ENSCORESW-914: idesc should really be xref.description field

ilabel added for xref.display_label field

modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm

@@ -92,13 +92,13 @@ sub fetch_all_by_translation_id {
   my @features;
   my $analysis_adaptor = $self->db()->get_AnalysisAdaptor();
 
-  my $sth = $self->prepare("SELECT protein_feature_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.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.translation_id = ?");
+  my $sth = $self->prepare("SELECT protein_feature_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.translation_id = ?");
 
   $sth->bind_param(1, $translation_id, SQL_INTEGER);
   $sth->execute();
 
   while (my $row = $sth->fetchrow_arrayref) {
-	my ($dbID, $start, $end, $analysisid, $score, $perc_id, $evalue, $hstart, $hend, $hid, $hdesc, $desc, $interpro_ac) = @$row;
+	my ($dbID, $start, $end, $analysisid, $score, $perc_id, $evalue, $hstart, $hend, $hid, $hdesc, $desc, $ilabel, $interpro_ac) = @$row;
 
 	my $analysis = $analysis_adaptor->fetch_by_dbID($analysisid);
 
@@ -120,6 +120,7 @@ sub fetch_all_by_translation_id {
 												 -HSEQNAME     => $hid,
 												 -HDESCRIPTION => $hdesc,
 												 -IDESC        => $desc,
+                                                                                                 -ILABEL       => $ilabel,
 												 -INTERPRO_AC  => $interpro_ac);
 
 	push(@features, $feat);
@@ -146,13 +147,13 @@ sub fetch_all_by_translation_id {
 sub fetch_by_dbID {
   my ($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.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.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 = ?");
 
   $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, $interpro_ac) = $sth->fetchrow_array();
+      $hend, $hseqname, $idesc, $ilabel, $interpro_ac) = $sth->fetchrow_array();
 
   if($sth->rows == 0) {
     $sth->finish();
@@ -176,6 +177,7 @@ sub fetch_by_dbID {
 									  -P_VALUE     => $pvalue,
 									  -PERCENT_ID  => $perc_ident,
 									  -IDESC       => $idesc,
+                                                                          -ILABEL      => $ilabel,
 									  -INTERPRO_AC => $interpro_ac);
 } ## end sub fetch_by_dbID
 

modules/Bio/EnsEMBL/ProteinFeature.pm

@@ -86,13 +86,14 @@ sub new {
 
   my $class = ref($proto) || $proto;
 
-  my ($idesc, $interpro_ac, $translation_id) = rearrange(['IDESC', 'INTERPRO_AC', 'TRANSLATION_ID'], @_);
+  my ($idesc, $ilabel, $interpro_ac, $translation_id) = rearrange(['IDESC', 'ILABEL', 'INTERPRO_AC', 'TRANSLATION_ID'], @_);
 
   my $self = $class->SUPER::new(@_);
 
   # the strand of protein features is always 0
   $self->{'strand'}         = 0;
   $self->{'idesc'}          = $idesc || '';
+  $self->{'ilabel'}         = $ilabel || '';
   $self->{'interpro_ac'}    = $interpro_ac || '';
   $self->{'translation_id'} = $translation_id || '';
 
@@ -134,6 +135,25 @@ sub idesc {
   return $self->{'idesc'};
 }
 
+=head2 ilabel
+
+  Arg [1]    : (optional) string The interpro label
+  Example    : print $protein_feature->ilabel();
+  Description: Getter/Setter for the interpro label of this protein
+               feature.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub ilabel {
+  my $self = shift;
+  $self->{'ilabel'} = shift if (@_);
+  return $self->{'ilabel'};
+}
+
 =head2 interpro_ac
 
   Arg [1]    : (optional) string The interpro accession

modules/t/proteinFeature.t

@@ -41,6 +41,7 @@ my $hspecies = 'Mus_musculus';
 my $hdes = "Hit description";
 
 my $idesc = 'interpro description';
+my $ilabel = 'interpro label';
 my $interpro_ac = 'interpro accession';
 
 my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
@@ -60,6 +61,7 @@ my $f = Bio::EnsEMBL::ProteinFeature->new
    -HSPECIES    => $hspecies,
    -HDESCRIPTION=> $hdes,
    -IDESC       => $idesc,
+   -ILABEL      => $ilabel,
    -INTERPRO_AC => $interpro_ac);
 
 
@@ -81,6 +83,7 @@ ok($f->hspecies eq $hspecies);
 ok($f->hdescription eq $hdes);
 
 ok($f->idesc eq $idesc);
+ok($f->ilabel eq $ilabel);
 ok($f->interpro_ac eq $interpro_ac);
 
 # check that the strand is 0
@@ -90,6 +93,7 @@ ok($f->strand == 0);
 # Test setters
 #
 ok(test_getter_setter($f, 'idesc', 'interpro desc1'));
+ok(test_getter_setter($f, 'ilabel', 'interpro label1'));
 ok(test_getter_setter($f, 'interpro_ac',   'interpro ac1'));