From 76a646f8a38bab25919006b252b64173847f9550 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Mon, 12 Nov 2012 16:43:44 +0000
Subject: [PATCH] POD cleanup
---
modules/Bio/EnsEMBL/Feature.pm | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm
index f83de136e2..ebc712c200 100644
--- a/modules/Bio/EnsEMBL/Feature.pm
+++ b/modules/Bio/EnsEMBL/Feature.pm
@@ -28,7 +28,8 @@ Bio::EnsEMBL::Feature - Ensembl specific sequence feature.
-start => 100,
-end => 220,
-strand => -1,
- -slice => $slice -analysis => $analysis
+ -slice => $slice,
+ -analysis => $analysis
);
my $start = $feat->start();
@@ -273,7 +274,6 @@ sub strand {
Arg [1] : int start
Arg [2] : int end
Arg [3] : (optional) int strand
- Example : None
Description: Sets the start, end and strand in one call rather than in
3 seperate calls to the start(), end() and strand() methods.
This is for convenience and for speed when this needs to be
@@ -1412,7 +1412,7 @@ sub get_overlapping_Genes{
=head2 get_nearest_Gene
- Description: Get all the nearest gene to the feature
+ Description: Get the nearest gene to the feature
Returntype : Bio::EnsEMBL::Gene
Caller : general
Status : UnStable
@@ -1434,7 +1434,7 @@ sub get_nearest_Gene {
Example : $feature_summary = $feature->summary_as_hash();
Description : Retrieves a textual summary of this Feature.
- Should be overidden by subclasses for specific tweaking
+ Should be overidden by subclasses for specific tweaking
Returns : hashref of arrays of descriptive strings
Status : Intended for internal use
=cut
@@ -1474,7 +1474,7 @@ sub species {
=head2 contig
- This method is deprecated and included for backwards compatibility only.
+ Deprecated - Included for backwards compatibility only.
Use slice() instead
=cut
sub contig {
@@ -1486,7 +1486,7 @@ sub contig {
=head2 sub_SeqFeature
- This method is deprecated and only for genebuild backwards compatibility.
+ Deprecated - For genebuild backwards compatibility.
Avoid using it if possible
=cut
sub sub_SeqFeature{
@@ -1496,7 +1496,7 @@ sub sub_SeqFeature{
=head2 add_sub_SeqFeature
- This method is deprecated and only for genebuild backwards compatibility.
+ Deprecated - only for genebuild backward compatibility.
Avoid using it if possible
=cut
sub add_sub_SeqFeature{
@@ -1530,8 +1530,8 @@ sub add_sub_SeqFeature{
=head2 flush_sub_SeqFeature
- This method is deprecated and only for genebuild backwards compatibility.
- Avoid using it isf possible
+ Deprecated - Only for genebuild backwards compatibility.
+ Avoid using it if possible
=cut
sub flush_sub_SeqFeature {
my ($self) = @_;
@@ -1572,7 +1572,7 @@ sub _deprecated_transform {
=head2 id
-This method is deprecated and only included for backwards compatibility.
+Deprecated - only included for backwards compatibility.
Use display_id, hseqname, dbID or stable_id instead
=cut
--
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