From 7501f3cd5239a02311e4da8e472aa2b39698b124 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 Jan 2008 11:43:45 +0000
Subject: [PATCH] Add POD descriptions for the two coverage binning methods,
and code stubs. Move some code around.
---
modules/Bio/EnsEMBL/Collection.pm | 52 ++++++++++++++++++++++---------
1 file changed, 38 insertions(+), 14 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Collection.pm b/modules/Bio/EnsEMBL/Collection.pm
index 6b34a8e7c3..d6b57fd957 100644
--- a/modules/Bio/EnsEMBL/Collection.pm
+++ b/modules/Bio/EnsEMBL/Collection.pm
@@ -60,7 +60,7 @@ classes.
-method => 'indices'
) };
- # Retrieve only the bin counts.
+ # Retrieve only the bin counts/densities.
my @bin_counts = @{ $collection->get_bins( -nbins => 100 ) };
=head1 DESCRIPTION
@@ -186,6 +186,19 @@ Returns an array of bins, each bin containing an array of entries
method) allocated to that bin. The 'entry' binning method is equivalent
to 'entries'.
+=item 'coverage1'
+
+Returns an array of bins, each bin containing the sum of the fractions
+of features overlapping that bin. A feature fully inside a bin will
+contribute 1 to the sum while a feature spanning exactly three bins
+(from the very start of the first to the very end of the third) will
+contribute 1/3 to the sum of each bin.
+
+=item 'coverage2'
+
+Returns an array of bins, each bin containing the fraction of the bin
+that is coverage by any feature.
+
=back
=head1 CONTACT
@@ -232,6 +245,17 @@ our $SLICE;
our %SEGMENTS;
our %SEQ_REG_MAP;
+our %VALID_BINNING_METHODS = (
+ 'count' => 0,
+ 'density' => 0, # Same as 'count'.
+ 'indices' => 1,
+ 'index' => 1, # Same as 'indices'.
+ 'entries' => 2,
+ 'entry' => 2, # Same as 'entries'.
+ 'coverage1' => 3, # FIXME: find better name
+ 'coverage2' => 4 # FIXME: find better name
+);
+
=head1 METHODS (constructor)
=head2 new
@@ -651,14 +675,6 @@ sub flush {
=cut
-our %valid_binning_methods = ( 'count' => 0,
- 'density' => 0, # Same as 'count'.
- 'indices' => 1,
- 'index' => 1, # Same as 'indices'.
- 'entries' => 2,
- 'entry' => 2, # Same as 'entries'.
- 'coverage' => 3 );
-
sub get_bins {
my $this = shift;
my ( $nbins, $method_name ) = rearrange( [ 'NBINS', 'METHOD' ], @_ );
@@ -669,14 +685,14 @@ sub get_bins {
}
$method_name ||= 'count';
- if ( !exists( $valid_binning_methods{$method_name} ) ) {
+ if ( !exists( $VALID_BINNING_METHODS{$method_name} ) ) {
throw(
sprintf(
"Invalid binning method '%s', valid methods are: %s",
- $method_name, join( ', ', keys(%valid_binning_methods) )
+ $method_name, join( ', ', keys(%VALID_BINNING_METHODS) )
) );
}
- my $method = $valid_binning_methods{$method_name};
+ my $method = $VALID_BINNING_METHODS{$method_name};
my $slice = $this->slice();
my $slice_start = $slice->start();
@@ -734,9 +750,17 @@ sub get_bins {
} elsif ( $method == 3 ) {
- # For 'coverage'.
+ # For 'coverage1'.
+
+ throw("The 'coverage1' binning method is not yet implemented");
+
+ # FIXME
+
+ } elsif ( $method == 4 ) {
+
+ # For 'coverage2'.
- throw("The 'coverage' binning method is not yet implemented");
+ throw("The 'coverage2' binning method is not yet implemented");
# FIXME
--
GitLab