From 335364e6d5ae00e62a2d33514eaded969cd41e78 Mon Sep 17 00:00:00 2001
From: jason <jason@bioperl.org>
Date: Fri, 22 Jan 2010 19:14:12 +0000
Subject: [PATCH] add an alphabet init arg and get/setter

svn path=/bioperl-live/trunk/; revision=16737
---
 Bio/AlignIO.pm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/Bio/AlignIO.pm b/Bio/AlignIO.pm
index 6fcbde71a..089d94e8e 100644
--- a/Bio/AlignIO.pm
+++ b/Bio/AlignIO.pm
@@ -380,9 +380,10 @@ sub fh {
 
 sub _initialize {
   my($self,@args) = @_;
-  my ($flat) = $self->_rearrange([qw(DISPLAYNAME_FLAT)],
+  my ($flat,$alphabet) = $self->_rearrange([qw(DISPLAYNAME_FLAT ALPHABET)],
 				 @args);
   $self->force_displayname_flat($flat) if defined $flat;
+  $self->alphabet($alphabet);
   $self->_initialize_io(@args);
   1;
 }
@@ -522,4 +523,27 @@ sub force_displayname_flat{
     return $self->{'_force_displayname_flat'} || 0;
 }
 
+=head2 alphabet
+
+ Title   : alphabet
+ Usage   : $obj->alphabet($newval)
+ Function: Get/Set alphabet for purpose of passing to Bio::LocatableSeq creation
+ Example : $obj->alphabet('dna');
+ Returns : value of alphabet (a scalar)
+ Args    : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub alphabet {
+    my $self = shift;
+    my $value = shift;
+    if ( defined $value ) {
+        $self->throw("Invalid alphabet $value") unless $value eq 'rna' || $value eq 'protein' || $value eq 'dna';
+        $self->{'_alphabet'} = $value;
+    }
+    return $self->{'_alphabet'};
+}
+
+
 1;
-- 
2.11.4.GIT