X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=dae8f82c53e85a616edf484f5de098ce0d84df06;hb=6897b5d861a256c94b23167254c3f4e2ab6acb3a;hp=4fb2516873b74e99d53dfa747ac56565da6591aa;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 4fb2516..dae8f82 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  *
  * This file is part of Jalview.
  *
@@ -30,6 +30,8 @@ import java.io.IOException;
  */
 public class IdentifyFile
 {
+  public static final String GFF3File = "GFF v2 or v3";
+
   /**
    * Identify a datasource's file content.
    *
@@ -96,7 +98,7 @@ public class IdentifyFile
       }
       while ((data = source.nextLine()) != null)
       {
-        length += data.length();
+        length += data.trim().length();
         if (!lineswereskipped)
         {
           for (int i = 0; !isBinary && i < data.length(); i++)
@@ -130,26 +132,50 @@ public class IdentifyFile
         }
         data = data.toUpperCase();
 
-        if ((data.indexOf("# STOCKHOLM") > -1))
+        if (data.startsWith("##GFF-VERSION"))
         {
-          reply = "STH";
-
+          reply = GFF3File;
           break;
         }
-        // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
-        if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+        if (data.indexOf("# STOCKHOLM") > -1)
         {
-          reply = "HTML";
+          reply = "STH";
           break;
         }
 
-        if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+        if ((data.indexOf("<") > -1)) // possible Markup Language data i.e HTML,
+                                      // RNAML, XML
         {
-          reply = "RNAML";
+          boolean identified = false;
+          do
+          {
+            if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+            {
+              reply = HtmlFile.FILE_DESC;
+              identified = true;
+              break;
+            }
 
-          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;
+         break;
+         }
         if ((data.length() < 1) || (data.indexOf("#") == 0))
         {
           lineswereskipped = true;