From 4dd6b741adffa9b56f5a592f1b92f48f08bc5040 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 19 Dec 2007 15:03:24 +0000
Subject: [PATCH] Correct some of the examples in the SYNOPSIS, and make some
POD code lines shorter.
---
modules/Bio/EnsEMBL/Collection.pm | 20 +++++++++++++-------
1 file changed, 13 insertions(+), 7 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Collection.pm b/modules/Bio/EnsEMBL/Collection.pm
index d0936e960d..4d66b48c1f 100644
--- a/modules/Bio/EnsEMBL/Collection.pm
+++ b/modules/Bio/EnsEMBL/Collection.pm
@@ -43,16 +43,21 @@ classes.
my @entries = @{ $collection->entries() };
# Retrieve a binned representation of the entries using 100 bins.
- my @binned_entries = @{ $collection->get_bin_entries(100) };
+ my @binned_entries = @{
+ $collection->get_bins( -nbins => 100,
+ -method => 'entries'
+ ) };
# Retrieve a binned representation of the entries using 100 bins,
# where each entry is represented by its index in the feature
# collection array (@entries above).
- my @binned_entry_indicies =
- @{ $collection->get_bin_entry_indices(100) };
+ my @binned_entry_indicies = @{
+ $collection->get_bins( -nbins => 100,
+ -method => 'indices'
+ ) };
# Retrieve only the bin counts.
- my @bin_counts = @{ $collection->get_bin_counts(100) };
+ my @bin_counts = @{ $collection->get_bins( -nbins => 100 ) };
=head1 DESCRIPTION
@@ -225,8 +230,8 @@ use constant { ENTRY_DBID => 0,
Example : my $collection =
Bio::EnsEMBL::Collection::<feature_type>->new(
- -slice => $slice,
- -light => 1 );
+ -slice => $slice,
+ -light => 1 );
Description : When called for a sub-class, creates a feature
collection object and associates a slice with it.
@@ -434,7 +439,8 @@ sub is_populated {
If unset, will use the 'lightweight' boolean set
when calling new().
- Example : $collection->populate( -sorted => 1, -light => 0 );
+ Example : $collection->populate( -sorted => 1,
+ -light => 0 );
Description : Populates the collection with a compact
representation of the features overlapping the
--
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