[Bioperl-guts-l] [15622] bioperl-live/trunk/Bio/SimpleAlign.pm: uniq_seq: removed commented print STDERR lines

Mark Allen Jensen maj at dev.open-bio.org
Thu Apr 2 00:20:36 EDT 2009


Revision: 15622
Author:   maj
Date:     2009-04-02 00:20:36 -0400 (Thu, 02 Apr 2009)

Log Message:
-----------
uniq_seq: removed commented print STDERR lines
changed POD to reflect the correct way to obtain
ST output. 
See the thread:
http://lists.open-bio.org/pipermail/bioperl-l/2009-April/029691.html

Modified Paths:
--------------
    bioperl-live/trunk/Bio/SimpleAlign.pm

Modified: bioperl-live/trunk/Bio/SimpleAlign.pm
===================================================================
--- bioperl-live/trunk/Bio/SimpleAlign.pm	2009-04-01 17:25:18 UTC (rev 15621)
+++ bioperl-live/trunk/Bio/SimpleAlign.pm	2009-04-02 04:20:36 UTC (rev 15622)
@@ -620,7 +620,8 @@
              differences.
  Function  : Make a new alignment of unique sequence types (STs)
  Returns   : 1. a new Bio::SimpleAlign object (all sequences renamed as "ST")
-             2. ST of each sequence in STDERR
+             2. if $aln->verbose > 0, ST of each sequence is sent to 
+                STDERR
  Argument  : None
 
 =cut
@@ -684,12 +685,10 @@
 					 -end  =>$end
 					 );
 	$aln->add_seq($new);
-#	print STDERR "ST".$order{$str}, "\t=>";
 	foreach (@{$member{$str}}) {
         $self->debug($_->id(), "\t", "ST", $order{$str}, "\n");
+        }
     }
-#	print STDERR "\n";
-    }
     return $aln;
 }
 




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