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POD fixes

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Brian O
Brian O committed Mar 23, 2007
1 parent 374fbea commit 4f99b08be9ed44d2c1430546f716fc85b731d23c
@@ -1,7 +1,5 @@
# BioPerl module for Bio::DB::BioSQL::BioDatabaseAdaptor
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Modified by Vsevolod (Simon) Ilyushchenko (simonf@cshl.edu)
#
# Copyright Ewan Birney
@@ -28,19 +26,18 @@ Private class.
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.
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bio.perl.org
=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 email or the web:
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/
http://bugzilla.bioperl.org
=head1 AUTHORS - Ewan Birney, Vsevolod (Simon) Ilyushchenko
@@ -5,18 +5,20 @@ Bio::DB::Das::BioSQL::DBAdaptor - class that helps to use custom object adaptors
=head1 SYNOPSIS
This is a private class.
=head1 DESCRIPTION
In order to use custom object adaptors in BioSQL, first one has to provide a custom
"driver" class. Then the method _get_object_adaptor_class has to be overloaded to return
In order to use custom object adaptors in BioSQL, first one has to
provide a custom "driver" class. Then the method
_get_object_adaptor_class has to be overloaded to return
custom adaptors.
=head1 AUTHOR - Vsevolod (Simon) Ilyushchenko
Email simonf@cshl.edu
=cut
package Bio::DB::Das::BioSQL::DBAdaptor;
use strict;
@@ -5,24 +5,30 @@ Bio::DB::Das::BioSQL::PartialSeqAdaptor - class that helps to use custom object
=head1 SYNOPSIS
This is a private class.
=head1 DESCRIPTION
This is a custom driver class for sequence objects retrieved from BioDB.
We don't want to retrieve all the features at initialization time, because
it may be slow. Thus, they are fetched by calling slow_attach_children if necessary.
it may be slow. Thus, they are fetched by calling slow_attach_children
if necessary.
=head1 CHANGES
=head2 Mon Mar 15 10:21:17 EST 2004
=over 1
=item Fixed slow_attach_children() to retrieve partially overlapping features.
=back
=head1 AUTHOR - Vsevolod (Simon) Ilyushchenko
Email simonf@cshl.edu
=cut
package Bio::DB::Das::BioSQL::PartialSeqAdaptor;
use strict;
@@ -1,4 +1,4 @@
# $Id%
=head1 NAME
Bio::DB::Das::BioSQL::Segment - DAS-style access to a BioSQL database
@@ -8,7 +8,7 @@ Bio::DB::Das::BioSQL::Segment - DAS-style access to a BioSQL database
# Get a Bio::Das::SegmentI object from a Bio::DB::Das::BioSQL database...
#Should be created through Bio::DB::Das::BioSQL.
@features = $segment->overlapping_features(-type=>['type1','type2']);
# each feature is a Bio::SeqFeatureI-compliant object
@@ -21,7 +21,6 @@ Bio::DB::Das::BioSQL::Segment - DAS-style access to a BioSQL database
# do something with feature
}
=head1 DESCRIPTION
Bio::DB::Das::BioSQL::Segment is a simplified alternative interface to
@@ -314,7 +313,7 @@ sub features {
}
}
=head2 seq
=head2 top_SeqFeatures
Title : top_SeqFeatures
Usage : $s->top_SeqFeatures
@@ -327,6 +326,7 @@ First, make the adaptor retrieve the feature objects from the database.
Then, get the actual objects and adjust the features' locations if necessary.
=cut
sub top_SeqFeatures
{
my ($self) = @_;
@@ -490,4 +490,5 @@ sub overlaps {
# compatibility with Bio::DB::GFF::RelSegment
*abs_ref = \&accession_number;
1;
View
@@ -1,5 +1,4 @@
# $Id: Chado.pm,v 1.68.4.9.2.12.2.1 2007-03-22 02:24:25 scottcain Exp $
# Das adaptor for Chado
# $Id: Chado.pm,v 1.68.4.9.2.12.2.2 2007-03-23 21:02:38 briano Exp $
=head1 NAME
@@ -28,7 +27,6 @@ Bio::DB::Das::Chado - DAS-style access to a chado database
-callback => sub { ... }
);
# get all feature types
@types = $db->types;
@@ -1184,12 +1182,9 @@ attributes depend on implementation) and returns a list of
$description is a human-readable description such as a locus line, and
$score is the match strength.
=cut
=head2
search_notes is the sub to support keyword wildcard searching
=cut
sub search_notes {
my $self = shift;
@@ -324,7 +324,7 @@ sub uniquename {
=head1 SeqFeatureI methods
Bio::DB::Das::Chado::Segment::Feature implements the Bio::SeqFeatureI
interface. Methods described below, L<Bio:SeqFeatureI> for more
interface. Methods described below, see Bio:SeqFeatureI for more
details.
=cut
@@ -6,18 +6,19 @@ package Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcr
use Bio::DB::GFF::Aggregator;
=head1 DESCRIPTION
Bio::DB::GFF::Aggregator::retranscript was written to make the compound feature,
"reftranscript" for use with Gbrowse editing software developed outside of the GMOD
development group. It can be used to aggregate "reftranscripts" from "refexons",
loaded as second copy features. These features, in contrast to "transcripts",
are usually implemented as features which cannot be edited and serve as starting
point references for annotations added using Gbrowse for feature visualization.
Bio::DB::GFF::Aggregator::retranscript was written to make the compound
feature, "reftranscript" for use with Gbrowse editing software
developed outside of the GMOD development group. It can be used to
aggregate "reftranscripts" from "refexons", loaded as second copy
features. These features, in contrast to "transcripts", are usually
implemented as features which cannot be edited and serve as starting
point references for annotations added using Gbrowse for feature
visualization.
Adding features to the compound feature, "reftranscript", can be done by adding
to the "part_names" call (i.e. "refCDS").
Adding features to the compound feature, "reftranscript", can be done
by adding to the "part_names" call (i.e. "refCDS").
=cut
@@ -69,6 +70,7 @@ sub part_names {
Status : Public
=cut
sub main_name {
return 'reftranscript';
}
@@ -1,18 +1,18 @@
# $Id: GFFhelper.pm,v 1.22 2004-06-15 18:03:04 sheldon_mckay Exp $
# $Id: GFFhelper.pm,v 1.22.14.1 2007-03-23 21:02:39 briano Exp $
=head1 NAME
Bio::Graphics::Browser::GFFhelper -- Helps gbrowse plugins handle GFF
=head1 SYNOPSIS
package Bio::Graphics::Browser::Plugin::MyPlugin;
use vars qw/@ISA $ROLLBACK/;
@ISA = qw/ Bio::Graphics::Browser::Plugin
Bio::Graphics::Browser::GFFhelper /;
$ROLLBACK = '/tmp/';
# other plugin subs skipped...
@@ -31,9 +31,9 @@ Bio::Graphics::Browser::GFFhelper -- Helps gbrowse plugins handle GFF
# don't save a persistent rb_id, look for a CGI param each time
my $rollback = $self->config_param('rb_id');
my $gff = $self->rollback($rollback);
# this is a rollback to an earlier version of an existing segment
# we don't need DNA, just the GFF
$gff;
@@ -49,12 +49,12 @@ Bio::Graphics::Browser::GFFhelper -- Helps gbrowse plugins handle GFF
# set sequence name in case the GFF does not have it
$self->refseq('L16622');
# process the GFF, convert it to GFF3, get the sequence
my ($newGFF, $dna) = $self->read_gff($gff);
return ($newGFF, $dna);
}
=head1 DESCRIPTION
This modules helps process GFF prior to loading into the database and provides
@@ -69,17 +69,20 @@ feature and attribute handling across different input/output formats.
=head2 Sequence Extraction
If DNA is appended to the GFF, it will be extracted. The read_gff method returns a
string containing processed GFF and also a sequence string
If DNA is appended to the GFF, it will be extracted. The read_gff
method returns a string containing processed GFF and also a sequence
string.
=head2 Rollbacks
The state of a segment can be captured and saved in case the user wishes to revert
to an earlier version of the segment after editing/deleting features. The last
10 modified segments are saved in a round-robin rotation. In plugins that inherit
methods from this module, the $ROLLBACK variable must be defined with a string
containing the path to a directory where the web user ('apache', 'nobody', etc.)
has write access. If $ROLLBACK is undefined, the rollback functionality is disabled.
The state of a segment can be captured and saved in case the user
wishes to revert to an earlier version of the segment after
editing/deleting features. The last 10 modified segments are saved
in a round-robin rotation. In plugins that inherit
methods from this module, the $ROLLBACK variable must be defined
with a string containing the path to a directory where the web
user ('apache', 'nobody', etc.) has write access. If $ROLLBACK
is undefined, the rollback functionality is disabled.
=head1 FEEDBACK
@@ -1,6 +1,5 @@
package Bio::Graphics::Browser::Plugin;
# $Id: Plugin.pm,v 1.12.4.6.2.2 2006-02-08 21:55:07 lstein Exp $
# base class for plugins for the Generic Genome Browser
# $Id: Plugin.pm,v 1.12.4.6.2.2.2.1 2007-03-23 21:02:39 briano Exp $
=head1 NAME
@@ -105,13 +104,13 @@ and allows the user to select among them. Example: BLAST search.
=item 3) annotators
These plugins receive the genomic segment object and either 1) return a list
of features which are overlayed on top of the detailed view (Example: restriction
site annotator) or 2) update the database with new or modified features
and return nothing (Example: basic editor)
These plugins receive the genomic segment object and either 1) return
a list of features which are overlayed on top of the detailed view
(Example: restriction site annotator) or 2) update the database with
new or modified features and return nothing (Example: basic editor)
=back
All plug-ins inherit from Bio::Graphics::Browser::Plugin, which
defines reasonable (but uninteresting) defaults for each of the
methods. Specific behavior is then implemented by selectively
@@ -431,7 +430,7 @@ and reconfigure() methods.
NOTE: If you need to use auxiliary files like BLAST files, you can
store the location of those files in the gbrowse .conf file under the
stanza [YourPlugin:plugin]:
[YourPlugin:plugin]
blast_path = /usr/local/blast/databases
@@ -1,6 +1,6 @@
package Bio::Graphics::Glyph::trace;
# $Id: trace.pm,v 1.1.2.9 2006-08-29 14:53:32 mwz444 Exp $
# $Id: trace.pm,v 1.1.2.9.2.1 2007-03-23 21:02:39 briano Exp $
use strict;
use GD;
@@ -827,7 +827,7 @@ The following additional options are available to the "image" glyph:
multiplied against the max
trace value to determine the
hight of peaks.
=head2 Specifying the Trace

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