From ea402c168ecf73c1824d023a91331494939f2641 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 12 Jul 2012 06:55:20 +0000 Subject: [PATCH] in progress --- forester/java/src/org/forester/msa/MsaCompactor.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) 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 opts = new ArrayList(); - 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 ); } -- 1.7.10.2