From 85b9cea078a9838ac1a8cc0f1e5ff770c2a292e4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 27 Aug 2010 10:38:25 +0000
Subject: [PATCH] In map_coordinates(): Fix documentation and argument
checking error message. From Michael S.
Also, reformat method.
---
modules/Bio/EnsEMBL/Mapper.pm | 347 +++++++++++++++++-----------------
1 file changed, 170 insertions(+), 177 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index 2b07b5b4bd..a60dc33cc8 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -138,7 +138,7 @@ sub flush {
end coordinate of 'source' sequence
Arg 4 int $strand
raw contig orientation (+/- 1)
- Arg 5 int $type
+ Arg 5 string $type
nature of transform - gives the type of
coordinates to be transformed *from*
Function generic map method
@@ -149,209 +149,202 @@ sub flush {
=cut
-sub map_coordinates{
- my ($self, $id, $start, $end, $strand, $type) = @_;
-
- unless(defined($id) && defined($start) && defined($end) &&
- defined($strand) && defined($type) ) {
- throw("Must start,end,strand,id,type as coordinates");
- }
-
-
-
-
-
- # special case for handling inserts:
- if($start == $end + 1) {
- return $self->map_insert($id, $start, $end, $strand, $type);
- }
-
- if( ! $self->{'_is_sorted'} ) { $self->_sort() }
-
- my $hash = $self->{"_pair_$type"};
+sub map_coordinates {
+ my ( $self, $id, $start, $end, $strand, $type ) = @_;
- my ($from, $to, $cs);
+ unless ( defined($id)
+ && defined($start)
+ && defined($end)
+ && defined($strand)
+ && defined($type) )
+ {
+ throw("Expecting 5 arguments");
+ }
- if($type eq $self->{'to'}) {
- $from = 'to';
- $to = 'from';
- $cs = $self->{'from_cs'};
- } else {
- $from = 'from';
- $to = 'to';
- $cs = $self->{'to_cs'};
- }
+ # special case for handling inserts:
+ if ( $start == $end + 1 ) {
+ return $self->map_insert( $id, $start, $end, $strand, $type );
+ }
- unless(defined $hash) {
- throw("Type $type is neither to or from coordinate systems");
- }
+ if ( !$self->{'_is_sorted'} ) { $self->_sort() }
- if( !defined $hash->{uc($id)} ) {
- # one big gap!
- my $gap = Bio::EnsEMBL::Mapper::Gap->new($start, $end);
- return $gap;
- }
+ my $hash = $self->{"_pair_$type"};
- my $last_used_pair;
- my @result;
+ my ( $from, $to, $cs );
- my ( $start_idx, $end_idx, $mid_idx, $pair, $self_coord );
- my $lr = $hash->{uc($id)};
-
- $start_idx = 0;
- $end_idx = $#$lr;
-
- # binary search the relevant pairs
- # helps if the list is big
- while(( $end_idx - $start_idx ) > 1 ) {
- $mid_idx = ($start_idx+$end_idx)>>1;
- $pair = $lr->[$mid_idx];
- $self_coord = $pair->{$from};
- if( $self_coord->{'end'} < $start ) {
- $start_idx = $mid_idx;
- } else {
- $end_idx = $mid_idx;
- }
- }
+ if ( $type eq $self->{'to'} ) {
+ $from = 'to';
+ $to = 'from';
+ $cs = $self->{'from_cs'};
+ } else {
+ $from = 'from';
+ $to = 'to';
+ $cs = $self->{'to_cs'};
+ }
-
- my $rank = 0;
- my $orig_start = $start;
- my $last_target_coord = undef;
- for( my $i = $start_idx; $i<=$#$lr; $i++ ) {
- $pair = $lr->[$i];
- my $self_coord = $pair->{$from};
- my $target_coord = $pair->{$to};
+ unless ( defined $hash ) {
+ throw("Type $type is neither to or from coordinate systems");
+ }
+ if ( !defined $hash->{ uc($id) } ) {
+ # one big gap!
+ my $gap = Bio::EnsEMBL::Mapper::Gap->new( $start, $end );
+ return $gap;
+ }
+ my $last_used_pair;
+ my @result;
-#
-# But not the case for haplotypes!! need to test for this case???
-# so removing this till a better solution is found
-#
-#
-# if($self_coord->{'start'} < $start){
-# $start = $orig_start;
-# $rank++;
-# }
+ my ( $start_idx, $end_idx, $mid_idx, $pair, $self_coord );
+ my $lr = $hash->{ uc($id) };
+ $start_idx = 0;
+ $end_idx = $#$lr;
- if(defined($last_target_coord) and $target_coord->{'id'} ne $last_target_coord){
- if($self_coord->{'start'} < $start){ # i.e. the same bit is being mapped to another assembled bit
- $start = $orig_start;
- }
- }
- else{
- $last_target_coord = $target_coord->{'id'};
- }
+ # binary search the relevant pairs
+ # helps if the list is big
+ while ( ( $end_idx - $start_idx ) > 1 ) {
+ $mid_idx = ( $start_idx + $end_idx ) >> 1;
+ $pair = $lr->[$mid_idx];
+ $self_coord = $pair->{$from};
+ if ( $self_coord->{'end'} < $start ) {
+ $start_idx = $mid_idx;
+ } else {
+ $end_idx = $mid_idx;
+ }
+ }
+ my $rank = 0;
+ my $orig_start = $start;
+ my $last_target_coord = undef;
+ for ( my $i = $start_idx; $i <= $#$lr; $i++ ) {
+ $pair = $lr->[$i];
+ my $self_coord = $pair->{$from};
+ my $target_coord = $pair->{$to};
+
+ #
+ # But not the case for haplotypes!! need to test for this case???
+ # so removing this till a better solution is found
+ #
+ #
+ # if($self_coord->{'start'} < $start){
+ # $start = $orig_start;
+ # $rank++;
+ # }
+
+ if ( defined($last_target_coord)
+ and $target_coord->{'id'} ne $last_target_coord )
+ {
+ if ( $self_coord->{'start'} < $start )
+ { # i.e. the same bit is being mapped to another assembled bit
+ $start = $orig_start;
+ }
+ } else {
+ $last_target_coord = $target_coord->{'id'};
+ }
+ # if we haven't even reached the start, move on
+ if ( $self_coord->{'end'} < $orig_start ) {
+ next;
+ }
+ # if we have over run, break
+ if ( $self_coord->{'start'} > $end ) {
+ last;
+ }
+ if ( $start < $self_coord->{'start'} ) {
+ # gap detected
+ my $gap = Bio::EnsEMBL::Mapper::Gap->new( $start,
+ $self_coord->{'start'} - 1, $rank );
+ push( @result, $gap );
+ $start = $gap->{'end'} + 1;
+ }
+ my ( $target_start, $target_end, $target_ori );
+ my $res;
+ if ( exists $pair->{'indel'} ) {
+ # When next pair is an IndelPair and not a Coordinate, create the
+ # new mapping Coordinate, the IndelCoordinate.
+ $target_start = $target_coord->{'start'};
+ $target_end = $target_coord->{'end'};
+
+ #create a Gap object
+ my $gap = Bio::EnsEMBL::Mapper::Gap->new( $start,
+ ( $self_coord->{'end'} < $end ? $self_coord->{'end'} : $end ) );
+ #create the Coordinate object
+ my $coord =
+ Bio::EnsEMBL::Mapper::Coordinate->new( $target_coord->{'id'},
+ $target_start, $target_end, $pair->{'ori'}*$strand, $cs );
+ #and finally, the IndelCoordinate object with
+ $res = Bio::EnsEMBL::Mapper::IndelCoordinate->new( $gap, $coord );
+ } else {
+ # start is somewhere inside the region
+ if ( $pair->{'ori'} == 1 ) {
+ $target_start =
+ $target_coord->{'start'} +
+ ( $start - $self_coord->{'start'} );
+ } else {
+ $target_end =
+ $target_coord->{'end'} - ( $start - $self_coord->{'start'} );
+ }
- # if we haven't even reached the start, move on
- if( $self_coord->{'end'} < $orig_start ) {
- next;
- }
-
- # if we have over run, break
- if( $self_coord->{'start'} > $end ) {
- last;
- }
-
- if( $start < $self_coord->{'start'} ) {
- # gap detected
- my $gap = Bio::EnsEMBL::Mapper::Gap->new($start,
- $self_coord->{'start'}-1, $rank);
+ # Either we are enveloping this map or not. If yes, then end
+ # point (self perspective) is determined solely by target. If
+ # not we need to adjust.
+
+ if ( $end > $self_coord->{'end'} ) {
+ # enveloped
+ if ( $pair->{'ori'} == 1 ) {
+ $target_end = $target_coord->{'end'};
+ } else {
+ $target_start = $target_coord->{'start'};
+ }
+ } else {
+ # need to adjust end
+ if ( $pair->{'ori'} == 1 ) {
+ $target_end =
+ $target_coord->{'start'} +
+ ( $end - $self_coord->{'start'} );
+ } else {
+ $target_start =
+ $target_coord->{'end'} - ( $end - $self_coord->{'start'} );
+ }
+ }
- push(@result,$gap);
- $start = $gap->{'end'}+1;
- }
- my ($target_start,$target_end,$target_ori);
- my $res;
- if (exists $pair->{'indel'}){
- #when next pair is an IndelPair and not a Coordinate, create the new mapping Coordinate, the IndelCoordinate
- $target_start = $target_coord->{'start'};
- $target_end = $target_coord->{'end'};
-
- #create a Gap object
- my $gap = Bio::EnsEMBL::Mapper::Gap->new($start, ($self_coord->{'end'} < $end ? $self_coord->{'end'} : $end));
- #create the Coordinate object
- my $coord = Bio::EnsEMBL::Mapper::Coordinate->new($target_coord->{'id'},
- $target_start,
- $target_end,
- $pair->{'ori'} * $strand,
- $cs);
- #and finally, the IndelCoordinate object with
- $res = Bio::EnsEMBL::Mapper::IndelCoordinate->new($gap,$coord);
- }
- else{
- # start is somewhere inside the region
- if( $pair->{'ori'} == 1 ) {
- $target_start =
- $target_coord->{'start'} + ($start - $self_coord->{'start'});
- } else {
- $target_end =
- $target_coord->{'end'} - ($start - $self_coord->{'start'});
- }
-
- # either we are enveloping this map or not. If yes, then end
- # point (self perspective) is determined solely by target. If not
- # we need to adjust
-
- if( $end > $self_coord->{'end'} ) {
- # enveloped
- if( $pair->{'ori'} == 1 ) {
- $target_end = $target_coord->{'end'};
- } else {
- $target_start = $target_coord->{'start'};
- }
- } else {
- # need to adjust end
- if( $pair->{'ori'} == 1 ) {
- $target_end =
- $target_coord->{'start'} + ($end - $self_coord->{'start'});
- } else {
- $target_start =
- $target_coord->{'end'} - ($end - $self_coord->{'start'});
- }
- }
-
- $res = Bio::EnsEMBL::Mapper::Coordinate->new($target_coord->{'id'},
- $target_start,
- $target_end,
- $pair->{'ori'} * $strand,
- $cs, $rank);
+ $res =
+ Bio::EnsEMBL::Mapper::Coordinate->new( $target_coord->{'id'},
+ $target_start, $target_end, $pair->{'ori'}*$strand,
+ $cs, $rank );
- }
+ } ## end else [ if ( exists $pair->{'indel'...})]
- push(@result,$res);
-
- $last_used_pair = $pair;
- $start = $self_coord->{'end'}+1;
+ push( @result, $res );
- }
+ $last_used_pair = $pair;
+ $start = $self_coord->{'end'} + 1;
- if( !defined $last_used_pair ) {
- my $gap = Bio::EnsEMBL::Mapper::Gap->new($start, $end);
- push(@result,$gap);
+ } ## end for ( my $i = $start_idx...)
- } elsif( $last_used_pair->{$from}->{'end'} < $end ) {
- # gap at the end
- my $gap = Bio::EnsEMBL::Mapper::Gap->new(
- $last_used_pair->{$from}->{'end'} + 1,
- $end, $rank);
- push(@result,$gap);
- }
+ if ( !defined $last_used_pair ) {
+ my $gap = Bio::EnsEMBL::Mapper::Gap->new( $start, $end );
+ push( @result, $gap );
- if ( $strand == -1 ) {
- @result = reverse ( @result);
- }
+ } elsif ( $last_used_pair->{$from}->{'end'} < $end ) {
+ # gap at the end
+ my $gap =
+ Bio::EnsEMBL::Mapper::Gap->new(
+ $last_used_pair->{$from}->{'end'} + 1,
+ $end, $rank );
+ push( @result, $gap );
+ }
+ if ( $strand == -1 ) {
+ @result = reverse(@result);
+ }
- return @result;
-}
+ return @result;
+} ## end sub map_coordinates
--
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