Properly formatted SYNOPSIS code, and removed syntax error.

Updated list of allowed linkage types with list from the Ensembl Core
schema.

Updated rest of package code to conform to relatively common Core API
coding practices.

modules/Bio/EnsEMBL/GoXref.pm

-
-#
-# EnsEMBL module for GoXref.pl
-#
-# Cared for by Arne Stabenau <stabenau@ebi.ac.uk>
-#
 # Copyright EnsEMBL 2000-2003
 #
 # You may distribute this module under the same terms as perl itself
@@ -16,38 +10,38 @@ Bio::EnsEMBL::GoXref
 
 =head1 DESCRIPTION
 
-This class extends the DBEntry in order to associate Evidence Tags to the 
-relationship between EnsEMBL objects and GO identifiers.  The relationship
-to GO that is stored in the database is actually derived through the 
-relationship of EnsEMBL peptides to SwissProt peptides.
+This class extends the DBEntry in order to associate Evidence Tags
+to the relationship between EnsEMBL objects and GO identifiers.  The
+relationship to GO that is stored in the database is actually derived
+through the relationship of EnsEMBL peptides to SwissProt peptides.
 
 I.e. The relationship is derived like this:
 
-ENSP  -> SWISSPROT -> GO
-                   
-An the evidence tag describes the relationship between the SWISSPROT Peptide 
-and the GO entry.
+ENSP -> SWISSPROT -> GO
+
+An the evidence tag describes the relationship between the SWISSPROT
+Peptide and the GO entry.
 
 In reality, however, we store this in the database like this:
 
 ENSP -> SWISSPROT
 ENSP -> GO
 
-and the evidence tag hangs off of the relationship between the ENSP and
-the GO identifier. Some ENSPs are associated with multiple closely related 
-Swissprot entries which may both be associated with the same GO identifier but
-with different evidence tags.  For this reason a single 'GoXref' can have 
-multiple evidence tags.
+and the evidence tag hangs off of the relationship between the ENSP
+and the GO identifier. Some ENSPs are associated with multiple closely
+related Swissprot entries which may both be associated with the same GO
+identifier but with different evidence tags.  For this reason a single
+'GoXref' can have multiple evidence tags.
 
 
 =head1 SYNOPSIS
 
-my $goxref = Bio::EnsEMBL::GoXref->new;
-$goxref->add_linkage_type('IEA')
+  my $goxref = Bio::EnsEMBL::GoXref->new;
+  $goxref->add_linkage_type('IEA');
 
-foreach my $evtag (@{$goxref->get_all_linkage_types()}) {
-  print "$evtag\n";
-}
+  foreach my $evtag ( @{ $goxref->get_all_linkage_types() } ) {
+    print "$evtag\n";
+  }
 
 =head1 CONTACT
 
@@ -61,15 +55,14 @@ package Bio::EnsEMBL::GoXref;
 use vars qw(@ISA);
 use strict;
 
-
 @ISA = qw( Bio::EnsEMBL::DBEntry );
 
-
 =head2 add_linkage_type
 
   Arg [1]    : string $value
-    allowed are "IC", "IDA", "IEA", "IEP", "IGI", "IMP", "IPI", "ISS",
-                "NAS", "NS", "TAS", "NR"
+               allowed values:
+               'IC', 'IDA', 'IEA', 'IEP', 'IGI', 'IMP', 'IPI',
+               'ISS', NAS', 'ND', 'TAS', 'NR', 'RCA'
   Arg [2]    : (optional) Bio::EnsEMBL::DBEntry $source
   Example    : $go_xref->add_linkage_type('IGI');
   Description: Associates a linkage type and source DBEntry with this go_xref
@@ -82,17 +75,20 @@ use strict;
 =cut
 
 sub add_linkage_type {
-  my $self = shift;
-  my $lt = shift;
-  my $source_dbentry = shift || undef();
-  
-  $self->throw("linkage type argument required") if(!$lt);
-  $self->throw("source_xref must be a Bio::EnsEMBL::DBEntry")
-      if($source_dbentry 
-	 and ! UNIVERSAL::isa($source_dbentry,'Bio::EnsEMBL::DBEntry'));
+  my ( $self, $lt, $source_dbentry ) = @_;
+
+  $self->throw("linkage type argument required") if ( !$lt );
+
+  if ( defined($source_dbentry)
+       && !$source_dbentry->isa('Bio::EnsEMBL::DBEntry') )
+  {
+    $self->throw("source_dbentry must be a Bio::EnsEMBL::DBEntry");
+  }
 
   $self->{'linkage_types'} ||= [];
-  push @{$self->{'linkage_types'}}, [$lt, ( $source_dbentry || () )];
+
+  push @{ $self->{'linkage_types'} },
+    [ $lt, ( $source_dbentry || () ) ];
 }
 
 
@@ -111,7 +107,7 @@ sub add_linkage_type {
 =cut
 
 sub get_all_linkage_info {
-  my $self = shift;
+  my ($self) = @_;
 
   return $self->{'linkage_types'} || [];
 }
@@ -120,7 +116,9 @@ sub get_all_linkage_info {
 =head2 get_all_linkage_types
 
   Arg [1]    : none
-  Example    : foreach my $et (@{$goxr->get_all_linkage_types}){ print "$et ";}
+  Example    : print( join( ' ',
+                            @{ $goxr->get_all_linkage_types() } ),
+                      "\n" );
   Description: Retrieves a unique list of evidence tags associated with 
                this go_xref
   Returntype : none
@@ -131,9 +129,12 @@ sub get_all_linkage_info {
 =cut
 
 sub get_all_linkage_types {
-  my $self = shift;
+  my ($self) = @_;
+
   my %seen;
-  return[ grep{!$seen{$_}++} map{$_->[0]} @{$self->{'linkage_types'}} ];
+  return [ grep  { !$seen{$_}++ }
+             map { $_->[0] } @{ $self->{'linkage_types'} } ];
+
   #return [ map{ $_->[0]} @{ $self->{'linkage_types'} || [] } ];
 }
 
@@ -151,8 +152,8 @@ sub get_all_linkage_types {
 =cut
 
 sub flush_linkage_types {
-  my $self = shift;
-  
+  my ($self) = @_;
+
   $self->{'linkage_types'} = [];
 }