From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 3 Jun 2022 13:15:04 +0000 (+0100)
Subject: JAL-1953 JAL-2889 don’t read additional lines when looking for phyloxml header
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3c7d4cf5ef1331e2fad9c617c228486badf6f6a0;p=jalview.git

JAL-1953 JAL-2889 don’t read additional lines when looking for phyloxml header
---

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index d2c586a..cab3e60 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -394,10 +394,8 @@ public class IdentifyFile
         }
         else // phylogenetic file
         {
-          String identifier = data.toLowerCase();
-          String secondLine = source.nextLine().toLowerCase();
-          if (identifier.startsWith("<phyloxml")
-                  || secondLine.startsWith("<phyloxml"))
+          // may also have a <xml header before hand, probably need to check it 
+          if (data.toLowerCase(Locale.ROOT).startsWith("<phyloxml"))
           {
             reply = FileFormat.PhyloXML;
             break;