X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=2679b484dc27cea46a3261a743982c84814a2db5;hb=12b928f827972f429471a5bf7a832fa634259a16;hp=f1f51b15c845d921dbbddce67efbf9378630eacc;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index f1f51b1..2679b48 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -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)
@@ -201,6 +209,16 @@ public class IdentifyFile
           reply = "PDB";
           break;
         }
+        /*// TODO comment out SimpleBLAST identification for Jalview 2.4.1
+        else if (!lineswereskipped && data.indexOf("BLAST")<4)
+        {
+          reply = "SimpleBLAST";
+          break;
+            
+        }
+        // end comments for Jalview 2.4.1
+         * 
+         */
         else if (!lineswereskipped && data.charAt(0) != '*'
                 && data.charAt(0) != ' '
                 && data.indexOf(":") < data.indexOf(",")) // &&