[Bioperl-guts-l] [14837] bioperl-live/trunk/Bio/Assembly/Contig.pm: Fixed bug for add_seq: $seq->end now based on ungapped length

[Florent E Angly]

Revision: 14837
Author:   fangly
Date:     2008-08-29 10:36:03 -0400 (Fri, 29 Aug 2008)

Log Message:
-----------
Fixed bug for add_seq: $seq->end now based on ungapped length

Modified Paths:
--------------
    bioperl-live/trunk/Bio/Assembly/Contig.pm

Modified: bioperl-live/trunk/Bio/Assembly/Contig.pm
===================================================================
--- bioperl-live/trunk/Bio/Assembly/Contig.pm	2008-08-29 14:17:13 UTC (rev 14836)
+++ bioperl-live/trunk/Bio/Assembly/Contig.pm	2008-08-29 14:36:03 UTC (rev 14837)
@@ -813,9 +813,9 @@
     $self->{'_consensus_sequence'} = $seq;
 
     $seq->start(1);
+    $seq->end($seq->_ungapped_len);
+
     my $con_len = $seq->length;
-    my $nof_gaps = scalar(@{$self->{'_consensus_gaps'}});
-    $seq->end($con_len-$nof_gaps);
 
     return $con_len;
 }
@@ -1116,7 +1116,8 @@
     }
 
     # Our locatable sequences are always considered to be complete sequences
-    $seq->start(1); $seq->end($seq->length());
+    $seq->start(1);
+    $seq->end($seq->_ungapped_len);
 
     $self->warn("Adding non-nucleotidic sequence ".$seqID)
         if (lc($seq->alphabet) ne 'dna' && lc($seq->alphabet) ne 'rna');