From 034e87858efb904a11646568bb5626863d42e0eb Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Thu, 21 Dec 2017 16:25:55 +0000
Subject: [PATCH] JAL-281 added file identify criteria for PhyloXML and Nexus

---
 src/jalview/io/IdentifyFile.java |   19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index ff959b0..a4d6e8b 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -334,15 +334,26 @@ public class IdentifyFile
           reply = FileFormat.Phylip;
           break;
         }
-        else
+        else if (!lineswereskipped && looksLikeJnetData(data))
         {
-          if (!lineswereskipped && looksLikeJnetData(data))
-          {
             reply = FileFormat.Jnet;
             break;
+
+        }
+        else // phylogenetic file?
+        {
+          if (source.nextLine().startsWith("<phyloxml"))
+          {
+            reply = FileFormat.PhyloXML;
+            break;
           }
+          else if (( ( data.startsWith( "nexus" ) ) || ( data.startsWith( "#nexus" ) )
+                || ( data.startsWith( "# nexus" ) ) || ( data.startsWith( "begin" ) ) ) ) 
+          {
+          reply = FileFormat.Nexus;      
+           break;
+        }
         }
-
         lineswereskipped = true; // this means there was some junk before any
         // key file signature
       }
-- 
1.7.10.2