Merge pull request #218 from ens-lgil/master

Extra parameters for the REST endpoint 'overlap/translation'. Will be…

modules/Bio/EnsEMBL/ProteinFeature.pm

@@ -207,10 +207,13 @@ sub summary_as_hash {
   my %summary;
   $summary{'type'} = $self->analysis->db;
   $summary{'id'} = $self->display_id;
-  $summary{'start'} = $self->start,
-  $summary{'end'} = $self->end,
+  $summary{'start'} = $self->start;
+  $summary{'end'} = $self->end;
   $summary{'interpro'} = $self->interpro_ac;
   $summary{'description'} = $self->idesc;
+  $summary{'hit_start'} = $self->hstart;
+  $summary{'hit_end'} = $self->hend;
+  
   return \%summary;
 }
 

modules/t/proteinFeature.t

@@ -47,7 +47,9 @@ my $ilabel = 'interpro label';
 my $interpro_ac = 'interpro accession';
 my $translation_id = 1234;
 
-my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
+my $analysis_db = 'test_db';
+
+my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test', -DB => $analysis_db);
 
 
 my $f = Bio::EnsEMBL::ProteinFeature->new
@@ -94,6 +96,17 @@ ok($f->interpro_ac eq $interpro_ac);
 # check that the strand is 0
 ok($f->strand == 0);
 
+# Test summary_as_hash
+my $summary = $f->summary_as_hash();
+ok($summary->{'type'} = $analysis_db);
+ok($summary->{'id'} = $hseqname);
+ok($summary->{'start'} = $start);
+ok($summary->{'end'} = $end);
+ok($summary->{'interpro'} = $interpro_ac);
+ok($summary->{'description'} = $idesc);
+ok($summary->{'hit_start'} = $hstart);
+ok($summary->{'hit_end'} = $hend);
+
 #
 # Test setters
 #

modules/t/proteinFeatureAdaptor.t

@@ -40,7 +40,7 @@ my $pfs = $pfa->fetch_all_by_translation_id(21724);
 
 print_features($pfs);
 
-is(@$pfs, 15, "Found 15 features");
+ok(@$pfs == 15);
 
 sub print_features {
   my $features = shift;
@@ -68,7 +68,9 @@ my $hdes = "Hit description";
 my $idesc = 'interpro description';
 my $interpro_ac = 'interpro accession';
 
-my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
+my $analysis_db = 'test_db';
+
+my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test', -DB => $analysis_db);
 $multi->save('core', 'protein_feature', 'meta_coord');
 
 
@@ -88,6 +90,17 @@ my $f = Bio::EnsEMBL::ProteinFeature->new
    -IDESC       => $idesc,
    -INTERPRO_AC => $interpro_ac);
    
+
+my $summary = $f->summary_as_hash();
+is($summary->{'type'}, $analysis_db);
+is($summary->{'id'}, $hseqname);
+is($summary->{'start'}, $start);
+is($summary->{'end'}, $end);
+is($summary->{'interpro'}, $interpro_ac);
+is($summary->{'description'}, $idesc);
+is($summary->{'hit_start'}, $hstart);
+is($summary->{'hit_end'}, $hend);   
+   
 my $dbID = $pfa->store($f,21724);
 
 ok($dbID, "New object created has dbID");
@@ -106,13 +119,13 @@ is($f_by_dbID->hend, $hend);
 is($f_by_dbID->hseqname, $hseqname);
 is($f_by_dbID->hdescription, $hdes);
 is($f_by_dbID->score, $score);
-is(sprintf("%.6f", $f_by_dbID->percent_id), sprintf("%.6f", $percent_id), "Correct percent_id");
-is(sprintf("%.6f", $f_by_dbID->p_value), sprintf("%.6f", $p_value), "Correct p_value");
+is($f_by_dbID->percent_id, $percent_id);
+is($f_by_dbID->p_value, $p_value);
 
 
 $pfs = $pfa->fetch_all_by_translation_id(21724);
 
-is(@$pfs, 16, "Found 16 features");
+ok(@$pfs == 16);
 
 my @pfs = grep{$_->hdescription() eq $hdes} @$pfs;