try to fall back to gene analysis when storing transcript that doesn't have an...

try to fall back to gene analysis when storing transcript that doesn't have an analysis object attached

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -886,7 +886,7 @@ sub store {
     my $new = $transcripts->[$i];
     my $old = $original_transcripts->[$i];
 
-    $transcript_adaptor->store($new, $gene_dbID );
+    $transcript_adaptor->store($new, $gene_dbID, $analysis_id);
 
     # update the original transcripts since we may have made copies of
     # them by transforming the gene

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -504,6 +504,11 @@ sub fetch_all_by_exon_stable_id {
   Arg [2]    : int $gene_dbID
                The identifier of the gene that this transcript is associated 
                with
+  Arg [3]    : (optional) int $analysis_id
+               The analysis_id to use when storing this gene. This is for 
+               backward compatibility only and used to fall back to the gene
+               analysis_id if no analysis object is attached to the transcript
+               (which you should do for new code).
   Example    : $transID = $transcriptAdaptor->store($transcript, $gene->dbID);
   Description: Stores a transcript in the database and returns the new
                internal identifier for the stored transcript.
@@ -515,7 +520,7 @@ sub fetch_all_by_exon_stable_id {
 =cut
 
 sub store {
-  my ($self, $transcript, $gene_dbID) = @_;
+  my ($self, $transcript, $gene_dbID, $analysis_id) = @_;
 
   if( ! ref $transcript || !$transcript->isa('Bio::EnsEMBL::Transcript') ) {
     throw("$transcript is not a EnsEMBL transcript - not storing");
@@ -532,15 +537,21 @@ sub store {
 
   # store analysis
   my $analysis = $transcript->analysis();
-  throw("Transcript should have an analysis object.") if(!defined($analysis));
+  my $new_analysis_id;
 
-  my $analysis_id = 0;
   if ($analysis) {
     if($analysis->is_stored($db)) {
-      $analysis_id = $analysis->dbID();
+      $new_analysis_id = $analysis->dbID;
     } else {
-      $analysis_id = $db->get_AnalysisAdaptor->store($analysis);
+      $new_analysis_id = $db->get_AnalysisAdaptor->store($analysis);
     }
+  } elsif ($analysis_id) {
+    # Fall back to analysis passed in (usually from gene) if analysis wasn't
+    # set explicitely for the transcript. This is deprectated though.
+    warning("You should explicitely attach an analysis object to the Transcript. Will fall back to Gene analysis, but this behaviour is deprecated.");
+    $new_analysis_id = $analysis_id;
+  } else {
+    throw("Need an analysis_id to store the Transcript.");
   }
 
   #
@@ -578,7 +589,7 @@ sub store {
   ));
 
   $tst->bind_param(1,$gene_dbID,SQL_INTEGER);
-  $tst->bind_param(2,$analysis_id,SQL_INTEGER);
+  $tst->bind_param(2,$new_analysis_id,SQL_INTEGER);
   $tst->bind_param(3,$seq_region_id,SQL_INTEGER);
   $tst->bind_param(4,$transcript->start,SQL_INTEGER);
   $tst->bind_param(5,$transcript->end,SQL_INTEGER);