From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 19 Dec 2017 14:10:26 +0000 (+0000)
Subject: JAL-281 added phyloxml and nexus to jalview fileformats
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f4171449d8dffb595a7e92a6336ede141edc3871;p=jalview.git

JAL-281 added phyloxml and nexus to jalview fileformats
---

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 4b33dbf..718370a 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -373,8 +373,57 @@ public enum FileFormat implements FileFormatI
     {
       return false;
     }
-  };
+  },
+  Nexus("Nexus", "nex,nexus,nx,tre", true, true)
+  {
+
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      // TODO Auto-generated method stub
+      return null;
+    }
 
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      // TODO Auto-generated method stub
+      return null;
+    }
+
+    @Override
+    public boolean isTextFormat()
+    {
+      return true;
+    }
+
+  },
+  PhyloXML("PhyloXML", "phyloxml,phylo.xml,pxml", true, true)
+  {
+
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      // TODO Auto-generated method stub
+      return null;
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      // TODO Auto-generated method stub
+      return null;
+    }
+
+    @Override
+    public boolean isTextFormat()
+    {
+      return true;
+    }
+
+  };
   private boolean writable;
 
   private boolean readable;