Moved comment so it doesn't break jalopy (this is not good!)

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 4337cf6..3dd95b6 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -41,7 +41,14 @@ public class IdentifyFile
         if(data.indexOf("#")==0 || data.length()<1)\r
           continue;\r
 \r
-        if(data.indexOf("PILEUP")>-1 || data.indexOf("//")>-1)\r
+        if(data.indexOf("PILEUP")>-1)\r
+        {\r
+          reply = "PileUp";\r
+          break;\r
+        }\r
+        if((data.indexOf("//")==0)\r
+           || ((data.indexOf("!!")>-1)\r
+           && (data.indexOf("!!")<data.indexOf("_MULTIPLE_ALIGNMENT "))))\r
         {\r
           reply = "MSF";\r
           break;\r
@@ -70,7 +77,8 @@ public class IdentifyFile
       }\r
       reader.close();\r
     }\r
-    catch(Exception ex){ex.printStackTrace();}\r
+    catch(Exception ex){\r
+      System.err.println("File Identification failed!"); ex.printStackTrace();}\r
 \r
     return reply;\r
   }\r