added a stableId generator for Pristionchus pacificus using WormBase ids

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

+=head1 LICENSE
+
+  Copyright 2010, The WormBase Consortium. All rights reserved.
+
+  Redistribution and use in source and binary forms, with or without modification, are
+  permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, this list of
+      conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, this list
+      of conditions and the following disclaimer in the documentation and/or other materials
+      provided with the distribution.
+
+  THIS SOFTWARE IS PROVIDED BY THE WORMBASE CONSORTIUM ``AS IS'' AND ANY EXPRESS OR IMPLIED
+  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> OR
+  CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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+  NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+  The views and conclusions contained in the software and documentation are those of the
+  authors and should not be interpreted as representing official policies, either expressed
+  or implied, of The WormBase Consortium.
+
+=head1 CONTACT
+
+  Please email comments or questions to the public WormBase
+  help list at <help@wormbase.org>.
+
+=cut
+
+package Bio::EnsEMBL::IdMapping::StableIdGenerator::PristionchusPacificus;
+
+# Class to generate WormBase conform Pristionchus IDs to be injected into the mapper
+
+use strict;
+use warnings;
+
+use base qw(Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric);
+
+# PPAxxxxx
+# ups the id by one
+sub increment_stable_id {
+  my ( $self, $lastId ) = @_;
+
+  throw("invalid stable ID: $lastId.") unless ($lastId=~/PPA/);
+
+  $lastId =~ /^PPA(\d+)/;
+
+  my $number = $1+1;
+  my $stable_id = sprintf("PPA%05d",$number);
+
+  return $stable_id;
+}
+
+# just in case it is actually used somewhere
+sub is_valid {
+  my ( $self, $stableId ) = @_;
+
+  if ( defined($stableId) && $stableId =~ /^PPA\d+/)
+     {return 1} else {return undef}
+}
+
+1;