Made name a private attribute, added a getter/setter for it and also …

…created two aliases for name: info and seqname.
cjfields · Apr 1, 2011 · 8db42eb · 8db42eb
1 parent d0a6cda
commit 8db42eb
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 11 deletions.
diff --git a/lib/Bio/SeqFeature/Lite.pm b/lib/Bio/SeqFeature/Lite.pm
@@ -3,9 +3,7 @@ class Bio::SeqFeature::Lite {
 # use base qw(Bio::Root::Root Bio::SeqFeatureI Bio::LocationI Bio::SeqI Bio::RangeI);
 
 # alias for functions    
-# *stop        = \&end;
-# *info        = \&name;
-# *seqname     = \&name;
+
 # *exons       = *sub_SeqFeature = *merged_segments = \&segments;
 # *get_all_SeqFeatures = *get_SeqFeatures = \&segments;
 # *method         = \&primary_tag;
@@ -65,7 +63,7 @@ has $!phase is rw;
 has $!seq is rw;
 has $!class is rw;
 
-has $.name is rw;
+has $!name is rw;
 has $.desc is rw;
 has $!subtype is rw;
 
@@ -207,12 +205,15 @@ method primary_tag($value?) {
     }
     return $!type;
 }
-# method name            {
-#   my $self = shift;
-#   my $d    = self->{name};
-#   self->{name} = shift if @_;
-#   $d;
-# }
+method name($value?)            {
+    my $d    = $!name;
+    $!name = $value if $value;
+    $d;
+}
+#alias for name
+method info($value?) { self.name($value);}
+method seqname($value?) { self.name($value);}
+
 
 method seq_id($value?){
    my $d    = $.ref;

diff --git a/t/SeqFeature/Lite.t b/t/SeqFeature/Lite.t
@@ -4,7 +4,7 @@ BEGIN {
 }
 
 use Test;
-plan 66;
+plan 75;
 eval_lives_ok 'use Bio::SeqFeature::Lite', 'Can use Bio::SeqFeature::Lite';
 
 use Bio::SeqFeature::Lite;
@@ -24,6 +24,9 @@ is($lite.stop,2000,'correct stop');
 is($lite.type,'transcript','Got correct transcript');
 is($lite.desc,'an enzyme inhibitor','Got desc');
 is($lite.display_name,"alpha-1 antitrypsin");
+is($lite.name,'alpha-1 antitrypsin');
+is($lite.seqname,'alpha-1 antitrypsin');
+is($lite.info,'alpha-1 antitrypsin');
 is($lite.display_id,"alpha-1 antitrypsin");
 is($lite.dna,'');
 is($lite.start_pos_type,"EXACT");
@@ -50,6 +53,7 @@ is($lite.length,1001);
 is($lite.type,'gapped_alignment');
 is($lite.desc,Any);
 is($lite.display_name,"ABC-3");
+is($lite.name,'ABC-3');
 is($lite.display_id,"ABC-3");
 is($lite.dna,'');
 is($lite.start_pos_type,"EXACT");
@@ -92,6 +96,7 @@ $lite  = Bio::SeqFeature::Lite.new(segments=>[$e1,$e2,$e3],type=>'gene',seq_id=>
 is($e1.type,'exon');
 is($e2.type,'exon');
 is($e3.type,'exon');
+is($e3.name,Any);
 
 is($lite.start,1,'correct start');
 is($lite.stop,500,'correct stop');
@@ -102,6 +107,7 @@ is($lite.high(),'500');
 is($lite.location_string,'1..100,150..200,300..500');
 is($lite.score,Any);
 is($lite.length,500);
+is($lite.name,Any);
 
 #they should still keep their type as 'exon'
 for ($lite.segments) -> $x {