JAL-2416 parse score matrices in either NCBI or AAindex format

[jalview.git] / src / jalview / io / IdentifyFile.java

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 4b6f8e4..035c1fa 100755 (executable)
--- 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();
@@ -146,6 +149,15 @@ public class IdentifyFile
           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!