From 75f18f091bd0cc54bc1c8114e5913d6afb22fdfb Mon Sep 17 00:00:00 2001
From: Web Admin <w3adm@sanger.ac.uk>
Date: Wed, 9 Mar 2005 10:15:13 +0000
Subject: [PATCH] Merge from branch-ensembl-29 to head
---
modules/Bio/EnsEMBL/Slice.pm | 61 ++++++++++++++++++++++++++++++------
1 file changed, 52 insertions(+), 9 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 14502f0694..84aa6a8f88 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -790,10 +790,31 @@ sub _constrain_to_region {
coordinate by. Positive values make the slice larger,
negative make the slice smaller.
Default = 0.
+ Arg [3] : (optional) bool $force_expand
+ if set to 1, then the slice will be contracted even in the case
+ when shifts $five_prime_expand and $three_prime_expand overlap.
+ In that case $five_prime_expand and $three_prime_expand will be set
+ to a maximum possible number and that will result in the slice
+ which would have only 2pbs.
+ Default = 0.
+ Arg [4] : (optional) int* $fpref
+ The reference to a number of basepairs to shift this slices five_prime
+ coordinate by. Normally it would be set to $five_prime_expand.
+ But in case when $five_prime_expand shift can not be applied and
+ $force_expand is set to 1, then $$fpref will contain the maximum possible
+ shift
+ Arg [5] : (optional) int* $tpref
+ The reference to a number of basepairs to shift this slices three_prime
+ coordinate by. Normally it would be set to $three_prime_expand.
+ But in case when $five_prime_expand shift can not be applied and
+ $force_expand is set to 1, then $$tpref will contain the maximum possible
+ shift
Example : my $expanded_slice = $slice->expand( 1000, 1000);
my $contracted_slice = $slice->expand(-1000,-1000);
my $shifted_right_slice = $slice->expand(-1000, 1000);
my $shifted_left_slice = $slice->expand( 1000,-1000);
+ my $forced_contracted_slice = $slice->expand(-1000,-1000, 1, \$five_prime_shift, \$three_prime_shift);
+
Description: Returns a slice which is a resized copy of this slice. The
start and end are moved outwards from the center of the slice
if positive values are provided and moved inwards if negative
@@ -810,7 +831,10 @@ sub expand {
my $self = shift;
my $five_prime_shift = shift || 0;
my $three_prime_shift = shift || 0;
-
+ my $force_expand = shift || 0;
+ my $fpref = shift;
+ my $tpref = shift;
+
if($self->{'seq'}){
warning("Cannot expand a slice which has a manually attached sequence ");
return undef;
@@ -818,19 +842,38 @@ sub expand {
my $new_start;
my $new_end;
+ my $sshift = $five_prime_shift;
+ my $eshift = $three_prime_shift;
- if($self->{'strand'} == 1) {
- $new_start = $self->{'start'} - $five_prime_shift;
- $new_end = $self->{'end'} + $three_prime_shift;
- } else {
- $new_end = $self->{'end'} + $five_prime_shift;
- $new_start = $self->{'start'} - $three_prime_shift;
+ if($self->{'strand'} != 1) {
+ $eshift = $five_prime_shift;
+ $sshift = $three_prime_shift;
}
+ $new_start = $self->{'start'} - $sshift;
+ $new_end = $self->{'end'} + $eshift;
+
if($new_start > $new_end) {
- throw('Slice start cannot be greater than slice end');
+ if ($force_expand) { # Apply max possible shift, if force_expand is set
+ if ($sshift < 0) { # if we are contracting the slice from the start - move the start just before the end
+ $new_start = $new_end - 1;
+ $sshift = $self->{start} - $new_start;
+ }
+
+ if($new_start > $new_end) { # if the slice still has a negative length - try to move the end
+ if ($eshift < 0) {
+ $new_end = $new_start + 1;
+ $eshift = $new_end - $self->{end};
+ }
+ }
+ # return the values by which the primes were actually shifted
+ $$tpref = $self->{strand} == 1 ? $eshift : $sshift;
+ $$fpref = $self->{strand} == 1 ? $sshift : $eshift;
+ }
+ if($new_start > $new_end) {
+ throw('Slice start cannot be greater than slice end');
+ }
}
-
#fastest way to copy a slice is to do a shallow hash copy
my %new_slice = %$self;
$new_slice{'start'} = int($new_start);
--
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