From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 9 Jul 2015 12:57:12 +0000 (+0100)
Subject: JAL-1806 bug fix to loop through the entire data file to check for a html or rnaml... 
X-Git-Tag: Release_2_10_0~580
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a38c5f242641005b952e446b2ece5aa1fc9e1028;p=jalview.git

JAL-1806 bug fix to loop through the entire data file to check for a html or rnaml tag when the data file starts with <
---

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 4c83ac1..dae8f82 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -142,19 +142,35 @@ public class IdentifyFile
           reply = "STH";
           break;
         }
-        // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
-        if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
-        {
-          reply = HtmlFile.FILE_DESC;
-          break;
-        }
 
-        if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+        if ((data.indexOf("<") > -1)) // possible Markup Language data i.e HTML,
+                                      // RNAML, XML
         {
-          reply = "RNAML";
-          break;
+          boolean identified = false;
+          do
+          {
+            if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+            {
+              reply = HtmlFile.FILE_DESC;
+              identified = true;
+              break;
+            }
+
+            if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+            {
+              reply = "RNAML";
+              identified = true;
+              break;
+            }
+          } while ((data = source.nextLine()) != null);
+
+          if (identified)
+          {
+            break;
+          }
         }
 
+
          if (data.indexOf("{\"") > -1)
          {
          reply = JSONFile.FILE_DESC;