X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=4b6f8e40a9b0da997593a5f088033967ebfaf60d;hb=ff8c06845590fd9fd423aa59809dcce9610ab295;hp=72a1155d0630435c2dd1bb2de8ebcad20a77b655;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 72a1155..4b6f8e4 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -72,7 +72,7 @@ public class IdentifyFile
     // preserves original behaviour prior to version 2.3
   }
 
-  public FileFormatI identify(AlignmentFileI file, boolean closeSource)
+  public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource)
           throws IOException
   {
     FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
@@ -141,6 +141,11 @@ public class IdentifyFile
         }
         data = data.toUpperCase();
 
+        if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
+        {
+          reply = FileFormat.ScoreMatrix;
+          break;
+        }
         if (data.startsWith("##GFF-VERSION"))
         {
           // GFF - possibly embedded in a Jalview features file!