From 044f5660380de4409902bd98954f112aff9633e3 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Thu, 18 Sep 2014 15:05:34 +0100
Subject: [PATCH] Code tidy in AssemblyExceptionFeatureAdaptor
---
.../DBSQL/AssemblyExceptionFeatureAdaptor.pm | 134 +++++++-----------
1 file changed, 54 insertions(+), 80 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
index 550c4f40de..3006351e15 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
@@ -286,7 +286,6 @@ sub _remap {
$features->[0]->slice == $slice)) {
return $features;
}
-
# remapping has not been done, we have to do our own conversion from
# to slice coords
@@ -333,14 +332,6 @@ sub _remap {
# create new copies of successfully mapped feaatures with shifted start,
# end and strand
my ($new_start, $new_end);
- # if($slice_strand == -1) {
- # $new_start = $slice_end - $end + 1;
- # $new_end = $slice_end - $start + 1;
- # } else {
- # $new_start = $start - $slice_start + 1;
- # $new_end = $end - $slice_start + 1;
- # }
-
my $seq_region_len = $slice->seq_region_length();
if ($slice_strand == 1) { # Positive strand
@@ -349,92 +340,75 @@ sub _remap {
$new_end = $end - $slice_start + 1;
if ($slice->is_circular()) {
- # Handle circular chromosomes.
-
- if ($new_start > $new_end) {
- # Looking at a feature overlapping the chromsome origin.
-
- if ($new_end > $slice_start) {
-
- # Looking at the region in the beginning of the
- # chromosome.
- $new_start -= $seq_region_len;
- }
-
- if ($new_end < 0) {
- $new_end += $seq_region_len;
- }
-
- } else {
-
- if ( $slice_start > $slice_end
- && $new_end < 0) {
- # Looking at the region overlapping the chromosome
- # origin and a feature which is at the beginning of the
- # chromosome.
- $new_start += $seq_region_len;
- $new_end += $seq_region_len;
- }
- }
-
- } ## end if ($dest_slice->is_circular...)
-
- } else { # Negative strand
+ # Handle circular chromosomes.
+
+ if ($new_start > $new_end) {
+ # Looking at a feature overlapping the chromsome origin.
+ if ($new_end > $slice_start) {
+ # Looking at the region in the beginning of the chromosome.
+ $new_start -= $seq_region_len;
+ }
+ if ($new_end < 0) {
+ $new_end += $seq_region_len;
+ }
+ } else {
+ if ( $slice_start > $slice_end && $new_end < 0) {
+ # Looking at the region overlapping the chromosome
+ # origin and a feature which is at the beginning of the
+ # chromosome.
+ $new_start += $seq_region_len;
+ $new_end += $seq_region_len;
+ }
+ }
+ } ## end if ($dest_slice->is_circular...)
+ } else { # Negative strand
my $new_start = $slice_end - $end + 1;
my $new_end = $slice_end - $start + 1;
if ($slice->is_circular()) {
- if ($slice_start > $slice_end) {
- # slice spans origin or replication
-
- if ($start >= $slice_start) {
- $new_end += $seq_region_len;
- $new_start += $seq_region_len
- if $end > $slice_start;
+ if ($slice_start > $slice_end) {
+ # slice spans origin or replication
- } elsif ($start <= $slice_end) {
- # do nothing
- } elsif ($end >= $slice_start) {
- $new_start += $seq_region_len;
- $new_end += $seq_region_len;
+ if ($start >= $slice_start) {
+ $new_end += $seq_region_len;
+ $new_start += $seq_region_len if $end > $slice_start;
- } elsif ($end <= $slice_end) {
+ } elsif ($start <= $slice_end) {
+ # do nothing
+ } elsif ($end >= $slice_start) {
+ $new_start += $seq_region_len;
+ $new_end += $seq_region_len;
- $new_end += $seq_region_len
- if $new_end < 0;
+ } elsif ($end <= $slice_end) {
+ $new_end += $seq_region_len if $new_end < 0;
+ } elsif ($start > $end) {
+ $new_end += $seq_region_len;
+ } else {
- } elsif ($start > $end) {
-
- $new_end += $seq_region_len;
+ }
+
+ } else {
- } else {
-
- }
-
- } else {
+ if ($start <= $slice_end and $end >= $slice_start) {
+ # do nothing
+ } elsif ($start > $end) {
+ if ($start <= $slice_end) {
+
+ $new_start -= $seq_region_len;
- if ($start <= $slice_end and $end >= $slice_start) {
- # do nothing
- } elsif ($start > $end) {
- if ($start <= $slice_end) {
-
- $new_start -= $seq_region_len;
+ } elsif ($end >= $slice_start) {
+ $new_end += $seq_region_len;
+ } else {
- } elsif ($end >= $slice_start) {
- $new_end += $seq_region_len;
-
- } else {
-
- }
- }
- }
+ }
+ }
+ }
}
- } ## end else [ if ($dest_slice_strand...)]
-
+ } ## end else [ if ($dest_slice_strand...)]
push @out, Bio::EnsEMBL::AssemblyExceptionFeature->new(
'-dbID' => $f->dbID,
'-start' => $new_start,
@@ -445,7 +419,7 @@ sub _remap {
'-alternate_slice' => $f->alternate_slice,
'-type' => $f->type,
);
- }
+ } # end foreach assembly exception
return \@out;
}
--
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