When Transcripts are removed, ensure transcript attributes, transcript

supporting features and translation attributes are removed

modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm

@@ -475,6 +475,8 @@ sub store_on_Translation {
 
   Arg [1]    : Bio::EnsEMBL::Slice $slice
                The Slice to remove attributes from
+  Arg [2]    : (optional) dbID $attrib_type_id
+               Database id of attributes to remove
   Example    : $attribute_adaptor->remove_from_Slice($slice);
   Description: Removes all attributes which are stored in the database on
                the provided Slice.
@@ -557,6 +559,106 @@ sub remove_from_MiscFeature {
 }
 
 
+=head2 remove_from_Transcript
+
+  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
+               The Transcript to remove attributes from
+  Arg [2]    : (optional) dbID $attrib_type_id
+               Database id of attributes to remove
+  Example    : $attribute_adaptor->remove_from_Transcript($transcript);
+  Description: Removes all attributes which are stored in the database on
+               the provided Transcript.
+  Returntype : none
+  Exceptions : throw on incorrect arguments
+               throw if transcript not stored
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub remove_from_Transcript {
+  my $self = shift;
+  my $transcript = shift;
+  my $attrib_type_id = shift;
+
+  if(!ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript')) {
+    throw("Bio::EnsEMBL::Transcript argument expected.");
+  }
+
+  my $db = $self->db();
+
+  if (! $transcript->is_stored($db)) {
+    throw("Transcript is not stored in the database.");
+  }
+  
+  if (defined $attrib_type_id) {
+    my $sth = $self->prepare("DELETE FROM transcript_attrib " .
+        "WHERE transcript_id = ? AND attrib_type_id = ?");
+    $sth->execute($transcript->dbID, $attrib_type_id);
+    $sth->finish;
+  } else {
+    my $sth = $self->prepare("DELETE FROM transcript_attrib " .
+        "WHERE transcript_id = ?");
+    $sth->execute($transcript->dbID);
+    $sth->finish();
+  }
+
+  return;
+}
+
+
+
+=head2 remove_from_Translation
+
+  Arg [1]    : Bio::EnsEMBL::Translation $translation
+               The Translation to remove attributes from
+  Arg [2]    : (optional) dbID $attrib_type_id
+               Database id of attributes to remove
+  Example    : $attribute_adaptor->remove_from_Transcript($transcript);
+  Description: Removes all attributes which are stored in the database on
+               the provided Transcript.
+  Returntype : none
+  Exceptions : throw on incorrect arguments
+               throw if transcript not stored
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub remove_from_Translation {
+  my $self = shift;
+  my $translation = shift;
+  my $attrib_type_id = shift;
+
+  if(!ref($translation) || !$translation->isa('Bio::EnsEMBL::Translation')) {
+    throw("Bio::EnsEMBL::Translation argument expected.");
+  }
+
+  my $db = $self->db();
+
+  if (! $translation->is_stored($db)) {
+    throw("Transcript is not stored in the database.");
+  }
+  
+  if (defined $attrib_type_id) {
+    my $sth = $self->prepare("DELETE FROM translation_attrib " .
+        "WHERE translation_id = ? AND attrib_type_id = ?");
+    $sth->execute($translation->dbID, $attrib_type_id);
+    $sth->finish;
+  } else {
+    my $sth = $self->prepare("DELETE FROM translation_attrib " .
+        "WHERE translation_id = ?");
+    $sth->execute($translation->dbID);
+    $sth->finish();
+  }
+
+  return;
+}
+
+
+
+
+
 
 # _store_type
 

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -838,6 +838,36 @@ sub remove {
     return;
   }
 
+  # remove the supporting features of this transcript
+
+  my $prot_adp = $self->db->get_ProteinAlignFeatureAdaptor;
+  my $dna_adp = $self->db->get_DnaAlignFeatureAdaptor;
+
+  my $sfsth = $self->prepare("SELECT feature_type, feature_id  " .
+                             "FROM transcript_supporting_feature " .
+                             "WHERE transcript_id = ?");
+  $sfsth->execute($transcript->dbID);
+  while(my ($type, $feature_id) = $sfsth->fetchrow()){
+    if($type eq 'protein_align_feature'){
+      my $f = $prot_adp->fetch_by_dbID($feature_id);
+      $prot_adp->remove($f);
+    }
+    elsif($type eq 'dna_align_feature'){
+      my $f = $dna_adp->fetch_by_dbID($feature_id);
+      $dna_adp->remove($f);
+    }
+    else {
+      warning("Unknown supporting feature type $type. Not removing feature.");
+    }
+  }
+  $sfsth->finish();
+
+  # delete the association to supporting features
+
+  $sfsth = $self->prepare("DELETE FROM transcript_supporting_feature WHERE transcript_id = ?");
+  $sfsth->execute( $transcript->dbID );
+  $sfsth->finish();
+
   # remove all xref linkages to this transcript
 
   my $dbeAdaptor = $self->db->get_DBEntryAdaptor();
@@ -845,17 +875,21 @@ sub remove {
     $dbeAdaptor->remove_from_object($dbe, $transcript, 'Transcript');
   }
 
-  my $exonAdaptor = $self->db->get_ExonAdaptor();
-  my $translationAdaptor = $self->db->get_TranslationAdaptor();
+  # remove the attributes associated with this transcript
+
+  $attrib_adp->remove_from_Transcript($transcript);
+  my $attrib_adp = $self->db->get_AttributeAdaptor;  
 
   # remove the translation associated with this transcript
 
+  my $translationAdaptor = $self->db->get_TranslationAdaptor();
   if( defined($transcript->translation()) ) {
     $translationAdaptor->remove( $transcript->translation );
   }
 
   # remove exon associations to this transcript
 
+  my $exonAdaptor = $self->db->get_ExonAdaptor();
   foreach my $exon ( @{$transcript->get_all_Exons()} ) {
     # get the number of transcript references to this exon
     # only remove the exon if this is the last transcript to

modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm

@@ -314,6 +314,10 @@ sub remove {
     return;
   }
 
+  # remove athe attributes associated with this translation
+  my $attrib_adp = $self->db->get_AttributeAdaptor;
+  $attrib_adp->remove_from_Translation($translation);
+
   # remove all xref associations to this translation
   my $dbe_adaptor = $self->db()->get_DBEntryAdaptor();
   foreach my $dbe (@{$translation->get_all_DBEntries()}) {