X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=035c1fa8fbbd3b0a0321f1003a31211934683704;hb=7abcbfb6619828a810ed1a9dddd870f70bf8bcd1;hp=0556e76a20248be0a0ad19fc9e92eaeb4a255689;hpb=35ce4609cc8a776b1d85a1f2c2c70aaa106c1a3b;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 0556e76..035c1fa 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -98,12 +98,15 @@ 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();
       }
+      boolean aaIndexHeaderRead = false;
+
       while ((data = source.nextLine()) != null)
       {
         bytesRead += data.length();
@@ -141,6 +144,20 @@ public class IdentifyFile
         }
         data = data.toUpperCase();
 
+        if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
+        {
+          reply = FileFormat.ScoreMatrix;
+          break;
+        }
+        if (data.startsWith("H ") && !aaIndexHeaderRead)
+        {
+          aaIndexHeaderRead = true;
+        }
+        if (data.startsWith("D ") && aaIndexHeaderRead)
+        {
+          reply = FileFormat.ScoreMatrix;
+          break;
+        }
         if (data.startsWith("##GFF-VERSION"))
         {
           // GFF - possibly embedded in a Jalview features file!