Jira ENSCORESW-1381

stable_id_version setter/getter for core object types, sets stable_id with a . delimited version or fetches stable_id with .version concatonated (if version is set)

modules/Bio/EnsEMBL/Exon.pm

@@ -1210,6 +1210,34 @@ sub version {
   return $self->{'version'};
 }
 
+=head2 stable_id_version
+
+  Arg [1]    : (optional) String - the stable ID with version to set
+  Example    : $exon->stable_id("ENSE0000000001.3");
+  Description: Getter/setter for stable id with version for this exon.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub stable_id_version {
+    my $self = shift;
+    if(my $stable_id = shift) {
+	# See if there's an embedded period, assume that's a
+	# version, might not work for some species but you
+	# should use ->stable_id() and version() if you're worried
+	# about ambiguity
+	my $vindex = rindex($stable_id, '.');
+	# Set the stable_id and version pair depending on if
+	# we found a version delimiter in the stable_id
+	($self->{stable_id}, $self->{version}) = ($vindex > 0 ?
+						  (substr($stable_id,0,$vindex), substr($stable_id,$vindex+1)) :
+						  $stable_id, undef);
+    }
+    return $self->{stable_id} . ($self->{version} ? ".$self->{version}" : '');
+}
 
 =head2 is_current
 

modules/Bio/EnsEMBL/Gene.pm

@@ -1078,6 +1078,34 @@ sub stable_id {
   return $self->{'stable_id'};
 }
 
+=head2 stable_id_version
+
+  Arg [1]    : (optional) String - the stable ID with version to set
+  Example    : $gene->stable_id("ENSG0000000001.3");
+  Description: Getter/setter for stable id with version for this gene.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub stable_id_version {
+    my $self = shift;
+    if(my $stable_id = shift) {
+	# See if there's an embedded period, assume that's a
+	# version, might not work for some species but you
+	# should use ->stable_id() and version() if you're worried
+	# about ambiguity
+	my $vindex = rindex($stable_id, '.');
+	# Set the stable_id and version pair depending on if
+	# we found a version delimiter in the stable_id
+	($self->{stable_id}, $self->{version}) = ($vindex > 0 ?
+						  (substr($stable_id,0,$vindex), substr($stable_id,$vindex+1)) :
+						  $stable_id, undef);
+    }
+    return $self->{stable_id} . ($self->{version} ? ".$self->{version}" : '');
+}
 
 =head2 is_current
 

modules/Bio/EnsEMBL/Operon.pm

@@ -210,6 +210,35 @@ sub version {
   return $self->{'version'};
 }
 
+=head2 stable_id_version
+
+  Arg [1]    : (optional) String - the stable ID with version to set
+  Example    : $operon->stable_id("accR2.3");
+  Description: Getter/setter for stable id with version for this operon.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub stable_id_version {
+    my $self = shift;
+    if(my $stable_id = shift) {
+	# See if there's an embedded period, assume that's a
+	# version, might not work for some species but you
+	# should use ->stable_id() and version() if you're worried
+	# about ambiguity
+	my $vindex = rindex($stable_id, '.');
+	# Set the stable_id and version pair depending on if
+	# we found a version delimiter in the stable_id
+	($self->{stable_id}, $self->{version}) = ($vindex > 0 ?
+						  (substr($stable_id,0,$vindex), substr($stable_id,$vindex+1)) :
+						  $stable_id, undef);
+    }
+    return $self->{stable_id} . ($self->{version} ? ".$self->{version}" : '');
+}
+
 =head2 get_all_OperonTranscripts
 
   Example    : my $ots = $operon->get_all_OperonTranscripts();

modules/Bio/EnsEMBL/OperonTranscript.pm

@@ -199,6 +199,35 @@ sub version {
   return $self->{'version'};
 }
 
+=head2 stable_id_version
+
+  Arg [1]    : (optional) String - the stable ID with version to set
+  Example    : $operon->stable_id("accR2A.3");
+  Description: Getter/setter for stable id with version.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub stable_id_version {
+    my $self = shift;
+    if(my $stable_id = shift) {
+	# See if there's an embedded period, assume that's a
+	# version, might not work for some species but you
+	# should use ->stable_id() and version() if you're worried
+	# about ambiguity
+	my $vindex = rindex($stable_id, '.');
+	# Set the stable_id and version pair depending on if
+	# we found a version delimiter in the stable_id
+	($self->{stable_id}, $self->{version}) = ($vindex > 0 ?
+						  (substr($stable_id,0,$vindex), substr($stable_id,$vindex+1)) :
+						  $stable_id, undef);
+    }
+    return $self->{stable_id} . ($self->{version} ? ".$self->{version}" : '');
+}
+
 =head2 operon
 
   Example    : $operon = $ot->operon();

modules/Bio/EnsEMBL/Transcript.pm

@@ -2310,7 +2310,6 @@ sub version {
   return $self->{'version'};
 }
 
-
 =head2 stable_id
 
  Title   : stable_id
@@ -2328,6 +2327,34 @@ sub stable_id {
   return $self->{'stable_id'};
 }
 
+=head2 stable_id_version
+
+  Arg [1]    : (optional) String - the stable ID with version to set
+  Example    : $transcript->stable_id("ENST0000000001.3");
+  Description: Getter/setter for stable id with version for this transcript.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub stable_id_version {
+    my $self = shift;
+    if(my $stable_id = shift) {
+	# See if there's an embedded period, assume that's a
+	# version, might not work for some species but you
+	# should use ->stable_id() and version() if you're worried
+	# about ambiguity
+	my $vindex = rindex($stable_id, '.');
+	# Set the stable_id and version pair depending on if
+	# we found a version delimiter in the stable_id
+	($self->{stable_id}, $self->{version}) = ($vindex > 0 ?
+						  (substr($stable_id,0,$vindex), substr($stable_id,$vindex+1)) :
+						  $stable_id, undef);
+    }
+    return $self->{stable_id} . ($self->{version} ? ".$self->{version}" : '');
+}
 
 =head2 is_current
 

modules/Bio/EnsEMBL/Translation.pm

@@ -474,6 +474,35 @@ sub stable_id {
   return $self->{'stable_id'};
 }
 
+=head2 stable_id_version
+
+  Arg [1]    : (optional) String - the stable ID with version to set
+  Example    : $translation->stable_id("ENSP0059890.3");
+  Description: Getter/setter for stable id with version for this translation.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub stable_id_version {
+    my $self = shift;
+    if(my $stable_id = shift) {
+	# See if there's an embedded period, assume that's a
+	# version, might not work for some species but you
+	# should use ->stable_id() and version() if you're worried
+	# about ambiguity
+	my $vindex = rindex($stable_id, '.');
+	# Set the stable_id and version pair depending on if
+	# we found a version delimiter in the stable_id
+	($self->{stable_id}, $self->{version}) = ($vindex > 0 ?
+						  (substr($stable_id,0,$vindex), substr($stable_id,$vindex+1)) :
+						  $stable_id, undef);
+    }
+    return $self->{stable_id} . ($self->{version} ? ".$self->{version}" : '');
+}
+
 =head2 created_date
 
   Arg [1]    : (optional) string $created_date - created date to set

modules/t/exon.t

@@ -242,6 +242,16 @@ $exon = $exonad->fetch_by_stable_id('ENSE00001109603');
 debug("fetch_by_stable_id");
 ok( $exon->dbID == 162033 );
 
+$exon->stable_id_version('ENSE00000171455.4');
+is($exon->stable_id, 'ENSE00000171455', 'Stable id set with stable_id_version');
+is($exon->version, 4, 'Version set with stable_id_version');
+is($exon->stable_id_version, 'ENSE00000171455.4', 'Stable id and version from stable_id_version');
+
+$exon->stable_id_version('ENSE00000171456');
+is($exon->stable_id, 'ENSE00000171456', 'Stable id set with stable_id_version');
+is($exon->version, undef, 'Version undef from stable_id_version');
+is($exon->stable_id_version, 'ENSE00000171456', 'Stable id and no version from stable_id_version');
+
 $exon = $exonad->fetch_by_stable_id('ENSE00001109603.1');
 ok($exon->dbID == 162033, 'fetch_by_stable_id with version');
 

modules/t/gene.t

@@ -840,6 +840,16 @@ $gene = $ga->fetch_by_stable_id('ENSG00000355555');
 debug("fetch_by_stable_id");
 ok($gene->dbID == 18275);
 
+$gene->stable_id_version('ENSG00000171455.4');
+is($gene->stable_id, 'ENSG00000171455', 'Stable id set with stable_id_version');
+is($gene->version, 4, 'Version set with stable_id_version');
+is($gene->stable_id_version, 'ENSG00000171455.4', 'Stable id and version from stable_id_version');
+
+$gene->stable_id_version('ENSG00000171456');
+is($gene->stable_id, 'ENSG00000171456', 'Stable id set with stable_id_version');
+is($gene->version, undef, 'Version undef from stable_id_version');
+is($gene->stable_id_version, 'ENSG00000171456', 'Stable id and no version from stable_id_version');
+
 $gene = $ga->fetch_by_stable_id("ENSG00000171456.1");
 ok($gene->stable_id eq 'ENSG00000171456', "Fetch by stable_id with version");
 

modules/t/operon.t

@@ -99,6 +99,16 @@ $operon = $operon_adaptor->fetch_by_stable_id('16152-16153-4840');
 debug( "Operon->fetch_by_stable_id()" );
 ok( $operon );
 
+$operon->stable_id_version('16152-16153-4841.4');
+is($operon->stable_id, '16152-16153-4841', 'Stable id set with stable_id_version');
+is($operon->version, 4, 'Version set with stable_id_version');
+is($operon->stable_id_version, '16152-16153-4841.4', 'Stable id and version from stable_id_version');
+
+$operon->stable_id_version('16152-16153-4842');
+is($operon->stable_id, '16152-16153-4842', 'Stable id set with stable_id_version');
+is($operon->version, undef, 'Version undef from stable_id_version');
+is($operon->stable_id_version, '16152-16153-4842', 'Stable id and no version from stable_id_version');
+
 $operon = $operon_adaptor->fetch_by_stable_id('16152-16153-4840.1');
 ok($operon->stable_id eq '16152-16153-4840', 'fetch_by_stable_id with version');
 

modules/t/operon_transcript.t

@@ -237,6 +237,16 @@ $operon_transcript = $ota->fetch_by_stable_id('T16152-16153-4840');
 debug( "OperonTranscript->fetch_by_stable_id()" );
 ok( $operon_transcript );
 
+$operon_transcript->stable_id_version('T16152-16153-4841.4');
+is($operon_transcript->stable_id, 'T16152-16153-4841', 'Stable id set with stable_id_version');
+is($operon_transcript->version, 4, 'Version set with stable_id_version');
+is($operon_transcript->stable_id_version, 'T16152-16153-4841.4', 'Stable id and version from stable_id_version');
+
+$operon_transcript->stable_id_version('T16152-16153-4842');
+is($operon_transcript->stable_id, 'T16152-16153-4842', 'Stable id set with stable_id_version');
+is($operon_transcript->version, undef, 'Version undef from stable_id_version');
+is($operon_transcript->stable_id_version, 'T16152-16153-4842', 'Stable id and no version from stable_id_version');
+
 $operon_transcript = $ota->fetch_by_stable_id('T16152-16153-4840.1');
 ok($operon_transcript->stable_id eq 'T16152-16153-4840', 'fetch_by_stable_id with version');
 

modules/t/transcript.t

@@ -609,6 +609,16 @@ is( scalar(@transcripts), 1, 'Fetched all transcripts by stable_id' );
 $tr = $ta->fetch_by_translation_stable_id('ENSP00000355555');
 is( $tr->dbID, 21740, 'Fetched transcript by translation stable id' );
 
+$tr->stable_id_version('ENSP00000171455.4');
+is($tr->stable_id, 'ENSp00000171455', 'Stable id set with stable_id_version');
+is($tr->version, 4, 'Version set with stable_id_version');
+is($tr->stable_id_version, 'ENSP00000171455.4', 'Stable id and version from stable_id_version');
+
+$tr->stable_id_version('ENSP00000171456');
+is($tr->stable_id, 'ENSP00000171456', 'Stable id set with stable_id_version');
+is($tr->version, undef, 'Version undef from stable_id_version');
+is($tr->stable_id_version, 'ENSP00000171456', 'Stable id and no version from stable_id_version');
+
 $tr = $ta->fetch_by_translation_stable_id('ENSP00000355555.1');
 is( $tr->dbID, 21740, 'Fetched transcript by translation stable id with version' );
 
@@ -681,18 +691,6 @@ is($tr->is_current, 1, 'Transcript is now current');   # 151
 
 $multi->restore;
 
-$tr = $ta->fetch_by_stable_id('ENST00000310998.1');
-ok($tr->stable_id eq 'ENST00000310998', 'Fetch by stable_id with version');
-
-$tr = $ta->fetch_by_stable_id('ENST00000310998.1a');
-ok(! defined($tr), 'Fetch by stable_id with bad version');
-
-$tr = $ta->fetch_by_stable_id_version('ENST00000310998', 1);
-ok($tr->stable_id eq 'ENST00000310998', 'fetch_by_stable_id_version');
-
-$tr = $ta->fetch_by_stable_id_version('ENST00000310998', '1a');
-ok(! defined($tr), 'fetch_by_stable_id_version with bad version');
-
 # UTR Tests
 {
   my $utr_testing = sub {

modules/t/translation.t

@@ -107,6 +107,16 @@ ok($translation && $translation->stable_id() eq 'ENSP00000201961');
 $translation = $ta->fetch_by_stable_id('ENSP00000201961');
 ok($translation && $translation->dbID() == 21734);
 
+$translation->stable_id_version('ENSP00000201962.4');
+is($translation->stable_id, 'ENSP00000201962', 'Stable id set with stable_id_version');
+is($translation->version, 4, 'Version set with stable_id_version');
+is($translation->stable_id_version, 'ENSP00000201962.4', 'Stable id and version from stable_id_version');
+
+$translation->stable_id_version('ENSP00000201963');
+is($translation->stable_id, 'ENSP00000201963', 'Stable id set with stable_id_version');
+is($translation->version, undef, 'Version undef from stable_id_version');
+is($translation->stable_id_version, 'ENSP00000201963', 'Stable id and no version from stable_id_version');
+
 $translation = $ta->fetch_by_stable_id('ENSP00000201961.1');
 ok($translation && $translation->dbID() == 21734, 'fetch_by_stable_id with version');