diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 5cfdb540e91e078e1d761f905963106fe972b4d6..7fec7c192b3fb398a674289eb167bb8a354b1ce9 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -566,153 +566,158 @@ sub store {
$tst->bind_param(7,$transcript->status,SQL_VARCHAR);
$tst->bind_param(8,$transcript->description,SQL_LONGVARCHAR);
- $tst->execute();
+ $tst->execute();
+ $tst->finish();
- $tst->finish();
+ my $transc_dbID = $tst->{'mysql_insertid'};
+
+ # set dbID and adaptor of transcript here - you'll need this when storing
+ # xrefs
+ $transcript->dbID($transc_dbID);
+ $transcript->adaptor($self);
- my $transc_dbID = $tst->{'mysql_insertid'};
+ #
+ # store translation
+ #
+ my $translation = $transcript->translation();
+ if( defined $translation ) {
+ #make sure that the start and end exon are set correctly
+ my $start_exon = $translation->start_Exon();
+ my $end_exon = $translation->end_Exon();
+
+ if(!$start_exon) {
+ throw("Translation does not define a start exon.");
+ }
- #
- # store translation
- #
- my $translation = $transcript->translation();
- if( defined $translation ) {
- #make sure that the start and end exon are set correctly
- my $start_exon = $translation->start_Exon();
- my $end_exon = $translation->end_Exon();
-
- if(!$start_exon) {
- throw("Translation does not define a start exon.");
- }
-
- if(!$end_exon) {
- throw("Translation does not defined an end exon.");
- }
-
- #If the dbID is not set, this means the exon must have been a different
- #object in memory than the the exons of the transcript. Try to find the
- #matching exon in all of the exons we just stored
- if(!$start_exon->dbID()) {
- my $key = $start_exon->hashkey();
- ($start_exon) = grep {$_->hashkey() eq $key} @$exons;
-
- if($start_exon) {
- $translation->start_Exon($start_exon);
- } else {
- throw("Translation's start_Exon does not appear to be one of the " .
- "exons in its associated Transcript");
- }
- }
-
- if(!$end_exon->dbID()) {
- my $key = $end_exon->hashkey();
- ($end_exon) = grep {$_->hashkey() eq $key} @$exons;
-
- if($start_exon) {
- $translation->end_Exon($end_exon);
- } else {
- throw("Translation's end_Exon does not appear to be one of the " .
- "exons in its associated Transcript.");
- }
- }
-
- $db->get_TranslationAdaptor()->store( $translation, $transc_dbID );
- # set values of the original translation, we may have copied it
- # when we transformed the transcript
- $original_translation->dbID($translation->dbID());
- $original_translation->adaptor($translation->adaptor());
- }
+ if(!$end_exon) {
+ throw("Translation does not defined an end exon.");
+ }
- #
- # store the xrefs/object xref mapping
- #
- my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
+ #If the dbID is not set, this means the exon must have been a different
+ #object in memory than the the exons of the transcript. Try to find the
+ #matching exon in all of the exons we just stored
+ if(!$start_exon->dbID()) {
+ my $key = $start_exon->hashkey();
+ ($start_exon) = grep {$_->hashkey() eq $key} @$exons;
+
+ if($start_exon) {
+ $translation->start_Exon($start_exon);
+ } else {
+ throw("Translation's start_Exon does not appear to be one of the " .
+ "exons in its associated Transcript");
+ }
+ }
- foreach my $dbe ( @{$transcript->get_all_DBEntries} ) {
- $dbEntryAdaptor->store( $dbe, $transc_dbID, "Transcript" );
- }
+ if(!$end_exon->dbID()) {
+ my $key = $end_exon->hashkey();
+ ($end_exon) = grep {$_->hashkey() eq $key} @$exons;
- #
- # Update transcript to point to display xref if it is set
- #
- if(my $dxref = $transcript->display_xref) {
- my $dxref_id;
-
- if($dxref->is_stored($db)) {
- $dxref_id = $dxref->dbID();
- } else {
- $dxref_id = $dbEntryAdaptor->exists($dxref);
- }
-
- if(defined($dxref_id)) {
- my $sth = $self->prepare( "update transcript set display_xref_id = ?".
- " where transcript_id = ?");
- $sth->bind_param(1,$dxref_id,SQL_INTEGER);
- $sth->bind_param(2,$transc_dbID,SQL_INTEGER);
- $sth->execute();
- $dxref->dbID($dxref_id);
- $dxref->adaptor($dbEntryAdaptor);
- $sth->finish();
- } else {
- warning("Display_xref ".$dxref->dbname().":".$dxref->display_id() .
- " is not stored in database.\nNot storing " .
- "relationship to this transcript.");
- $dxref->dbID(undef);
- $dxref->adaptor(undef);
- }
- }
+ if($start_exon) {
+ $translation->end_Exon($end_exon);
+ } else {
+ throw("Translation's end_Exon does not appear to be one of the " .
+ "exons in its associated Transcript.");
+ }
+ }
- #
- # Link transcript to exons in exon_transcript table
- #
- my $etst =
- $self->prepare("insert into exon_transcript (exon_id,transcript_id,rank)"
- ." values (?,?,?)");
- my $rank = 1;
- foreach my $exon ( @{$transcript->get_all_Exons} ) {
- $etst->bind_param(1,$exon->dbID,SQL_INTEGER);
- $etst->bind_param(2,$transc_dbID,SQL_INTEGER);
- $etst->bind_param(3,$rank,SQL_INTEGER);
- $etst->execute();
- $rank++;
- }
+ $db->get_TranslationAdaptor()->store( $translation, $transc_dbID );
+ # set values of the original translation, we may have copied it
+ # when we transformed the transcript
+ $original_translation->dbID($translation->dbID());
+ $original_translation->adaptor($translation->adaptor());
+ }
- $etst->finish();
+ #
+ # store the xrefs/object xref mapping
+ #
+ my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
+
+ foreach my $dbe ( @{$transcript->get_all_DBEntries} ) {
+ $dbEntryAdaptor->store( $dbe, $transcript, "Transcript" );
+ }
+
+ #
+ # Update transcript to point to display xref if it is set
+ #
+ if(my $dxref = $transcript->display_xref) {
+ my $dxref_id;
+
+ if($dxref->is_stored($db)) {
+ $dxref_id = $dxref->dbID();
+ } else {
+ $dxref_id = $dbEntryAdaptor->exists($dxref);
+ }
+
+ if(defined($dxref_id)) {
+ my $sth = $self->prepare( "update transcript set display_xref_id = ?".
+ " where transcript_id = ?");
+ $sth->bind_param(1,$dxref_id,SQL_INTEGER);
+ $sth->bind_param(2,$transc_dbID,SQL_INTEGER);
+ $sth->execute();
+ $dxref->dbID($dxref_id);
+ $dxref->adaptor($dbEntryAdaptor);
+ $sth->finish();
+ } else {
+ warning("Display_xref ".$dxref->dbname().":".$dxref->display_id() .
+ " is not stored in database.\nNot storing " .
+ "relationship to this transcript.");
+ $dxref->dbID(undef);
+ $dxref->adaptor(undef);
+ }
+ }
+
+ #
+ # Link transcript to exons in exon_transcript table
+ #
+ my $etst =
+ $self->prepare("insert into exon_transcript (exon_id,transcript_id,rank)"
+ ." values (?,?,?)");
+ my $rank = 1;
+ foreach my $exon ( @{$transcript->get_all_Exons} ) {
+ $etst->bind_param(1,$exon->dbID,SQL_INTEGER);
+ $etst->bind_param(2,$transc_dbID,SQL_INTEGER);
+ $etst->bind_param(3,$rank,SQL_INTEGER);
+ $etst->execute();
+ $rank++;
+ }
+
+ $etst->finish();
+
+ #
+ # Store stable_id
+ #
+ if (defined($transcript->stable_id)) {
+ if (!defined($transcript->version)) {
+ throw("Trying to store incomplete stable id information for " .
+ "transcript");
+ }
+
+ my $statement =
+ "INSERT INTO transcript_stable_id ".
+ "SET transcript_id = ?, ".
+ " stable_id = ?, ".
+ "version = ?, ";
+
+ if( $transcript->created_date() ) {
+ $statement .= "created_date = from_unixtime( ".$transcript->created_date()."),";
+ } else {
+ $statement .= "created_date = \"0000-00-00 00:00:00\",";
+ }
+
+ if( $transcript->modified_date() ) {
+ $statement .= "modified_date = from_unixtime( ".$transcript->modified_date().")";
+ } else {
+ $statement .= "modified_date = \"0000-00-00 00:00:00\"";
+ }
+
+ my $sth = $self->prepare($statement);
+ $sth->bind_param(1,$transc_dbID,SQL_INTEGER);
+ $sth->bind_param(2,$transcript->stable_id,SQL_VARCHAR);
+ $sth->bind_param(3,$transcript->version,SQL_INTEGER);
+ $sth->execute();
+ $sth->finish();
+ }
- #
- # Store stable_id
- #
- if (defined($transcript->stable_id)) {
- if (!defined($transcript->version)) {
- throw("Trying to store incomplete stable id information for " .
- "transcript");
- }
-
- my $statement =
- "INSERT INTO transcript_stable_id ".
- "SET transcript_id = ?, ".
- " stable_id = ?, ".
- "version = ?, ";
-
- if( $transcript->created_date() ) {
- $statement .= "created_date = from_unixtime( ".$transcript->created_date()."),";
- } else {
- $statement .= "created_date = \"0000-00-00 00:00:00\",";
- }
-
- if( $transcript->modified_date() ) {
- $statement .= "modified_date = from_unixtime( ".$transcript->modified_date().")";
- } else {
- $statement .= "modified_date = \"0000-00-00 00:00:00\"";
- }
-
- my $sth = $self->prepare($statement);
- $sth->bind_param(1,$transc_dbID,SQL_INTEGER);
- $sth->bind_param(2,$transcript->stable_id,SQL_VARCHAR);
- $sth->bind_param(3,$transcript->version,SQL_INTEGER);
- $sth->execute();
- $sth->finish();
- }
# Now the supporting evidence
@@ -752,18 +757,17 @@ sub store {
- #update the original transcript object - not the transfered copy that
- #we might have created
- $original->dbID( $transc_dbID );
- $original->adaptor( $self );
-
- # store transcript attributes if there are any
- my $attr_adaptor = $db->get_AttributeAdaptor();
- $attr_adaptor->store_on_Transcript($transcript,
- $transcript->get_all_Attributes);
+ #update the original transcript object - not the transfered copy that
+ #we might have created
+ $original->dbID( $transc_dbID );
+ $original->adaptor( $self );
+ # store transcript attributes if there are any
+ my $attr_adaptor = $db->get_AttributeAdaptor();
+ $attr_adaptor->store_on_Transcript($transcript,
+ $transcript->get_all_Attributes);
- return $transc_dbID;
+ return $transc_dbID;
}