protein feature converters

modules/Bio/EnsEMBL/Utils/Converter/bio_ens.pm

@@ -81,12 +81,14 @@ sub _initialize {
     my ($dbadaptor, 
         $dbdriver, $dbhost, $dbport, $dbuser, $dbpass, $dbname,
         $analysis, $analysis_dbid, $analysis_logic_name, 
-        $contig, $contig_dbid, $contig_name) =
+        $contig, $contig_dbid, $contig_name, 
+        $translation_id) =
         
         $self->_rearrange([qw(DBADAPTOR 
             DBDRIVER DBHOST DBPORT DBUSER DBPASS DBNAME
             ANALYSIS ANALYSIS_DBID ANALYSIS_LOGIC_NAME 
-            CONTIG CONTIG_DBID CONTIG_NAME)], @args);
+            CONTIG CONTIG_DBID CONTIG_NAME
+            TRANSLATION_ID)], @args);
 
     
     if(defined $dbadaptor){

modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm

@@ -56,7 +56,9 @@ use Bio::EnsEMBL::Utils::Converter::bio_ens;
 sub _initialize {
     my ($self, @args) = @_;
     $self->SUPER::_initialize(@args);
-
+    my ($translation_id) = $self->_rearrange([qw(TRANSLATION_ID)], @args);
+    $self->translation_id($translation_id);
+    
     # internal converter for seqFeature
     $self->{_bio_ens_seqFeature} = new Bio::EnsEMBL::Utils::Converter (
         -in => 'Bio::SeqFeature::Generic',
@@ -104,6 +106,7 @@ sub _convert_single_to_proteinFeature {
         -feature1 => $featurePair->feature1,
         -feature2 => $featurePair->feature2
     );
+    $proteinFeature->seqname($self->translation_id);
     return $proteinFeature;
 }
 
@@ -155,5 +158,10 @@ sub _create_consensus{
     return $consensus;
 }
 
+sub translation_id {
+    my ($self, $arg) = @_;
+    return $self->{_translation_id} = $arg if(defined($arg));
+    return $self->{_translation_id};
+}
         
 1;

modules/Bio/EnsEMBL/Utils/Converter/bio_ens_seqFeature.pm

@@ -64,16 +64,38 @@ sub _convert_single {
         $self->warn("No seq_id value. EnsEMBL SeqFeature will validate it");
         $seq_id = 'Unknown';
     }
-        
+    
+    # Debated issue here. There are p_value and percent_id in EnsEMBL API and DB
+    # schema, but not in bioperl. If in bioperl there are tags called p_value or
+    # percent_id, then the values are passed, otherwise set the default 1.
+    #
+    # the problem arise when I try to converter the seqfeature for tmhmm to 
+    # EnsEMBL seqFeature.
+    # -- Juguang, 11 July '03
+    my $score = $in->score || 1;
+    my $percent_id;
+    if($in->has_tag('percent_id')){
+        ($percent_id) = @{$in->get_tag_values('percent_id')};
+    }else{
+        $percent_id ||= 1;
+    }
+    my $p_value;
+    if($in->has_tag('p_value')){
+        ($p_value) = @{$in->get_tag_values('p_value')};
+    }else{
+        $p_value ||= 1;
+    }
     my $ens_seqFeature;
     my @args = (
         -start => $in->start,
         -end => $in->end,
         -strand => $in->strand,
-        -score => $in->score,
+        -score => $score,
         -analysis => $self->analysis,
         -source_tag => $in->source_tag,
-        -seqname => $seq_id
+        -seqname => $seq_id,
+        -percent_id => $percent_id,
+        -p_value => $p_value
     );
 
     my $output_module = $self->out;