pir format ambiguity and todo regarding 'format override' parameter

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 071b6f2..a1ae26c 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -161,15 +161,17 @@ public class IdentifyFile
 
           break;
         }
-        else if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
-        {
-          reply = "PIR";
-
-          break;
-        }
         else if (data.indexOf(">") > -1)
         {
-          // could be BLC file, read next line to confirm
+          // FASTA, PIR file or BLC file
+          boolean checkPIR = false;
+          if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
+          {
+            // watch for PIR file attributes
+            checkPIR = true;
+            reply = "PIR";
+          }
+          // could also be BLC file, read next line to confirm
           data = source.nextLine();
 
           if (data.indexOf(">") > -1)
@@ -181,10 +183,13 @@ public class IdentifyFile
             // Is this a single line BLC file?
             source.nextLine();
             String data2 = source.nextLine();
-            if (data2 != null && data.indexOf("*") > -1
-                    && data.indexOf("*") == data2.indexOf("*"))
+            if (data2 != null && data.indexOf("*") > -1)
             {
+              if (data.indexOf("*") == data2.indexOf("*"))
+              {
               reply = "BLC";
+              }
+              // otherwise can still possibly be a PIR file
             }
             else
             {
@@ -192,8 +197,11 @@ public class IdentifyFile
               // TODO : AMSA File is indicated if there is annotation in the
               // FASTA file - but FASTA will automatically generate this at the
               // mo.
+              break;
             }
           }
+          // TODO final check for PIR content. require >P1;title\n<blah>\nterminated sequence to occur at least once. 
+          // the PIR/fasta ambiguity may be the use case that is needed to have a 'Parse as type XXX' parameter for the applet/application.
           break;
         }
         else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)