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small doc fixes

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1 parent 19147a7 commit 783e25d4fb5e6342b4b0e28910167d734a81000f Chris Fields committed Aug 21, 2009
Showing with 59 additions and 50 deletions.
  1. +2 −0 docs/class_template_komodo.pm
  2. +2 −0 docs/role_template_komodo.pm
  3. +6 −5 lib/Biome/Annotation/README
  4. +49 −45 lib/Biome/Role/Feature.pm
@@ -6,6 +6,8 @@ no Biome;
__PACKAGE__->meta->make_immutable;
+1;
+
__END__
=head1 NAME
@@ -6,6 +6,8 @@ no Biome::Role;
__PACKAGE__->meta->make_immutable;
+1;
+
__END__
=head1 NAME
@@ -1,9 +1,10 @@
Annotation and Annotation Collections
-This system is mainly inherited from BioPerl. Several users and devs
-have previously indicated that this could easily be replaced by something
-that creates a hierarchal structure with a predefined schema, along the lines
-of XML, JSON, or even using an Ontology.
+This system is mainly inherited from BioPerl. It long been suggested that this
+could easily be replaced by something with a hierarchal structure using a
+predefined schema, along the lines of XML, JSON, or even using an Ontology. This
+would possibly involve something along the lines of Data::Stag, XML::LibXML,
+JSON, or maybe a pluggable system that allows any of the above.
It is very possible this system will be overhauled with that in mind, with an
-eye towards a lightweight implementation with easy serialization.
+eye towards keeping a lightweight implementation with easy serialization.
View
@@ -7,13 +7,13 @@ requires qw(
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).
+ # instance (nodes in a tree or graph, columns in an alignment, indices in an
+ # array, etc). May need to be aliased as needed.
requires qw(
display_name
description
-); # Biome::Role::Describe
+); # possibly Biome::Role::Describe
requires qw(
add_tag_values
@@ -22,25 +22,45 @@ requires qw(
get_all_tags
has_tag
remove_tag
- get_tagset_values
-); # Biome::Role::CollectTags
+ get_tagset_values
+); # possibly 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
+ has_featured_instance
+ entire_featured_instance
+ attach_featured_instance
+ spliced_featured_instance
+); # customized roles for each parent (featured) instance
+ # should be aliased for the specific features instance name
+
+has [qw(primary_tag source_tag id)] => (
+ isa => 'Str',
+ is => 'rw'
+);
+
+has 'score' => (
+ isa => 'Num',
+ is => 'rw'
+);
+
+has 'sub_Features' => (
+ is => 'ro',
+ isa => 'ArrayRef[Obj]',
+ default => sub {[]},
+ lazy => 1,
+ metaclass => 'Collection::Array',
+ provides => {
+ 'push' => 'add_Features',
+ 'elements' => 'get_Features',
+ 'clear' => 'delete_Features',
+ 'count' => 'num_Features',
+ }
+);
no Biome::Role;
+1;
+
__END__
=head1 NAME
@@ -60,9 +80,6 @@ This documentation refers to Biome::Role::Feature version 0.01.
with 'Biome::Role::Feature';
# other comsumer-specific information
-
-
-
=head1 DESCRIPTION
@@ -72,21 +89,23 @@ CollectAnnotation, etc.).
=head1 SUBROUTINES/METHODS
+TODO
+
=head1 DIAGNOSTICS
-None; abstract class.
+TODO
=head1 CONFIGURATION AND ENVIRONMENT
-None
+TODO
=head1 DEPENDENCIES
Biome::Role (part of Biome)
=head1 INCOMPATIBILITIES
-None known
+TODO
=head1 BUGS AND LIMITATIONS
@@ -96,29 +115,20 @@ 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.
+TODO
=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.
+TODO
=head1 COMMON USAGE MISTAKES
+TODO
+
=head1 SEE ALSO
+TODO
+
=head1 (DISCLAIMER OF) WARRANTY
This program is distributed in the hope that it will be useful,
@@ -127,13 +137,7 @@ 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.
+TODO
=head1 AUTHOR

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