X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=ad5884c835530bea106f0d1752c730e215b914cb;hb=bd6ce8f5f9fc8e5bc8a6188d15987ce0ffd2c1ee;hp=7ad8fcd6dc7833f4e696c1389c797a231defe046;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 7ad8fcd..ad5884c 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -150,6 +150,11 @@ public class IdentifyFile
           reply = FileFormat.ScoreMatrix;
           break;
         }
+        if (data.startsWith("HMMER3"))
+        {
+          reply = FileFormat.HMMER3;
+          break;
+        }
         if (data.startsWith("H ") && !aaIndexHeaderRead)
         {
           aaIndexHeaderRead = true;
@@ -275,6 +280,11 @@ public class IdentifyFile
           // read as a FASTA (probably)
           break;
         }
+        if (data.indexOf("{\"") > -1)
+        {
+          reply = FileFormat.Json;
+          break;
+        }
         int lessThan = data.indexOf("<");
         if ((lessThan > -1)) // possible Markup Language data i.e HTML,
                              // RNAML, XML
@@ -292,11 +302,6 @@ public class IdentifyFile
           }
         }
 
-        if (data.indexOf("{\"") > -1)
-        {
-          reply = FileFormat.Json;
-          break;
-        }
         if ((data.length() < 1) || (data.indexOf("#") == 0))
         {
           lineswereskipped = true;