From dd7704036fce6e3bf52b728025ecb646b1b63524 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 7 May 2008 12:54:33 +0000
Subject: [PATCH] Reformatting, rearranging.
---
modules/Bio/EnsEMBL/Collection.pm | 104 ++++++++++++++++--------------
1 file changed, 54 insertions(+), 50 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Collection.pm b/modules/Bio/EnsEMBL/Collection.pm
index 09a3dd50fb..aa6c988209 100644
--- a/modules/Bio/EnsEMBL/Collection.pm
+++ b/modules/Bio/EnsEMBL/Collection.pm
@@ -143,17 +143,29 @@ use constant { FEATURE_DBID => 0,
FEATURE_END => 3,
FEATURE_STRAND => 4 };
+our %VALID_BINNING_METHODS = (
+ 'count' => 0,
+ 'density' => 0, # Same as 'count'.
+ # 'indices' => 1,
+ # 'index' => 1, # Same as 'indices'.
+ # 'features' => 2,
+ # 'feature' => 2, # Same as 'features'.
+ 'fractional_count' => 3,
+ 'weight' => 3, # Same as 'fractional_count'.
+ 'coverage' => 4 );
+
# ======================================================================
# The public interface added by Feature Collection
sub fetch_bins_by_Slice {
- my $this = shift;
+ my ( $this, @args ) = @_;
+
my ( $slice, $method, $nbins, $logic_name, $lightweight ) =
rearrange( [ 'SLICE', 'METHOD',
'NBINS', 'LOGIC_NAME',
'LIGHTWEIGHT'
],
- @_ );
+ @args );
# Temporarily set the colleciton to be lightweight.
my $old_value = $this->_lightweight();
@@ -173,7 +185,7 @@ sub fetch_bins_by_Slice {
$this->_lightweight($old_value);
return $bins;
-}
+} ## end sub fetch_bins_by_Slice
# ======================================================================
# Specialization of methods in Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
@@ -199,6 +211,7 @@ sub _create_feature {
my ( $dbid, $start, $end, $strand, $slice ) =
rearrange( [ 'DBID', 'START', 'END', 'STRAND', 'SLICE' ],
%{$args} );
+
my $feature =
[ $dbid, $slice->get_seq_region_id(), $start, $end, $strand ];
@@ -238,21 +251,11 @@ sub _lightweight {
return $this->{'lightweight'} || 0;
}
-our %VALID_BINNING_METHODS = (
- 'count' => 0,
- 'density' => 0, # Same as 'count'.
- # 'indices' => 1,
- # 'index' => 1, # Same as 'indices'.
- # 'features' => 2,
- # 'feature' => 2, # Same as 'features'.
- 'fractional_count' => 3,
- 'weight' => 3, # Same as 'fractional_count'.
- 'coverage' => 4 );
-
sub _bin_features {
- my $this = shift;
+ my ( $this, @args ) = @_;
+
my ( $slice, $nbins, $method_name, $features ) =
- rearrange( [ 'SLICE', 'NBINS', 'METHOD', 'FEATURES' ], @_ );
+ rearrange( [ 'SLICE', 'NBINS', 'METHOD', 'FEATURES' ], @args );
if ( !defined($features) || !@{$features} ) { return [] }
@@ -308,36 +311,37 @@ sub _bin_features {
# ----------------------------------------------------------------
# For 'count' and 'density'.
- for ( my $bin_index = $start_bin ;
- $bin_index <= $end_bin ;
+ for ( my $bin_index = $start_bin;
+ $bin_index <= $end_bin;
++$bin_index )
{
++$bins[$bin_index];
}
- } elsif ( $method == 1 ) {
- # ----------------------------------------------------------------
- # For 'indices' and 'index'
-
- for ( my $bin_index = $start_bin ;
- $bin_index <= $end_bin ;
- ++$bin_index )
- {
- push( @{ $bins[$bin_index] }, $feature_index );
- }
-
- ++$feature_index;
-
- } elsif ( $method == 2 ) {
- # ----------------------------------------------------------------
- # For 'features' and 'feature'.
-
- for ( my $bin_index = $start_bin ;
- $bin_index <= $end_bin ;
- ++$bin_index )
- {
- push( @{ $bins[$bin_index] }, $feature );
- }
+ # } elsif ( $method == 1 ) {
+ # # ----------------------------------------------------------------
+ # # For 'indices' and 'index'
+ #
+ # for ( my $bin_index = $start_bin ;
+ # $bin_index <= $end_bin ;
+ # ++$bin_index )
+ # {
+ # push( @{ $bins[$bin_index] }, $feature_index );
+ # }
+ #
+ # ++$feature_index;
+ #
+ # } elsif ( $method == 2 ) {
+ # # ----------------------------------------------------------------
+ # # For 'features' and 'feature'.
+ #
+ # for ( my $bin_index = $start_bin ;
+ # $bin_index <= $end_bin ;
+ # ++$bin_index )
+ # {
+ # push( @{ $bins[$bin_index] }, $feature );
+ # }
+ #
} elsif ( $method == 3 ) {
# ----------------------------------------------------------------
@@ -357,8 +361,8 @@ sub _bin_features {
$feature_length;
# The intermediate bins (if there are any)...
- for ( my $bin_index = $start_bin + 1 ;
- $bin_index <= $end_bin - 1 ;
+ for ( my $bin_index = $start_bin + 1;
+ $bin_index <= $end_bin - 1;
++$bin_index )
{
$bins[$bin_index] += $bin_length/$feature_length;
@@ -388,16 +392,16 @@ sub _bin_features {
# first).
my $bin_start = int( $start_bin*$bin_length );
my $bin_end = int( ( $start_bin + 1 )*$bin_length - 1 );
- for ( my $pos = $feature_start ;
- $pos <= $bin_end && $pos <= $feature_end ;
+ for ( my $pos = $feature_start;
+ $pos <= $bin_end && $pos <= $feature_end;
++$pos )
{
$bin_masks[$start_bin][ $pos - $bin_start ] = 1;
}
}
- for ( my $bin_index = $start_bin + 1 ;
- $bin_index <= $end_bin - 1 ;
+ for ( my $bin_index = $start_bin + 1;
+ $bin_index <= $end_bin - 1;
++$bin_index )
{
# Mark the middle bins between $start_bin and $end_bin as fully
@@ -416,8 +420,8 @@ sub _bin_features {
# first).
my $bin_start = int( $end_bin*$bin_length );
my $bin_end = int( ( $end_bin + 1 )*$bin_length - 1 );
- for ( my $pos = $bin_start ;
- $pos <= $feature_end && $pos <= $bin_end ;
+ for ( my $pos = $bin_start;
+ $pos <= $feature_end && $pos <= $bin_end;
++$pos )
{
$bin_masks[$end_bin][ $pos - $bin_start ] = 1;
@@ -436,7 +440,7 @@ sub _bin_features {
# For the 'coverage' method: Finish up by going through @bin_masks
# and sum up the arrays.
- for ( my $bin_index = 0 ; $bin_index < $nbins ; ++$bin_index ) {
+ for ( my $bin_index = 0; $bin_index < $nbins; ++$bin_index ) {
if ( defined( $bin_masks[$bin_index] ) ) {
if ( !ref( $bin_masks[$bin_index] ) ) {
$bins[$bin_index] = 1;
--
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