From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 28 Nov 2013 00:05:53 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9adbaa1f8ed31fbec2e285b694ac42a437d255a8;p=jalview.git

inprogress
---

diff --git a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
index ffabc45..e5bb182 100644
--- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
@@ -41,6 +41,9 @@ module Evoruby
     NORMALIZED_IDS_MAP_SUFFIX           = ".nim"
     PROTEINS_LIST_FILE_SEPARATOR        = "\t"
 
+    def initialize()
+      @file_to_msa = Hash.new
+    end
 
     def run()
 
@@ -464,8 +467,6 @@ module Evoruby
           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
         end
       end
-
-
     end
 
 
@@ -537,6 +538,10 @@ module Evoruby
     end
 
     def read_fasta_file( input )
+      if @file_to_msa.has_key?( input )
+        return @file_to_msa[ input ]
+      end
+
       f = MsaFactory.new()
       msa = nil
       begin
@@ -544,6 +549,9 @@ module Evoruby
       rescue Exception => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
       end
+      if @file_to_msa.size < 500
+        @file_to_msa[ input ] = msa
+      end
       msa
     end