is_chromosome uses karyotype rank attribute

modules/Bio/EnsEMBL/Slice.pm

@@ -798,10 +798,7 @@ sub assembly_exception_type {
 =head2 is_chromosome
 
   Example			: print ($slice->is_chromosome()) ? 'I am a chromosome' : 'Not one'; 
-  Description	: Uses a number of rules known to indicate a chromosome region 
-                other and takes into account those regions which can be 
-                placed on a Chromsome coordinate system but in fact are not
-                assembled into one.
+  Description	: A chromosome is a slice with a karyotype rank assigned to it.
   Returntype 	: Boolean indicates if the current object is a chromosome
   Exceptions 	: None
 
@@ -809,29 +806,8 @@ sub assembly_exception_type {
 
 sub is_chromosome {
   my ($self) = @_;
-  my $coord_system = $self->coord_system->name;
-  my $seq_name     = $self->seq_region_name;
-
-  if (($seq_name =~ /random
-                    |^Un\d{4}$
-                    |^Un\.\d{3}\.\d*$
-                    |E\d\d\w*$
-                    |_NT_
-                    |scaffold_
-                    |cutchr
-                    |unplaced 
-                    |chunk
-                    |clone
-                    |contig
-                    |genescaffold
-                    |reftig
-                    |supercontig
-                    |ultracontig        
-                    /x) or ( $coord_system !~ /^chromosome$/i && $coord_system !~ /^group$/i ) ) {
-    return 0;
-  }
-  
-  return 1;
+
+  return $self->has_karyotype();
 }
 
 

modules/t/slice.t

@@ -570,8 +570,8 @@ is($chr_one_slice->assembly_exception_type(), 'REF', 'Ensuring reference regions
 # Test slice attributes
 my $current_slice = $slice_adaptor->fetch_by_region('chromosome', $CHR, $START, $END);
 is($current_slice->is_chromosome, 1, "Slice is a chromosome");
-is($current_slice->has_karyotype, 0, "Slice has no karyotype attribute");
-is($current_slice->karyotype_rank, 0, "No karyotype rank could be found");
+is($current_slice->has_karyotype, 1, "Slice has a karyotype attribute");
+is($current_slice->karyotype_rank, 20, "Karyotype rank is 20 could be found");
 
 #
 # Test get_genome_component

modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt

@@ -16,3 +16,4 @@
 16	_selenocysteine	Selenocysteine	\N
 17	codon_table	Codon Table	Alternate codon table
 18	non_ref	Non Reference	Non Reference Sequence Region
+19	karyotype_rank	Rank in the karyotype	For a given seq_region, if it is part of the species karyotype, will indicate its rank

modules/t/test-genome-DBs/homo_sapiens/core/seq_region_attrib.txt

@@ -14,3 +14,4 @@
 965899	17	2
 965888	17	2
 469351	18	1
+469283	19	20