X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=46899da400da56c3b638fc245d130e16d64ce532;hb=cd5b2de469fb4c09242955cb4b74279e2da348d6;hp=7293ac6927a9310c8dc49e54f3ffca815efeb765;hpb=4932106f045349290d58ab38d216dff31fd9afce;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 7293ac6..46899da 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -40,6 +40,7 @@ public class IdentifyFile
    */
   public String Identify(String file, String protocol)
   {
+    String emessage = "UNIDENTIFIED FILE PARSING ERROR";
     FileParse parser = null;
     try {
       parser = new FileParse(file, protocol);
@@ -49,10 +50,11 @@ public class IdentifyFile
     } catch (Exception e) {
       System.err.println("Error whilst identifying");
       e.printStackTrace(System.err);
+      emessage = e.getMessage();
     }
     if (parser!=null)
       return parser.errormessage;
-    return "UNIDENTIFIED FILE PARSING ERROR";
+    return emessage;
   }
   public String Identify(FileParse source) {
     return Identify(source, true); // preserves original behaviour prior to version 2.3
@@ -70,6 +72,10 @@ public class IdentifyFile
     boolean lineswereskipped=false;
     boolean isBinary = false; // true if length is non-zero and non-printable characters are encountered
     try {
+      if (!closeSource)
+      {
+        source.mark();
+      }
       while ( (data = source.nextLine()) != null)
       {
         length+=data.length();
@@ -165,6 +171,7 @@ public class IdentifyFile
             else
             {
                 reply = "FASTA";
+                // TODO : AMSA File is indicated if there is annotation in the FASTA file - but FASTA will automatically generate this at the mo.
             }
           }
           break;