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commit e27d0d24861461fd54ad643d76c3cf631694b7f2 1 parent 8076cae
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3  lib/Bio/Community/IO.pm
@@ -5,8 +5,7 @@
# Copyright Florent Angly <florent.angly@gmail.com>
#
# You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
+
=head1 NAME
View
3  lib/Bio/Community/IO/dummy.pm
@@ -5,8 +5,7 @@
# Copyright Florent Angly <florent.angly@gmail.com>
#
# You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
+
=head1 NAME
View
3  lib/Bio/Community/IO/gaas.pm
@@ -5,8 +5,7 @@
# Copyright Florent Angly <florent.angly@gmail.com>
#
# You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
+
=head1 NAME
View
3  lib/Bio/Community/IO/generic.pm
@@ -5,8 +5,7 @@
# Copyright Florent Angly <florent.angly@gmail.com>
#
# You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
+
=head1 NAME
View
3  lib/Bio/Community/IO/qiime.pm
@@ -5,8 +5,7 @@
# Copyright Florent Angly <florent.angly@gmail.com>
#
# You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
+
=head1 NAME
View
74 lib/Bio/Community/Role/Classified.pm
@@ -1,8 +1,82 @@
+# BioPerl module for Bio::Community::Role::Classified
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Copyright Florent Angly <florent.angly@gmail.com>
+#
+# You may distribute this module under the same terms as perl itself
+
+
+=head1 NAME
+
+Bio::Community::Role::Classified - Role for objects that have a taxonomic classification
+
+=head1 SYNOPSIS
+
+ package My::Package;
+
+ use Moose;
+ with 'Bio::Community::Role::Classified';
+
+ # Use the taxon() method as needed
+ # ...
+
+ 1;
+
+=head1 DESCRIPTION
+
+This role provides the capability to add a taxonomic classification (Bio::Taxon
+object) to objects of the class that consumes this role.
+
+=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 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
+
+=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:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Florent Angly
+
+Email florent.angly@gmail.com
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
package Bio::Community::Role::Classified;
use Moose::Role;
use namespace::autoclean;
+
=head2 taxon
Title : taxon
View
75 lib/Bio/Community/Role/Described.pm
@@ -1,8 +1,83 @@
+# BioPerl module for Bio::Community::Role::Described
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Copyright Florent Angly <florent.angly@gmail.com>
+#
+# You may distribute this module under the same terms as perl itself
+
+
+=head1 NAME
+
+Bio::Community::Role::Described - Role for objects that have a description
+
+=head1 SYNOPSIS
+
+ package My::Package;
+
+ use Moose;
+ with 'Bio::Community::Role::Described';
+
+ # Use the desc() method as needed
+ # ...
+
+ 1;
+
+=head1 DESCRIPTION
+
+This role provides the capability to add an arbitrary description (a string)
+to objects of the class that consumes this role.
+
+=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 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
+
+=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:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Florent Angly
+
+Email florent.angly@gmail.com
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+
package Bio::Community::Role::Described;
use Moose::Role;
use namespace::autoclean;
+
=head2 desc
Title : desc
View
78 lib/Bio/Community/Role/IO.pm
@@ -1,8 +1,86 @@
+# BioPerl module for Bio::Community::Role::IO
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Copyright Florent Angly <florent.angly@gmail.com>
+#
+# You may distribute this module under the same terms as perl itself
+
+
+=head1 NAME
+
+Bio::Community::Role::IO - Role for IO layer
+
+=head1 SYNOPSIS
+
+ package My::Package;
+
+ use Moose;
+ with 'Bio::Community::Role::IO';
+
+ # ...
+
+ 1;
+
+=head1 DESCRIPTION
+
+This role is an IO layer to read and write community files. The only thing it
+does is define methods that the role-consuming class must implement.
+
+Input methods: next_member, next_community, _next_community_init, _next_community_finish
+Output methods: write_member, write_community, _write_community_init, _write_community_finish, sort_members
+
+=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 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
+
+=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:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Florent Angly
+
+Email florent.angly@gmail.com
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+
package Bio::Community::Role::IO;
use Moose::Role;
use namespace::autoclean;
+# TODO: POD that describes each method and its inputs and outputs
+
requires 'next_member',
'next_community',
'_next_community_init',
View
75 lib/Bio/Community/Role/Sequenced.pm
@@ -1,8 +1,83 @@
+# BioPerl module for Bio::Community::Role::Sequenced
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Copyright Florent Angly <florent.angly@gmail.com>
+#
+# You may distribute this module under the same terms as perl itself
+
+
+=head1 NAME
+
+Bio::Community::Role::Sequenced - Role for objects that have a sequence
+
+=head1 SYNOPSIS
+
+ package My::Package;
+
+ use Moose;
+ with 'Bio::Community::Role::Sequenced';
+
+ # Use the seqs() method as needed
+ # ...
+
+ 1;
+
+=head1 DESCRIPTION
+
+This role provides the capability to add an arrayref of sequences (Bio::PrimarySeq
+compliant objects) to objects of the class that consumes this role.
+
+=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 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
+
+=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:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Florent Angly
+
+Email florent.angly@gmail.com
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+
package Bio::Community::Role::Sequenced;
use Moose::Role;
use namespace::autoclean;
+
=head2 seqs
Title : seqs
View
151 lib/Bio/Community/Role/Table.pm
@@ -1,15 +1,10 @@
-package Bio::Community::Role::Table;
-
-use Moose::Role;
-use MooseX::Method::Signatures;
-use namespace::autoclean;
-use Fcntl;
-
-
-# Consuming class has to inherit from Bio::Root::IO
-requires '_fh',
- '_readline',
- '_print';
+# BioPerl module for Bio::Community::Role::Table
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Copyright Florent Angly <florent.angly@gmail.com>
+#
+# You may distribute this module under the same terms as perl itself
=head1 NAME
@@ -19,28 +14,88 @@ access to their cells
=head1 SYNOPSIS
- package My::Class;
- use Moose;
- extends 'Bio::Root::IO';
- with 'Bio::Community::Role::Table';
- # Use the new(), _read_table(), _get_value(), _set_value() and _write_table()
- # methods as needed
- 1;
+ package My::Package;
+
+ use Moose;
+ extends 'Bio::Root::IO';
+ with 'Bio::Community::Role::Table';
+
+ # Use the new(), _read_table(), _get_value(), _set_value() and _write_table()
+ # methods as needed
+ # ...
+
+ 1;
=head1 DESCRIPTION
This role implements methods to read and write file structured as a table
-containing rows and columns. The consuming class must inherit from Bio::Root::IO.
-When reading a table from a file, an index is kept to provide random-access to
-any cell of the table. When writing a table to a file, cell data can also be
-given in any order. It is kept in memory until the file is written to disk.
-
-=head1 CONSTRUCTORS
+containing rows and columns. When reading a table from a file, an index is kept
+to provide random-access to any cell of the table. When writing a table to a file,
+cell data can also be given in any order. It is kept in memory until the file is
+written to disk.
Objects are constructed with the new() method. Since Table-consuming classes
must inherit from Bio::Root::IO, all Bio::Root::IO options are accepted, e.g.
--file, -fh, -string, -flush, etc. The following options specific to the Table
-role are also valid:
+-file, -fh, -string, -flush, etc. Other constructors are detailed in the
+L<APPENDIX>.
+
+=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 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
+
+=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:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Florent Angly
+
+Email florent.angly@gmail.com
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+package Bio::Community::Role::Table;
+
+use Moose::Role;
+use MooseX::Method::Signatures;
+use namespace::autoclean;
+use Fcntl;
+
+
+# Consuming class has to inherit from Bio::Root::IO
+requires '_fh',
+ '_readline',
+ '_print';
+
=head2 delim
@@ -130,48 +185,6 @@ has 'missing_string' => (
lazy => 1,
);
-=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 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
-
-=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:
-
- http://bugzilla.open-bio.org/
-
-=head1 AUTHOR - Florent Angly
-
-Email florent.angly@gmail.com
-
-=head1 APPENDIX
-
-The rest of the documentation details the methods available. Since this class is
-not meant to be used directly, but rather consumed by another class, its methods
-should not be directly accessed by users but by developers, and are thus preceded
-with a _
=head2 _max_line
View
74 lib/Bio/Community/Role/Weighted.pm
@@ -1,3 +1,77 @@
+# BioPerl module for Bio::Community::Role::Weighted
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Copyright Florent Angly <florent.angly@gmail.com>
+#
+# You may distribute this module under the same terms as perl itself
+
+
+=head1 NAME
+
+Bio::Community::Role::Weighted - Role for objects that have a weight
+
+=head1 SYNOPSIS
+
+ package My::Package;
+
+ use Moose;
+ with 'Bio::Community::Role::Weighted';
+
+ # Use the weights() method as needed
+ # ...
+
+ 1;
+
+=head1 DESCRIPTION
+
+This role provides the capability to add an arrayref of weights (strictly positive
+numbers) to objects of the class that consumes this role.
+
+=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 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
+
+=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:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Florent Angly
+
+Email florent.angly@gmail.com
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+
package Bio::Community::Role::Weighted;
use Moose::Role;
View
3  lib/Bio/Community/Types.pm
@@ -5,8 +5,7 @@
# Copyright Florent Angly <florent.angly@gmail.com>
#
# You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
+
=head1 NAME
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