From 3c7d4cf5ef1331e2fad9c617c228486badf6f6a0 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 3 Jun 2022 14:15:04 +0100
Subject: [PATCH] =?utf8?q?JAL-1953=20JAL-2889=20don=E2=80=99t=20read=20addit?=
 =?utf8?q?ional=20lines=20when=20looking=20for=20phyloxml=20header?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
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---
 src/jalview/io/IdentifyFile.java |    6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

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;
-- 
1.7.10.2