From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 22 Jan 2014 00:38:38 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5537afb612b104805a43dadf6f699dcf737aab42;hp=909718c34690db186df56680f8213727612d198f;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 45fa3ad..f16c57b 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -1711,7 +1711,7 @@ public class PhylogenyMethods {
             return my_s.indexOf( my_query ) >= 0;
         }
         else {
-            return Pattern.compile( "\\b" + my_query  + "\\b").matcher( my_s ).find();
+            return Pattern.compile( "(\\b|_)" + Pattern.quote(my_query)  + "(\\b|_)").matcher( my_s ).find();
         }
     }