From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 28 Sep 2013 03:40:50 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2a63b447bec39d34eea1b1bbd7504761ca603a8e;p=jalview.git

inprogress
---

diff --git a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb
index 5d03737..e9d0bf0 100644
--- a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb
@@ -388,8 +388,10 @@ module Evoruby
                   from = 1
                 end
                 to = to + ADD_TO_CLOSE_PAIRS
-                if to > in_msa.get_length
-                  to = in_msa.get_length
+                temp_seqs = in_msa.find_by_name_start( seq_name, true )
+                temp_seq = in_msa.get_sequence( temp_seqs[ 0 ] )
+                if to >  temp_seq.get_length
+                  to =  temp_seq.get_length
                 end
               end