Add subclass of StableIdGenerator::EnsemblGeneric to do Anopheles gambiae...

Add subclass of StableIdGenerator::EnsemblGeneric to do Anopheles gambiae stable ID incrementation and verification.

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

+package Bio::EnsEMBL::IdMapping::StableIdGenerator::AnophelesGambiae;
+
+# Package that implements incrementing and verification of Anopheles gambiae
+# stable IDs as used by the VectorBase project.
+# Based on Aedes_Aegypti.pm
+# Differs from Aedes in that Exon stable ids like Ennnnnn not AAEL.ennnnnn
+# and gene/transcript/translation start AGAP not AAEL
+# also needs to explicitly exclude old-style ids, as base will look at gene_archve and will consider ENSANGG to be a higher id than any AGAP, so will use that as starting pint fornew ids
+
+use strict;
+use warnings;
+
+use base qw(Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric);
+
+sub increment_stable_id {
+
+  # This method will increment a stable ID.  For Anopheles, it will
+  # pick out the numerical part of the stable ID (no matter what type of
+  # stable ID it is) and increment it by one.  It will then replace the
+  # numerical part by the incremented value and return the new stable
+  # ID.  The parsing of the stable ID is very naive.
+
+  my ( $self, $stable_id ) = @_;
+
+  if ( !$self->is_valid($stable_id) ) {
+    throw("Unknown or missing stable ID: $stable_id.");
+  }
+
+  $stable_id =~ /^(\D*)(\d+)(\D*)/;
+
+  my $number_as_string = "$2";
+  my $number           = $2 + 1;
+  $stable_id = sprintf( "%s"
+                          . sprintf( "%%0%dd", length($number_as_string)
+                          )
+                          . "%s",
+                        $1, $number, $3 );
+
+  return $stable_id;
+}
+
+sub is_valid {
+
+  # A stable ID is a valid Anopheles stable ID if it begins with the
+  # character string "AGAP" or (for exons) just "E"
+  # must make the exon one explicityly E+digits, so that will exclude old-style ENSANG ids
+  # otherwise these cause problems when initial_stable_id method checks archive tables
+
+  my ( $self, $stable_id ) = @_;
+
+  if ( !( defined($stable_id) && ( $stable_id =~ /^AGAP/ || $stable_id =~ /^E\d+$/ ) ) ) { return 0 }
+
+  return 1;
+}
+
+
+1;