Merge pull request #157 from Ensembl/ENSCORESW-1912

Updated the new call to create the ProteinFeature object in ProteinFe…

modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm

@@ -143,13 +143,20 @@ sub fetch_all_by_logic_name {
 sub fetch_by_dbID {
   my ($self, $protfeat_id) = @_;
 
-  my $sth = $self->prepare("SELECT p.seq_start, p.seq_end, p.analysis_id, " . "       p.score, p.perc_ident, p.evalue, " . "       p.hit_start, p.hit_end, p.hit_name, " . "       x.description, x.display_label, i.interpro_ac " . "FROM   protein_feature p " . "LEFT JOIN interpro AS i ON p.hit_name = i.id " . "LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac " . "WHERE  p.protein_feature_id = ?");
+  my $sth = $self->prepare("SELECT p.translation_id, p.seq_start, p.seq_end, p.analysis_id, "
+                            . "p.score, p.perc_ident, p.evalue, "
+                            . "p.hit_start, p.hit_end, p.hit_name, p.hit_description, "
+                            . "x.description, x.display_label, i.interpro_ac "
+                            . "FROM   protein_feature p "
+                            . "LEFT JOIN interpro AS i ON p.hit_name = i.id "
+                            . "LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac "
+                            . "WHERE  p.protein_feature_id = ?");
 
   $sth->bind_param(1, $protfeat_id, SQL_INTEGER);
   my $res = $sth->execute();
    
-  my ($start, $end, $analysis_id, $score, $perc_ident, $pvalue, $hstart, 
-      $hend, $hseqname, $idesc, $ilabel, $interpro_ac) = $sth->fetchrow_array();
+  my ($translation_id, $start, $end, $analysis_id, $score, $perc_ident, $pvalue, $hstart,
+      $hend, $hseqname, $hdesc, $idesc, $ilabel, $interpro_ac) = $sth->fetchrow_array();
 
   if($sth->rows == 0) {
     $sth->finish();
@@ -168,13 +175,15 @@ sub fetch_by_dbID {
 									  -HSTART      => $hstart,
 									  -HEND        => $hend,
 									  -HSEQNAME    => $hseqname,
+									  -HDESCRIPTION => $hdesc,
 									  -ANALYSIS    => $analysis,
 									  -SCORE       => $score,
 									  -P_VALUE     => $pvalue,
 									  -PERCENT_ID  => $perc_ident,
 									  -IDESC       => $idesc,
-                                                                          -ILABEL      => $ilabel,
-									  -INTERPRO_AC => $interpro_ac);
+                                      -ILABEL      => $ilabel,
+									  -INTERPRO_AC => $interpro_ac,
+									  -TRANSLATION_ID  => $translation_id);
 } ## end sub fetch_by_dbID
 
 =head2 store

modules/t/proteinFeature.t

@@ -45,6 +45,7 @@ my $hdes = "Hit description";
 my $idesc = 'interpro description';
 my $ilabel = 'interpro label';
 my $interpro_ac = 'interpro accession';
+my $translation_id = 1234;
 
 my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
 
@@ -64,7 +65,8 @@ my $f = Bio::EnsEMBL::ProteinFeature->new
    -HDESCRIPTION=> $hdes,
    -IDESC       => $idesc,
    -ILABEL      => $ilabel,
-   -INTERPRO_AC => $interpro_ac);
+   -INTERPRO_AC => $interpro_ac,
+   -TRANSLATION_ID     => $translation_id);
 
 
 
@@ -73,6 +75,7 @@ ok($f && $f->isa('Bio::EnsEMBL::ProteinFeature'));
 ok($f->start == $start);
 ok($f->end == $end);
 ok($f->analysis == $analysis);
+ok($f->translation_id == $translation_id);
 
 ok($f->hstart == $hstart);
 ok($f->hend   == $hend);

modules/t/proteinFeatureAdaptor.t

@@ -88,9 +88,29 @@ my $f = Bio::EnsEMBL::ProteinFeature->new
    -IDESC       => $idesc,
    -INTERPRO_AC => $interpro_ac);
    
-$pfa->store($f,21724);
+my $dbID = $pfa->store($f,21724);
 
-my $pfs = $pfa->fetch_all_by_translation_id(21724);
+ok($dbID, "New object created has dbID");
+
+#fetch protein feature object by dbID and compare the core attributes
+#deep comparison is not possible because all the attributes are not stored in the protein_feature table
+my $f_by_dbID = $pfa->fetch_by_dbID($dbID);
+
+is($f_by_dbID->translation_id, 21724);
+is($f_by_dbID->start, $start);
+is($f_by_dbID->end, $end);
+is($f_by_dbID->dbID, $dbID);
+is($f_by_dbID->analysis->logic_name, 'test');
+is($f_by_dbID->hstart, $hstart);
+is($f_by_dbID->hend, $hend);
+is($f_by_dbID->hseqname, $hseqname);
+is($f_by_dbID->hdescription, $hdes);
+is($f_by_dbID->score, $score);
+is($f_by_dbID->percent_id, $percent_id);
+is($f_by_dbID->p_value, $p_value);
+
+
+$pfs = $pfa->fetch_all_by_translation_id(21724);
 
 ok(@$pfs == 16);