Merge branch 'master' into reorganization_2.x

Make sure removed repos aren't carried over.
bioperl · Nov 29, 2011 · 6218096 · 6218096
2 parents 5b2a77b + 245f557
commit 6218096
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Showing 50 changed files with 3,145 additions and 4,939 deletions.
diff --git a/Bio/AlignIO.pm b/Bio/AlignIO.pm
@@ -375,6 +375,20 @@ sub fh {
   return $s;
 }
 
+
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the alignment format
+ Returns : alignment format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 # _initialize is where the heavy stuff will happen when new is called
 
 sub _initialize {

diff --git a/Bio/Assembly/IO.pm b/Bio/Assembly/IO.pm
@@ -141,6 +141,19 @@ sub new {
 }
 
 
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the assembly format
+ Returns : assembly format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 # _initialize is chained for all SeqIO classes
 sub _initialize {
     my($self, @args) = @_;

diff --git a/Bio/Assembly/IO/ace.pm b/Bio/Assembly/IO/ace.pm
@@ -814,25 +814,15 @@ sub write_footer {
 =head2 variant
 
  Title   : variant
- Usage   : $format  = $obj->variant();
+ Usage   : $variant = $ass_io->variant();
  Function: Get and set method for the assembly variant. This is important since
            not all assemblers respect the reference ACE format.
  Returns : string
  Args    : string: 'consed' (default) or '454'
 
 =cut
 
-sub variant {
-    my ($self, $enc) = @_;
-    if (defined $enc) {
-        $enc = lc $enc;
-        if (not exists $variant{$enc}) {
-            $self->throw('Not a valid ACE variant format');
-        }
-        $self->{variant} = $enc;
-    }
-    return $self->{variant};
-}
+# variant() method inherited from Bio::Root::IO
 
 
 =head2 _write_read

diff --git a/Bio/ClusterIO.pm b/Bio/ClusterIO.pm
@@ -186,6 +186,18 @@ sub new {
     }
 }
 
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the cluster format
+ Returns : cluster format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
 
 # _initialize is chained for all ClusterIO classes