install this module type the following:
+
+   perl Build.PL
+   ./Build
+   ./Build test
+   ./Build install
+
+DEPENDENCIES
+
+This module requires these other modules and libraries:
+
+  URI::Escape
+  XML::DOM::XPath
+
+COPYRIGHT AND LICENCE
+
+Copyright (C) 2010 by Christopher Fields and Allen Day
+
+This library is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself, either Perl version 5.10.1 or,
+at your option, any later version of Perl 5 you may have available.
+

lib/Bio/Factory/FeatureFactory.pm

@@ -0,0 +1,203 @@
+package Bio::Factory::FeatureFactory;
+
+use base qw(Bio::Root::Root Bio::Factory::ObjectFactoryI);
+
+sub unflattener {
+
+}
+
+sub 
+
+sub create_feature {
+
+}
+
+sub feature_collection {
+
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+Bio::Factory::FeatureFactory - <One-line description of module's purpose>
+
+=head1 VERSION
+
+This documentation refers to Bio::Factory::FeatureFactory version Bio::Root::Root.
+
+=head1 SYNOPSIS
+
+   use Bio::Factory::FeatureFactory;
+   # Brief but working code example(s) here showing the most common usage(s)
+
+   # This section will be as far as many users bother reading,
+
+   # so make it as educational and exemplary as possible.
+
+=head1 DESCRIPTION
+
+<TODO>
+A full description of the module and its features.
+May include numerous subsections (i.e., =head2, =head3, etc.).
+
+=head1 SUBROUTINES/METHODS
+
+<TODO>
+A separate section listing the public components of the module's interface.
+These normally consist of either subroutines that may be exported, or methods
+that may be called on objects belonging to the classes that the module provides.
+Name the section accordingly.
+
+In an object-oriented module, this section should begin with a sentence of the
+form "An object of this class represents...", to give the reader a high-level
+context to help them understand the methods that are subsequently described.
+
+=head1 DIAGNOSTICS
+
+<TODO>
+A list of every error and warning message that the module can generate
+(even the ones that will "never happen"), with a full explanation of each
+problem, one or more likely causes, and any suggested remedies.
+
+=head1 CONFIGURATION AND ENVIRONMENT
+
+<TODO>
+A full explanation of any configuration system(s) used by the module,
+including the names and locations of any configuration files, and the
+meaning of any environment variables or properties that can be set. These
+descriptions must also include details of any configuration language used.
+
+=head1 DEPENDENCIES
+
+<TODO>
+A list of all the other modules that this module relies upon, including any
+restrictions on versions, and an indication of whether these required modules are
+part of the standard Perl distribution, part of the module's distribution,
+or must be installed separately.
+
+=head1 INCOMPATIBILITIES
+
+<TODO>
+A list of any modules that this module cannot be used in conjunction with.
+This may be due to name conflicts in the interface, or competition for
+system or program resources, or due to internal limitations of Perl
+(for example, many modules that use source code filters are mutually
+incompatible).
+
+=head1 BUGS AND LIMITATIONS
+
+There are no known bugs in this module.
+
+User feedback is an integral part of the evolution of this and other Biome and
+BioPerl modules. Send your comments and suggestions preferably to one of the
+BioPerl mailing lists. Your participation is much appreciated.
+
+  bioperl-l@bioperl.org                  - General discussion
+  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
+
+Patches are always welcome.
+
+=head2 Support 
+ 
+Please direct usage questions or support issues to the mailing list:
+  
+L<bioperl-l@bioperl.org>
+  
+rather than to the module maintainer directly. Many experienced and reponsive
+experts will be able look at the problem and quickly address it. Please include
+a thorough description of the problem with code and data examples if at all
+possible.
+
+=head2 Reporting Bugs
+
+Preferrably, Biome bug reports should be reported to the GitHub Issues bug
+tracking system:
+
+  http://github.com/cjfields/biome/issues
+
+Bugs can also be reported using the BioPerl bug tracking system, submitted via
+the web:
+
+  http://bugzilla.open-bio.org/
+
+=head1 EXAMPLES
+
+<TODO>
+Many people learn better by example than by explanation, and most learn better
+by a combination of the two. Providing a /demo directory stocked with
+well-commented examples is an excellent idea, but your users might not have
+access to the original distribution, and the demos are unlikely to have been
+installed for them. Adding a few illustrative examples in the documentation
+itself can greatly increase the "learnability" of your code.
+
+=head1 FREQUENTLY ASKED QUESTIONS
+
+<TODO>
+Incorporating a list of correct answers to common questions may seem like extra
+work (especially when it comes to maintaining that list), but in many cases it
+actually saves time. Frequently asked questions are frequently emailed
+questions, and you already have too much email to deal with. If you find
+yourself repeatedly answering the same question by email, in a newsgroup, on a
+web site, or in person, answer that question in your documentation as well. Not
+only is this likely to reduce the number of queries on that topic you
+subsequently receive, it also means that anyone who does ask you directly can
+simply be directed to read the fine manual.
+
+=head1 COMMON USAGE MISTAKES
+
+<TODO>
+This section is really "Frequently Unasked Questions". With just about any kind
+of software, people inevitably misunderstand the same concepts and misuse the
+same components. By drawing attention to these common errors, explaining the
+misconceptions involved, and pointing out the correct alternatives, you can once
+again pre-empt a large amount of unproductive correspondence. Perl itself
+provides documentation of this kind, in the form of the perltrap manpage.
+
+=head1 SEE ALSO
+
+<TODO>
+Often there will be other modules and applications that are possible
+alternatives to using your software. Or other documentation that would be of use
+to the users of your software. Or a journal article or book that explains the
+ideas on which the software is based. Listing those in a "See Also" section
+allows people to understand your software better and to find the best solution
+for their problem themselves, without asking you directly.
+
+By now you have no doubt detected the ulterior motive for providing more
+extensive user manuals and written advice. User documentation is all about not
+having to actually talk to users.
+
+=head1 (DISCLAIMER OF) WARRANTY
+
+<TODO>
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+=head1 ACKNOWLEDGEMENTS
+
+<TODO>
+Acknowledging any help you received in developing and improving your software is
+plain good manners. But expressing your appreciation isn't only courteous; it's
+also enlightened self-interest. Inevitably people will send you bug reports for
+your software. But what you'd much prefer them to send you are bug reports
+accompanied by working bug fixes. Publicly thanking those who have already done
+that in the past is a great way to remind people that patches are always
+welcome.
+
+=head1 AUTHOR
+
+Chris Fields  (cjfields at bioperl dot org)
+
+=head1 LICENCE AND COPYRIGHT
+
+Copyright (c) 2010 Chris Fields (cjfields at bioperl dot org). All rights reserved.
+
+followed by whatever licence you wish to release it under.
+For Perl code that is often just:
+
+This module is free software; you can redistribute it and/or
+modify it under the same terms as Perl itself. See L<perlartistic>.