Bio::Tools::CodonTable: handle negative table ids as invalid (#386)

Without this extra check, negative table IDs were being counted from the end of the tables array.
bioperl · Apr 26, 2024 · 9f6beda · 9f6beda
1 parent 62ee9df
commit 9f6beda
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Showing 2 changed files with 14 additions and 10 deletions.
diff --git a/lib/Bio/Tools/CodonTable.pm b/lib/Bio/Tools/CodonTable.pm
@@ -277,7 +277,7 @@ sub new {
 sub id{
     my ($self,$value) = @_;
     if( defined $value) {
-        if (  not defined $TABLES[$value] or $TABLES[$value] eq '') {
+        if (! defined $TABLES[$value] || $TABLES[$value] eq '' || $value < 0) {
             $self->warn("Not a valid codon table ID [$value], using [1] instead ");
             $value = 1;
         }

diff --git a/t/SeqTools/CodonTable.t b/t/SeqTools/CodonTable.t
@@ -6,7 +6,7 @@ use strict;
 BEGIN {
     use Bio::Root::Test;
 
-    test_begin(-tests => 87);
+    test_begin(-tests => 89);
 
     use_ok('Bio::Tools::CodonTable');
     use_ok('Bio::CodonUsage::IO');
@@ -27,16 +27,20 @@ $myCodonTable = Bio::Tools::CodonTable->new();
 is $myCodonTable->id(), 1;
 is $myCodonTable->name(), "Standard";
 
-# invalid table should produce a warn and set default table (1)
-my $stderr = '';
+
+# Test invalid IDs warn and return table id=1
 {
-    # capture stderr output
-    local *STDERR;
-    open STDERR, '>', \$stderr;
-    $myCodonTable->id(99);
+    foreach my $invalid_id (99, -2) {
+        my $stderr = '';
+        # capture stderr output
+        local *STDERR;
+        open STDERR, '>', \$stderr;
+        $myCodonTable = Bio::Tools::CodonTable->new(-id => $invalid_id);
+        like $stderr, qr/Not a valid codon table ID/;
+        is $myCodonTable->id, 1;
+    }
 }
-like $stderr, qr/Not a valid codon table ID/;
-is $myCodonTable->id, 1;
+
 
 # change codon table
 $myCodonTable->id(10);