initial cut at an abstract Feature role (NYI)

cjfields · Aug 21, 2009 · 19147a7 · 19147a7
1 parent 67d7525
commit 19147a7
Showing 1 changed file with 150 additions and 0 deletions.
diff --git a/lib/Biome/Role/Feature.pm b/lib/Biome/Role/Feature.pm
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+package Biome::Role::Feature;
+
+use Biome::Role;
+
+requires qw(
+    start
+    end
+    length
+);  # possibly Biome::Role::Range, but may delineate start/end for a different
+    # range (nodes in a tree or graph, columns in an alignment, indices in an
+    # array, etc).
+
+requires qw(
+    display_name
+    description
+); # Biome::Role::Describe
+
+requires qw(
+    add_tag_values
+    get_tag_values
+    set_tag_values
+    get_all_tags
+    has_tag
+    remove_tag
+    get_tagset_values    
+); # Biome::Role::CollectTags
+
+requires qw(
+    primary_tag
+    source_tag
+    score
+    
+    get_Features
+    add_Features
+    attach_instance
+    entire_instance
+    spliced_instance
+    id
+    
+); # specific for this role
+
+no Biome::Role;
+
+__END__
+
+=head1 NAME
+
+Biome::Role::Feature - Role that describes the basic attributes specific
+for Features.
+
+=head1 VERSION
+
+This documentation refers to Biome::Role::Feature version 0.01.
+
+=head1 SYNOPSIS
+
+    package Biome::Foo;
+    use Biome;
+    
+    with 'Biome::Role::Feature';
+    
+    # other comsumer-specific information
+    
+    
+    
+
+=head1 DESCRIPTION
+
+This describes the basic abstract interface for a Feature. Methods expected in
+this interface may be defined in other roles (for instance, Range, CollectTags,
+CollectAnnotation, etc.).
+
+=head1 SUBROUTINES/METHODS
+
+=head1 DIAGNOSTICS
+
+None; abstract class.
+
+=head1 CONFIGURATION AND ENVIRONMENT
+
+None
+
+=head1 DEPENDENCIES
+
+Biome::Role (part of Biome)
+
+=head1 INCOMPATIBILITIES
+
+None known
+
+=head1 BUGS AND LIMITATIONS
+
+There are no known bugs in this module.
+Please report problems to the bioperl mailing list.
+Patches are welcome.
+
+=head1 EXAMPLES
+
+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
+
+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
+
+=head1 SEE ALSO
+
+=head1 (DISCLAIMER OF) WARRANTY
+
+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
+
+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) 2009 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>.