minor bug fixes and addition of method to get things by logic name in case...

minor bug fixes and addition of method to get things by logic name in case Fgenesh is being run at teh same time as genscan

modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm

@@ -109,6 +109,14 @@ sub fetch_by_Slice {
    $self->throw( "Not implemented yet" );
 }
 
+sub fetch_by_Slice_and_logic_name {
+   my $self = shift;
+   my $slice = shift;
+   my $logic_name = shift;
+
+   $self->throw( "Not implemented yet" );
+}
+
 
 =head2 fetch_by_Contig
 
@@ -151,6 +159,37 @@ sub fetch_by_Contig {
   return \@res;
 }
 
+sub fetch_by_Contig_and_logic_name {
+  my $self = shift;
+  my $contig = shift;
+  my $logic_name = shift;
+
+  my $query = qq {
+    SELECT  p.prediction_transcript_id
+      , p.contig_id
+      , p.contig_start
+      , p.contig_end
+      , p.contig_strand
+      , p.start_phase
+      , p.exon_rank
+      , p.score
+      , p.p_value	
+      , p.analysis_id
+      , p.exon_count
+
+    FROM prediction_transcript p, analysis a
+    WHERE p.contig_id = ? 
+    AND a.analysis_id = p.analysis_id
+    AND a.logic_name = ?
+    ORDER BY p.prediction_transcript_id, p.exon_rank
+  };
+
+  my $sth = $self->prepare( $query );
+  $sth->execute( $contig->dbID, $logic_name );
+
+  my @res = $self->_ptrans_from_sth( $sth );
+  return \@res;
+}
 
 
 =head2 _ptrans_from_sth
@@ -194,7 +233,6 @@ sub _ptrans_from_sth {
     my $exon = $self->_new_Exon_from_hashRef( $hashRef );
     $pre_trans->add_Exon( $exon, $hashRef->{'exon_rank'} );
   }
-
   return @result;
 }
 
@@ -282,10 +320,10 @@ sub store {
   my @exons = $pre_trans->get_all_Exons();
   my $dbID = undef;
   my $rank = 1;
-
+  
   for my $exon ( @exons ) {
     if( ! defined $exon ) { $rank++; next; }
-
+    
     my $contig_id = $exon->contig->dbID();
     my $contig_start = $exon->start();
     my $contig_end = $exon->end();
@@ -297,7 +335,7 @@ sub store {
     # this is only in PredictionExon
     my $score = $exon->score();
     my $p_value = $exon->p_value();
-
+    #print "storing exon with pvalue ".$exon->p_value." and score ".$exon->score."\n";
     my $analysis = $pre_trans->analysis->dbID;
 
     if( $rank == 1 ) {
@@ -306,7 +344,7 @@ sub store {
       $dbID =   $exonst->{'mysql_insertid'};
     } else {
       $exonst->execute( $dbID, $rank, $contig_id, $contig_start, $contig_end, $contig_strand,
-			$start_phase, $end_phase, $score, $analysis, scalar( @exons ) );
+			$start_phase, $score, $p_value, $analysis, scalar( @exons ) );
     }
     $rank++;
   }