diff --git a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
index c3c6311fb520fa0196baa82a9b06645b0af9350b..eb7966b62ef373237225fc01e024191621ae0922 100644
--- a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
@@ -2,20 +2,74 @@ package Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric;
=head1 NAME
+Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric - default Ensembl
+StableIdGenerator implementation
=head1 SYNOPSIS
+# inject the confiured StableIdGenerator plugin
+my $stable_id_generator = $conf->param('plugin_stable_id_generator');
+inject($stable_id_generator);
+
+# create a new StableIdGenerator object
+my $generator_instance = $stable_id_generator->new(
+ -LOGGER => $self->logger,
+ -CONF => $self->conf,
+ -CACHE => $self->cache
+);
+
+# determine starting stable ID for new assignments
+my $new_stable_id = $generator_instance->initial_stable_id('gene');
+
+# loop over genes
+foreach my $target_gene (@all_target_genes) {
+
+ # if the stable Id for this gene was mapped, assign it
+ if ($mapping_exists{$target_gene->id}) {
+ my $source_gene = $mappings{$target_gene->id};
+ $target_gene->stable_id($source_gene->stable_id);
+
+ # calculate and set version
+ my $version = $generator_instance->calculate_version($source_gene,
+ $target_gene);
+ $target_gene->version($version);
+
+ # no mapping exists, assign a new stable Id
+ } else {
+ $target_gene->stable_id($new_stable_id);
+ $target_gene->version('1');
+
+ # increment the stable Id (to be assigned to the next unmapped gene)
+ $new_stable_id = $generator_instance->increment_stable_id($new_stable_id);
+ }
+}
=head1 DESCRIPTION
+This is the default implementation for a StableIdGenerator, which is used by
+Bio::EnsEMBL::IdMapping::StableIdMapper to generate new stable Ids and increment
+versions on mapped stable Ids. Refer to the documentation in this module if you
+would like to implement your own StableIdGenerator.
+
+The stable Id mapping application allows you to plugin your own implementation
+by specifying it with the --plugin_stable_id_generator configuration parameter.
+
+Requirements for a StableIdGenerator plugin:
+
+ - inherit from Bio::EnsEMBL::IdMapping::BaseObject
+ - implement all methods listed in METHODS below (see method POD for
+ signatures)
=head1 METHODS
+initial_stable_id
+increment_stable_id
+calculate_version
=head1 LICENCE
This code is distributed under an Apache style licence. Please see
-http:#www.ensembl.org/info/about/code_licence.html for details.
+http://www.ensembl.org/info/about/code_licence.html for details.
=head1 AUTHOR
@@ -39,6 +93,20 @@ our @ISA = qw(Bio::EnsEMBL::IdMapping::BaseObject);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+=head2 initial_stable_id
+
+ Arg[1] : String $type - an entity type (gene|transcript|translation|exon)
+ Example : my $new_stable_id = $generator->initial_stable_id('gene');
+ Description : Determine the initial stable Id to use for new assignments. This
+ method is called once at the beginning of stable Id mapping.
+ Return type : String - a stable Id of appropriate type
+ Exceptions : none
+ Caller : Bio::EnsEMBL::IdMapping::StableIdMapper::map_stable_ids()
+ Status : At Risk
+ : under development
+
+=cut
+
sub initial_stable_id {
my $self = shift;
my $type = shift;
@@ -57,7 +125,13 @@ sub initial_stable_id {
$init_stable_id = $self->fetch_value_from_db($s_dbh, $sql);
if ($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");
+
} else {
$self->logger->warning("Can't find highest ${type}_stable_id in source db.\n");
}
@@ -66,6 +140,22 @@ sub initial_stable_id {
}
+=head2 increment_stable_id
+
+ Arg[1] : String $stable_id - the stable Id to increment
+ Example : $next_stable_id = $generator->increment_stable_id(
+ $current_stable_id);
+ Description : Increments the stable Id used for new assigments. This method is
+ called after each new stable Id assigment to generate the next
+ stable Id to be used.
+ Return type : String - the next new stable Id
+ Exceptions : thrown on missing or malformed argument
+ Caller : Bio::EnsEMBL::IdMapping::StableIdMapper::map_stable_ids()
+ Status : At Risk
+ : under development
+
+=cut
+
sub increment_stable_id {
my $self = shift;
my $stable_id = shift;
@@ -81,6 +171,27 @@ sub increment_stable_id {
}
+=head2 calculate_version
+
+ Arg[1] : Bio::EnsEMBL::IdMapping::TinyFeature $s_obj - source object
+ Arg[2] : Bio::EnsEMBL::IdMapping::TinyFeature $t_obj - target object
+ Example : my $version = $generator->calculate_version($source_gene,
+ $target_gene);
+ $target_gene->version($version);
+ Description : Determines the version for a mapped stable Id. For Ensembl
+ genes, the rules for incrementing the version number are:
+ - exons: if exon sequence changed
+ - transcript: if spliced exon sequence changed
+ - translation: if transcript changed
+ - gene: if any of its transcript changed
+ Return type : String - the version to be used
+ Exceptions : thrown on wrong argument
+ Caller : Bio::EnsEMBL::IdMapping::StableIdMapper::map_stable_ids()
+ Status : At Risk
+ : under development
+
+=cut
+
sub calculate_version {
my $self = shift;
my $s_obj = shift;
diff --git a/modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm b/modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
index 0878345a5b0c6910fc28033320bb7e5e001ee3be..5524df2dbd8dc23931891de57a28856bcd2fc133 100644
--- a/modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
@@ -260,8 +260,6 @@ sub map_stable_ids {
# no mapping was found, assign a new stable ID
} else {
- $new_stable_id = $self->stable_id_generator->increment_stable_id(
- $new_stable_id);
$t_obj->stable_id($new_stable_id);
$t_obj->version(1);
$t_obj->created_date($self->mapping_session_date);
@@ -281,6 +279,10 @@ sub map_stable_ids {
$self->add_stable_id_event('new', $key);
}
+ # increment the stable Id (to be assigned to the next unmapped gene)
+ $new_stable_id = $self->stable_id_generator->increment_stable_id(
+ $new_stable_id);
+
# stats
$stats{'new'}++;