From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 9 Jan 2018 11:18:07 +0000 (+0000)
Subject: JAL-2805 added nexus specific parser settings
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=324c8f8f1d1090664f6f49e86825c8543a55f08b;p=jalview.git

JAL-2805 added nexus specific parser settings
---

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index 0337829..f8347bd 100644
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -74,11 +74,6 @@ public final class AptxInit
   private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
           .getTaxonomyExtraction();
 
-
-
-
-
-
   public static TreeFrameI createInstanceFromCalculation(
           final TreeBuilder calculatedTree)
   {
diff --git a/src/jalview/ext/forester/io/ForesterParser.java b/src/jalview/ext/forester/io/ForesterParser.java
index a6d7831..4cd84b1 100644
--- a/src/jalview/ext/forester/io/ForesterParser.java
+++ b/src/jalview/ext/forester/io/ForesterParser.java
@@ -1,5 +1,6 @@
 package jalview.ext.forester.io;
 
+import jalview.ext.archaeopteryx.AptxInit;
 import jalview.ext.archaeopteryx.Tree;
 import jalview.ext.treeviewer.TreeI;
 import jalview.ext.treeviewer.TreeParserI;
@@ -30,6 +31,10 @@ public class ForesterParser
   public static ForesterParser createNexusParser(File file)
           throws PhylogenyParserException, IOException
   {
+    NexusPhylogeniesParser nxParser = new NexusPhylogeniesParser();
+    nxParser.setReplaceUnderscores(
+            AptxInit.APTX_CONFIG.isReplaceUnderscoresInNhParsing());
+    nxParser.setIgnoreQuotes(false);
     return new ForesterParser(new NexusPhylogeniesParser(), file);
   }