give bioperlflattener a default subroutine to use for fetching featur…

…e labels, which is actually the label-fetching code moved into there from flatfile-to-json.pl
Arabidopsis-Information-Portal · Feb 21, 2012 · c4a6a31 · c4a6a31
1 parent 4150791
commit c4a6a31
Show file tree

Hide file tree

Showing 2 changed files with 34 additions and 15 deletions.
diff --git a/bin/flatfile-to-json.pl b/bin/flatfile-to-json.pl
@@ -222,22 +222,13 @@ =head2 BED-SPECIFIC
     $nclChunk *= 4 if $compress;
 }
 
-#default label-extracting function, for GFF
-my $labelSub = sub {
-    return $_[0]->display_name if ($_[0]->can('display_name') && defined($_[0]->display_name));
-    if ($_[0]->can('attributes')) {
-	return $_[0]->attributes('load_id') if $_[0]->attributes('load_id');
-	return $_[0]->attributes('Alias') if $_[0]->attributes('Alias');
-    }
-    #return eval{$_[0]->primary_tag};
-};
-
 my $idSub = sub {
-    return $_[0]->load_id if ($_[0]->can('load_id') && defined($_[0]->load_id));
+    return $_[0]->load_id if $_[0]->can('load_id') && defined $_[0]->load_id;
     return $_[0]->can('primary_id') ? $_[0]->primary_id : $_[0]->id;
 };
 
 my $stream;
+my $labelStyle = 1;
 if ($gff) {
     my $io = Bio::FeatureIO->new(
         -format  => 'gff',
@@ -252,7 +243,7 @@ =head2 BED-SPECIFIC
         ($thinType ? ("-thin_type" => $thinType) : ()),
         ($thickType ? ("-thick_type" => $thickType) : ()),
        );
-    $labelSub = sub {
+    $labelStyle = sub {
         #label sub for features returned by Bio::FeatureIO::bed
         return $_[0]->name;
     };
@@ -283,7 +274,7 @@ =head2 BED-SPECIFIC
     {
         "idSub"  => $idSub,
         "label"  => ($getLabel || ($autocomplete ne "none"))
-                       ? $labelSub : 0,
+                       ? $labelStyle : 0,
         %style,
     },
     [], [] );
@@ -316,6 +307,9 @@ =head2 BED-SPECIFIC
     },
   );
 
+use Data::Dump;
+ddx( \@arrayrepr_classes );
+
 # build a filtering subroutine for the features
 my $filter = do {
     my @filters;

diff --git a/lib/BioperlFlattener.pm b/lib/BioperlFlattener.pm
@@ -97,7 +97,8 @@ sub new {
     @curMapHeaders = (@curMapHeaders, @$extraHeaders);
 
     if ($style{label}) {
-	push @curFeatMap, $style{label};
+        $style{label} = \&defaultLabelSub unless ref $style{label} eq 'CODE';
+        push @curFeatMap, $style{label};
 	push @curMapHeaders, "name";
     }
 
@@ -156,7 +157,7 @@ sub new {
 
     if ($self->{getLabel} || $self->{getAlias}) {
 	if ($self->{getLabel} && $self->{getAlias}) {
-	    unshift @nameMap, sub {[unique($style{label}->($_[0]),
+	    unshift @nameMap, sub {[unique( ($style{label} || \&defaultLabelSub)->($_[0]),
 					   $_[0]->get_tag_values("Alias"))]};
 	} elsif ($self->{getLabel}) {
 	    unshift @nameMap, sub {[$style{label}->($_[0])]};
@@ -257,4 +258,28 @@ sub unique {
     return (grep(defined($_) && !$saw{$_}++, @_));
 }
 
+
+###################
+
+sub defaultLabelSub {
+    my ( $f ) = @_;
+    if( $f->can('display_name') and defined( my $dn = $f->display_name )) {
+        return $dn
+    }
+    elsif( $f->can('get_tag_values') ) {
+        my $n = eval { ($f->get_tag_values('Name'))[0] };
+        return $n if defined $n;
+
+        my $a = eval { ($f->get_tag_values('Alias'))[0] };
+        return $a if defined $a;
+    }
+    elsif( $f->can('attributes') ) {
+	return $f->attributes('load_id') if defined $f->attributes('load_id');
+	return $f->attributes('Name')    if defined $f->attributes('Name');
+	return $f->attributes('Alias')   if defined $f->attributes('Alias');
+    }
+    return;
+}
+
+
 1;