From 019cdc780d01acddde69982b1526c1f81b807d48 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 8 Apr 2008 14:14:15 +0000
Subject: [PATCH] Add NAME and SYNOPSIS section.
---
modules/Bio/EnsEMBL/Collection.pm | 44 +++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Collection.pm b/modules/Bio/EnsEMBL/Collection.pm
index c5f590b088..425ba7923a 100644
--- a/modules/Bio/EnsEMBL/Collection.pm
+++ b/modules/Bio/EnsEMBL/Collection.pm
@@ -1,7 +1,51 @@
# $Id$
+# Ensembl module Bio::EnsEMBL::Collection
+#
+# You may distribute this module under the same terms as Perl itself.
+#
+
package Bio::EnsEMBL::Collection;
+=head1 NAME
+
+Bio::EnsEMBL::Collection - Abstract base class for feature collection
+classes.
+
+=head1 SYNOPSIS
+
+ # Create an exon collection adaptor.
+ my $collection =
+ $registry->get_adaptor( 'Human', 'Core', 'ExonCollection' );
+
+ # Create a slice.
+ my $slice =
+ $slice_adaptor->fetch_by_region( 'Chromosome', '2', 1, 300_000 );
+
+ # Fetch the exons, represented as simple arrays of attributes, on
+ # the slice.
+ my @exons = @{ $collection->fetch_all_by_Slice($slice) };
+
+
+ # Fetch the exons on the slice and count them into 50 bins (each
+ # bin contains the number of exons overlapping that bin).
+ my @bins = @{
+ $collection->fetch_bins_by_Slice( -slice => $slice,
+ -nbins => 50,
+ -method => 'density'
+ ) };
+
+ # Fetch the exons on the slice and calculate the coverage of 50
+ # bins (each bin contains the coverage of that bin by any exon as
+ # a number between 0 and 1).
+ my @bins = @{
+ $collection->fetch_bins_by_Slice( -slice => $slice,
+ -nbins => 50,
+ -method => 'coverage'
+ ) };
+
+=cut
+
use strict;
use warnings;
--
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