From a56dab3cea2628b469fdc1818b067e851f6101d6 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Thu, 18 Jan 2018 14:23:05 +0000
Subject: [PATCH 1/1] JAL-2805 disabled Nexus file identification(as its
 parser is unreliable)

---
 src/jalview/io/FileFormat.java   |   61 +++++++++++++++++++-------------------
 src/jalview/io/IdentifyFile.java |   18 ++++++-----
 2 files changed, 40 insertions(+), 39 deletions(-)

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 3b54f38..ceb72be 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -22,7 +22,6 @@ package jalview.io;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
-import jalview.ext.forester.io.NexusFile;
 import jalview.ext.forester.io.PhyloXmlFile;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
@@ -376,36 +375,36 @@ public enum FileFormat implements FileFormatI
       return false;
     }
   },
-  Nexus("Nexus", "nex,nexus,nx,tre", true, true)
-  {
-
-    @Override
-    public AlignmentFileReaderI getReader(FileParse source)
-            throws IOException
-    {
-      return new NexusFile(source);
-    }
-
-    @Override
-    public AlignmentFileWriterI getWriter(AlignmentI al)
-    {
-      // handle within Aptx?
-      return null;
-    }
-
-    @Override
-    public boolean isTextFormat()
-    {
-      return true;
-    }
-
-    @Override
-    public boolean isTreeFile()
-    {
-      return true;
-    }
-
-  },
+  // Nexus("Nexus", "nex,nexus,nx,tre", true, true)
+  // {
+  //
+  // @Override
+  // public AlignmentFileReaderI getReader(FileParse source)
+  // throws IOException
+  // {
+  // return new NexusFile(source);
+  // }
+  //
+  // @Override
+  // public AlignmentFileWriterI getWriter(AlignmentI al)
+  // {
+  // // handle within Aptx?
+  // return null;
+  // }
+  //
+  // @Override
+  // public boolean isTextFormat()
+  // {
+  // return true;
+  // }
+  //
+  // @Override
+  // public boolean isTreeFile()
+  // {
+  // return true;
+  // }
+  //
+  // },
   PhyloXML("PhyloXML", "phyloxml,phylo.xml,pxml", true, true)
   {
 
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index a7ed592..1d0a3d2 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -350,14 +350,16 @@ public class IdentifyFile
             reply = FileFormat.PhyloXML;
             break;
           }
-          else if (((identifier.startsWith("nexus"))
-                  || (identifier.startsWith("#nexus"))
-                  || (identifier.startsWith("# nexus"))
-                  || (identifier.startsWith("begin"))))
-          {
-          reply = FileFormat.Nexus;      
-           break;
-        }
+          // commented out, nexus parser is troublesome
+
+          // else if (((identifier.startsWith("nexus"))
+          // || (identifier.startsWith("#nexus"))
+          // || (identifier.startsWith("# nexus"))
+          // || (identifier.startsWith("begin"))))
+          // {
+          // reply = FileFormat.Nexus;
+          // break;
+          // }
         }
         lineswereskipped = true; // this means there was some junk before any
         // key file signature
-- 
1.7.10.2