is_ter_codon and is_start_codon do not behaves thesame. Now it does. …

…is_ter_codon was not verifying all unambiguous_codons, but only the first.

lib/Bio/Tools/CodonTable.pm

@@ -735,41 +735,18 @@ sub is_start_codon{
 =head2 is_ter_codon
 
  Title : is_ter_codon
- Usage : $obj->is_ter_codon('GAA')
+ Usage : $obj->is_ter_codon('TGA')
  Function: returns true (1) for all codons that can be used as a
  translation tarminator, false (0) for others.
- Example : $myCodonTable->is_ter_codon('ATG')
+ Example : $myCodonTable->is_ter_codon('TGA')
  Returns : boolean
  Args : codon
 
 =cut
 
 sub is_ter_codon{
  my ($self, $value) = @_;
- my $id = $self->{'id'};
-
- # We need to ensure U is mapped to T (ie. UAG)
- $value = uc $value;
- $value =~ tr/U/T/;
-
- if (length $value != 3 ) {
- # Incomplete codons are not stop codons
- return 0;
- } else {
- my $result = 0;
-
- # For all the possible codons, if any are not a stop
- # codon, fail immediately
- for my $c ( $self->unambiguous_codons($value) ) {
- my $m = substr( $TABLES[$id], $CODONS->{$c}, 1 );
- if($m eq $TERMINATOR) {
- $result = 1;
- } else {
- return 0;
- }
- }
- return $result;
- }
+ shift->_codon_is( shift, \@STARTS, '*' );
 }
 
 # desc: compares the passed value with a single entry in the given