added 2 new attributes in protein and dna alignFeatures to get the name of the...

added 2 new attributes in protein and dna alignFeatures to get the name of the external database and the displayable name

modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm

@@ -58,10 +58,14 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
 sub _tables {
   my $self = shift;
 
-  return ['dna_align_feature', 'daf'];
+  return (['dna_align_feature', 'daf'],['external_db','exdb']);
 }
 
 
+sub _left_join{
+    return (['external_db',"exdb.external_db_id = daf.external_db_id"]);
+}
+
 =head2 _columns
 
   Args       : none
@@ -95,7 +99,9 @@ sub _columns {
             daf.score
             daf.external_db_id
             daf.hcoverage
-	    daf.external_data);
+	    daf.external_data
+	    exdb.db_name
+	    exdb.db_display_name);
 }
 
 
@@ -326,13 +332,13 @@ sub _objs_from_sth {
   my($dna_align_feature_id, $seq_region_id, $analysis_id, $seq_region_start,
      $seq_region_end, $seq_region_strand, $hit_start, $hit_end, $hit_name,
      $hit_strand, $cigar_line, $evalue, $perc_ident, $score,
-     $external_db_id, $hcoverage, $extra_data );
+     $external_db_id, $hcoverage, $extra_data, $external_db_name, $external_display_db_name );
 
   $sth->bind_columns(
     \$dna_align_feature_id, \$seq_region_id, \$analysis_id, \$seq_region_start,
     \$seq_region_end, \$seq_region_strand, \$hit_start, \$hit_end, \$hit_name,
     \$hit_strand, \$cigar_line, \$evalue, \$perc_ident, \$score,
-    \$external_db_id, \$hcoverage, \$extra_data );
+    \$external_db_id, \$hcoverage, \$extra_data, \$external_db_name, \$external_display_db_name );
 
 
   my $asm_cs;
@@ -453,6 +459,8 @@ sub _objs_from_sth {
                                     'external_db_id' => $external_db_id,
                                     'hcoverage'      => $hcoverage,
 				    'extra_data'     => $extra_data ? $self->get_dumped_data($extra_data) : '',
+				    'dbname'         => $external_db_name,
+				    'db_display_name' => $external_display_db_name
                                   } ) );
 
   }

modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm

@@ -190,13 +190,13 @@ sub _objs_from_sth {
   my ($protein_align_feature_id, $seq_region_id, $seq_region_start,
       $seq_region_end, $analysis_id, $seq_region_strand, $hit_start,
       $hit_end, $hit_name, $cigar_line, $evalue, $perc_ident, $score,
-      $external_db_id, $hcoverage );
+      $external_db_id, $hcoverage, $external_db_name, $external_display_db_name );
 
   $sth->bind_columns(\$protein_align_feature_id, \$seq_region_id,
            \$seq_region_start,\$seq_region_end, \$analysis_id,
            \$seq_region_strand, \$hit_start,\$hit_end, \$hit_name,
            \$cigar_line, \$evalue, \$perc_ident, \$score,
-           \$external_db_id, \$hcoverage );
+           \$external_db_id, \$hcoverage, \$external_db_name, \$external_display_db_name );
 
   my $asm_cs;
   my $cmp_cs;
@@ -316,7 +316,9 @@ sub _objs_from_sth {
           'adaptor'      => $self,
           'dbID'           => $protein_align_feature_id,
           'external_db_id' => $external_db_id,
-          'hcoverage'      => $hcoverage
+          'hcoverage'      => $hcoverage,
+	  'dbname'         => $external_db_name,
+	  'db_display_name' => $external_display_db_name
         } ) );
 
   }
@@ -329,7 +331,7 @@ sub _objs_from_sth {
 sub _tables {
   my $self = shift;
 
-  return ['protein_align_feature', 'paf'];
+  return (['protein_align_feature', 'paf'], ['external_db','exdb']);
 }
 
 
@@ -351,7 +353,13 @@ sub _columns {
              paf.perc_ident
              paf.score
              paf.external_db_id
-             paf.hcoverage );
+             paf.hcoverage
+	     exdb.db_name
+	     exdb.db_display_name);
+}
+
+sub _left_join{
+    return (['external_db',"exdb.external_db_id = paf.external_db_id"]);
 }
 
 =head2 list_dbIDs

modules/Bio/EnsEMBL/FeaturePair.pm

@@ -119,10 +119,10 @@ sub new {
   my $self = $class->SUPER::new(@_);
 
   my ($hstart,$hend,$hstrand,$percent_id,$score, $species, $hspecies,
-      $p_value, $hseqname, $f1,$f2, $coverage, $hcoverage, $group_id,$level_id, $external_db_id, $extra_data) =
+      $p_value, $hseqname, $f1,$f2, $coverage, $hcoverage, $group_id,$level_id, $external_db_id, $extra_data, $external_db_name, $external_display_db_name) =
     rearrange(['HSTART','HEND','HSTRAND','PERCENT_ID','SCORE','SPECIES',
                'HSPECIES', 'P_VALUE', 'HSEQNAME', 'FEATURE1','FEATURE2',
-               'COVERAGE', 'HCOVERAGE', 'GROUP_ID','LEVEL_ID', 'EXTERNAL_DB_ID', 'EXTRA_DATA'], @_);
+               'COVERAGE', 'HCOVERAGE', 'GROUP_ID','LEVEL_ID', 'EXTERNAL_DB_ID', 'EXTRA_DATA', 'DBNAME', 'DB_DISPLAY_NAME'], @_);
 
   if(defined($hstart) && defined($hend) && ($hend < $hstart)) {
     throw('HSTART must be less than or equal to HEND');
@@ -147,6 +147,8 @@ sub new {
   $self->{'level_id'}   = $level_id;
   $self->{'external_db_id'} = $external_db_id;
   $self->{'extra_data'} = $extra_data;
+  $self->{'dbname'} = $external_db_name;
+  $self->{'db_display_name'} = $external_display_db_name;
 
   #
   # Feature1 and Feature2 arg handling for backwards compatibility
@@ -542,6 +544,43 @@ sub external_db_id {
 }
 
 
+=head2 dbname
+
+  Arg [1]    : string  $external_db_name (optional)
+  Example    : $ex_db_name = $fp->dbname();
+  Description: Getter/Setter for the external_db_name attribute, name of external database
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub db_name {
+  my $self = shift;
+  $self->{'dbname'} = shift if(@_);
+  return $self->{'dbname'};
+}
+
+=head2 db_display_name
+
+  Arg [1]    : string  $db_display_name (optional)
+  Example    : $ex_db_display_name = $fp->db_display_name();
+  Description: Getter/Setter for the db_display_name attribute 
+               The preferred display name for the external database. 
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub db_display_name {
+  my $self = shift;
+  $self->{'db_display_name'} = shift if(@_);
+  return $self->{'db_display_name'};
+}
+
 
 
 =head2 p_value