In add_map_coordinates(): Correct spelling in documentation and remove

mentioning of return values as none are returned (and the rest of the
API is not expecting anything).  From Michael S.


Also, reformat method.

modules/Bio/EnsEMBL/Mapper.pm

@@ -528,54 +528,56 @@ sub fastmap {
     Arg  4      int $strand
                 relative orientation of source and target (+/- 1)
     Arg  5      int $id
-                id of 'targe' sequence
+                id of 'target' sequence
     Arg  6      int $start
-                start coordinate of 'targe' sequence
+                start coordinate of 'target' sequence
     Arg  7      int $end
-                end coordinate of 'targe' sequence
-    Function    stores details of mapping between two regions:
-                'source' and 'target'. Returns 1 if the pair was added, 0 if it
-                was already in.
-    Returntype  int 0,1
+                end coordinate of 'target' sequence
+    Function    Stores details of mapping between
+                'source' and 'target' regions.
+    Returntype  none
     Exceptions  none
     Caller      Bio::EnsEMBL::Mapper
 
 =cut
 
-sub add_map_coordinates{
-  my ($self, $contig_id, $contig_start, $contig_end, 
-      $contig_ori, $chr_name, $chr_start, $chr_end) = @_;
-
-  unless(defined($contig_id) && defined($contig_start) && defined($contig_end)
-	 && defined($contig_ori) && defined($chr_name) && defined($chr_start)
-	 && defined($chr_end)) {
+sub add_map_coordinates {
+  my ( $self, $contig_id, $contig_start, $contig_end, $contig_ori,
+       $chr_name, $chr_start, $chr_end )
+    = @_;
+
+  unless (    defined($contig_id)
+           && defined($contig_start)
+           && defined($contig_end)
+           && defined($contig_ori)
+           && defined($chr_name)
+           && defined($chr_start)
+           && defined($chr_end) )
+  {
     throw("7 arguments expected");
   }
 
-  if( ($contig_end - $contig_start)  != ($chr_end - $chr_start) ) {
+  if ( ( $contig_end - $contig_start ) != ( $chr_end - $chr_start ) ) {
     throw("Cannot deal with mis-lengthed mappings so far");
   }
 
+  my $from = Bio::EnsEMBL::Mapper::Unit->new( $contig_id, $contig_start,
+                                              $contig_end );
+  my $to =
+    Bio::EnsEMBL::Mapper::Unit->new( $chr_name, $chr_start, $chr_end );
 
-  my $from =
-    Bio::EnsEMBL::Mapper::Unit->new($contig_id, $contig_start, $contig_end);
-  my $to   =
-    Bio::EnsEMBL::Mapper::Unit->new($chr_name, $chr_start, $chr_end);
-
-  my $pair = Bio::EnsEMBL::Mapper::Pair->new($from, $to, $contig_ori);
+  my $pair = Bio::EnsEMBL::Mapper::Pair->new( $from, $to, $contig_ori );
 
   # place into hash on both ids
-  my $map_to = $self->{'to'};
+  my $map_to   = $self->{'to'};
   my $map_from = $self->{'from'};
 
-  push( @{$self->{"_pair_$map_to"}->{uc($chr_name)}}, $pair );
-  push( @{$self->{"_pair_$map_from"}->{uc($contig_id)}}, $pair );
+  push( @{ $self->{"_pair_$map_to"}->{ uc($chr_name) } },    $pair );
+  push( @{ $self->{"_pair_$map_from"}->{ uc($contig_id) } }, $pair );
 
   $self->{'pair_count'}++;
-
   $self->{'_is_sorted'} = 0;
-
-}
+} ## end sub add_map_coordinates
 
 
 =head2 add_indel_coordinates