also look in gene_archive to determine initial_stable_id()

modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm

@@ -115,22 +115,34 @@ sub initial_stable_id {
 
   # use stable ID from configuration if set
   if ($init_stable_id = $self->conf->param("starting_${type}_stable_id")) {
-    $self->logger->debug("Using pre-configured $init_stable_id as base for new $type stable IDs\n");
+    $self->logger->debug("Using pre-configured $init_stable_id as base for new $type stable IDs.\n");
     return $init_stable_id;
   }
 
   my $s_dba = $self->cache->get_DBAdaptor('source');
   my $s_dbh = $s_dba->dbc->db_handle;
+
+  # look in the ${type}_stable_id table first
   my $sql = qq(SELECT MAX(stable_id) FROM ${type}_stable_id);
   $init_stable_id = $self->fetch_value_from_db($s_dbh, $sql);
 
+  # also look in gene_archive to make sure there are no larger Ids there
+  unless ($type eq 'exon') {
+    $sql = qq(SELECT MAX(${type}_stable_id) FROM gene_archive);
+    my $archived_stable_id = $self->fetch_value_from_db($s_dbh, $sql);
+    if ($archived_stable_id and $self->is_valid($archived_stable_id) and
+        ($archived_stable_id gt $init_stable_id)) {
+      $init_stable_id = $archived_stable_id;
+    }
+  }
+
   if ($init_stable_id) {
     # since $init_stable_id now is the highest existing stable Id for this
     # object type, we need to increment it to find the first one we want to use
     # for new assignments
     $init_stable_id = $self->increment_stable_id($init_stable_id);
     
-    $self->logger->debug("Using $init_stable_id as base for new $type stable IDs\n");
+    $self->logger->debug("Using $init_stable_id as base for new $type stable IDs.\n");
 
   } else {
     $self->logger->warning("Can't find highest ${type}_stable_id in source db.\n");
@@ -160,10 +172,11 @@ sub increment_stable_id {
   my $self = shift;
   my $stable_id = shift;
 
-  unless ($stable_id and ($stable_id =~ /ENS([A-Z]{1,4})(\d{11})/)) {
+  unless ($self->is_valid($stable_id)) {
     throw("Unknown or missing stable ID: $stable_id.");
   }
-
+  
+  $stable_id =~ /ENS([A-Z]{1,4})(\d{11})/;
   my $number = $2;
   my $new_stable_id = 'ENS'.$1.(++$number);
 
@@ -171,6 +184,28 @@ sub increment_stable_id {
 }
 
 
+=head2 is_valid
+
+  Arg[1]      : String $stable_id - the stable Id to check
+  Example     : unless ($generator->is_valid($stable_id)) {
+                  die "Invalid stable Id: $stable_id.\n";
+                }
+  Description : Tests a stable Id to be valid (according to the Ensembl stable
+                Id format definition).
+  Return type : Boolean - TRUE if valid, FALSE otherwise
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub is_valid {
+  my ($self, $stable_id) = @_;
+  return ($stable_id and ($stable_id =~ /ENS([A-Z]{1,4})(\d{11})/));
+}
+
+
 =head2 calculate_version
 
   Arg[1]      : Bio::EnsEMBL::IdMapping::TinyFeature $s_obj - source object