maint: fix POD for Bioperl's PodWeaver and DistZilla pluginbundles, a…

…nd remove tabs
bioperl · Apr 4, 2013 · 55cf1d3 · 55cf1d3
1 parent ce47658
commit 55cf1d3
Show file tree

Hide file tree

Showing 17 changed files with 333 additions and 1,104 deletions.
diff --git a/dist.ini b/dist.ini
@@ -1,13 +1,10 @@
-name    = Bio-Coordinate
-version = 2.000
-author  =  BioPerl Team <bioperl-l@bioperl.org>
-license = Perl_5
-copyright_holder = BioPerl Team
-
-main_module = lib/Bio/Coordinate/Chain.pm
+name              = Bio-Coordinate
+main_module       = lib/Bio/Coordinate/Chain.pm
+version           = 1.70
+author            = BioPerl Team <bioperl-l@bioperl.org>
+license           = Perl_5
+copyright_holder  = BioPerl Team
 
 [@Filter]
 -bundle = @BioPerl
--remove = NoTabsTests
-dist = Bio-Coordinate
-repository_at = github
+-remove = NoTabsTests ; because CoordinateMapper.t and GeneCoordinateMapper.t require tabs
diff --git a/lib/Bio/Coordinate/Chain.pm b/lib/Bio/Coordinate/Chain.pm
@@ -1,19 +1,15 @@
-#
-# bioperl module for Bio::Coordinate::Chain
-#
-# Please direct questions and support issues to <bioperl-l@bioperl.org>
-#
-# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
-#
-# Copyright Heikki Lehvaslaiho
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
+package Bio::Coordinate::Chain;
+use strict;
+use Bio::Root::Root;
+use Bio::Coordinate::Result;
+use base qw(Bio::Coordinate::Collection Bio::Coordinate::MapperI);
 
-=head1 NAME
+# ABSTRACT: Mapping locations through a chain of coordinate mappers.
+# AUTHOR:   Heikki Lehvaslaiho <heikki@bioperl.org>
+# OWNER:    Heikki Lehvaslaiho
+# LICENSE:  Perl_5
 
-Bio::Coordinate::Chain - Mapping locations through a chain of  coordinate mappers
+# CONTRIBUTOR: Ewan Birney <birney@ebi.ac.uk>
 
 =head1 SYNOPSIS
 
@@ -53,65 +49,9 @@ It would be neat to an internal function that would generate a new
 single step mapper from those included in the chain. It should speed
 things up considerably. Any volunteers?
 
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to 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
-
-=head2 Support
-
-Please direct usage questions or support issues to the mailing list:
-
-I<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
-
-Report bugs to the Bioperl bug tracking system to help us keep track
-the bugs and their resolution.  Bug reports can be submitted via the
-web:
-
-  https://redmine.open-bio.org/projects/bioperl/
-
-=head1 AUTHOR - Heikki Lehvaslaiho
-
-Email:  heikki-at-bioperl-dot-org
-
-=head1 CONTRIBUTORS
-
-Ewan Birney, birney@ebi.ac.uk
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object
-methods. Internal methods are usually preceded with a _
-
 =cut
 
-
-# Let the code begin...
-
-package Bio::Coordinate::Chain;
-use strict;
-
-# Object preamble - inherits from Bio::Root::Root
-use Bio::Root::Root;
-use Bio::Coordinate::Result;
-
-use base qw(Bio::Coordinate::Collection Bio::Coordinate::MapperI);
-
-
-=head2 map
+=method map
 
  Title   : map
  Usage   : $newpos = $obj->map($pos);
@@ -144,11 +84,8 @@ sub map {
    return $value;
 }
 
-
 =head2 Inherited methods
 
-=cut
-
 =head2 add_mapper
 
  Title   : add_mapper
@@ -159,8 +96,6 @@ sub map {
  Returns : 1 when succeeds, 0 for failure.
  Args    : mapper object
 
-=cut
-
 =head2 mappers
 
  Title   : mappers
@@ -170,8 +105,6 @@ sub map {
  Returns : array of mappers
  Args    : array of mappers
 
-=cut
-
 =head2 each_mapper
 
  Title   : each_mapper
@@ -181,8 +114,6 @@ sub map {
  Returns : array of mappers
  Args    : none
 
-=cut
-
 =head2 swap
 
  Title   : swap
@@ -192,8 +123,6 @@ sub map {
  Returns : 1
  Args    :
 
-=cut
-
 =head2 test
 
  Title   : test
@@ -206,7 +135,11 @@ sub map {
 
 =cut
 
+=method sort
 
+You do not really want to sort your chain, do you! This function does nothing
+other than a warning.
+=cut
 
 sub sort{
    my ($self) = @_;

diff --git a/lib/Bio/Coordinate/Collection.pm b/lib/Bio/Coordinate/Collection.pm
@@ -1,19 +1,15 @@
-#
-# bioperl module for Bio::Coordinate::Collection
-#
-# Please direct questions and support issues to <bioperl-l@bioperl.org>
-#
-# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
-#
-# Copyright Heikki Lehvaslaiho
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
+package Bio::Coordinate::Collection;
+use strict;
+use Bio::Coordinate::Result;
+use Bio::Coordinate::Result::Gap;
+use base qw(Bio::Root::Root Bio::Coordinate::MapperI);
 
-=head1 NAME
+# ABSTRACT: Noncontinuous match between two coordinate sets.
+# AUTHOR:   Heikki Lehvaslaiho <heikki@bioperl.org>
+# OWNER:    Heikki Lehvaslaiho
+# LICENSE:  Perl_5
 
-Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets
+# CONTRIBUTOR: Ewan Birney <birney@ebi.ac.uk>
 
 =head1 SYNOPSIS
 
@@ -52,65 +48,10 @@ To map coordinates to the other direction, you have to swap() the
 collection. Keeping track of the direction and ID restrictions
 are left to the calling code.
 
-
-
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to 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
-
-=head2 Support
-
-Please direct usage questions or support issues to the mailing list:
-
-I<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
-
-report bugs to the Bioperl bug tracking system to help us keep track
-the bugs and their resolution.  Bug reports can be submitted via the
-web:
-
-  https://redmine.open-bio.org/projects/bioperl/
-
-=head1 AUTHOR - Heikki Lehvaslaiho
-
-Email:  heikki-at-bioperl-dot-org
-
-=head1 CONTRIBUTORS
-
-Ewan Birney, birney@ebi.ac.uk
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object
-methods. Internal methods are usually preceded with a _
-
 =cut
 
-
-# Let the code begin...
-
-package Bio::Coordinate::Collection;
-use strict;
-
-# Object preamble - inherits from Bio::Root::Root
-use Bio::Coordinate::Result;
-use Bio::Coordinate::Result::Gap;
-
-use base qw(Bio::Root::Root Bio::Coordinate::MapperI);
-
+=method new
+=cut
 
 sub new {
     my($class,@args) = @_;
@@ -134,8 +75,7 @@ sub new {
     return $self; # success - we hope!
 }
 
-
-=head2 add_mapper
+=method add_mapper
 
  Title   : add_mapper
  Usage   : $obj->add_mapper($mapper)
@@ -163,7 +103,7 @@ sub add_mapper {
   push(@{$self->{'_mappers'}},$value);
 }
 
-=head2 mappers
+=attr mappers
 
  Title   : mappers
  Usage   : $obj->mappers();
@@ -189,8 +129,7 @@ sub mappers{
         return @{$self->{'_mappers'}};
 }
 
-
-=head2 each_mapper
+=attr each_mapper
 
  Title   : each_mapper
  Usage   : $obj->each_mapper();
@@ -206,7 +145,7 @@ sub each_mapper{
    return @{$self->{'_mappers'}};
 }
 
-=head2 mapper_count
+=attr mapper_count
 
  Title   : mapper_count
  Usage   : my $count = $collection->mapper_count;
@@ -216,16 +155,14 @@ sub each_mapper{
  Returns : integer
  Args    : none
 
-
 =cut
 
 sub mapper_count{
    my $self = shift;
    return scalar @{$self->{'_mappers'} || []};
 }
 
-
-=head2 swap
+=method swap
 
  Title   : swap
  Usage   : $obj->swap;
@@ -247,7 +184,7 @@ sub swap {
    1;
 }
 
-=head2 test
+=method test
 
  Title   : test
  Usage   : $obj->test;
@@ -275,8 +212,7 @@ sub test {
    $res;
 }
 
-
-=head2 map
+=method map
 
  Title   : map
  Usage   : $newpos = $obj->map($pos);
@@ -300,7 +236,6 @@ sub map {
 
    $self->sort unless $self->_is_sorted;
 
-
    if ($value->isa("Bio::Location::SplitLocationI")) {
 
        my $result = Bio::Coordinate::Result->new();
@@ -316,11 +251,9 @@ sub map {
        return $self->_map($value);
    }
 
-
 }
 
-
-=head2 _map
+=internal _map
 
  Title   : _map
  Usage   : $newpos = $obj->_map($simpleloc);
@@ -376,8 +309,7 @@ IDMATCH: {
    return $result;
 }
 
-
-=head2 sort
+=method sort
 
  Title   : sort
  Usage   : $obj->sort;
@@ -408,7 +340,7 @@ sub sort{
    $self->_is_sorted(1);
 }
 
-=head2 _is_sorted
+=internal _is_sorted
 
  Title   : _is_sorted
  Usage   : $newpos = $obj->_is_sorted;