From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 12 Jul 2012 06:55:20 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ea402c168ecf73c1824d023a91331494939f2641;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/msa/MsaCompactor.java b/forester/java/src/org/forester/msa/MsaCompactor.java
index 9529b82..a66c09b 100644
--- a/forester/java/src/org/forester/msa/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa/MsaCompactor.java
@@ -82,9 +82,9 @@ public class MsaCompactor {
     final private void mafft() throws IOException, InterruptedException {
         final MsaInferrer mafft = Mafft.createInstance( "/home/czmasek/bin/mafft" );
         final List<String> opts = new ArrayList<String>();
-        opts.add( "--maxiterate" );
-        opts.add( "1000" );
-        opts.add( "--localpair" );
+        // opts.add( "--maxiterate" );
+        // opts.add( "1000" );
+        // opts.add( "--localpair" );
         opts.add( "--quiet" );
         _msa = mafft.infer( _msa.asSequenceList(), opts );
     }