From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 20 Feb 2014 15:18:28 +0000 (+0000)
Subject: JAL-1447 patch to correctly recognise FASTA files containing '*'
X-Git-Tag: Jalview_2_9~206^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c2128745577234fbee1f276f3db96776e1533d9e;p=jalview.git

JAL-1447 patch to correctly recognise FASTA files containing '*'
---

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 63d8d63..93f9a98 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -182,16 +182,19 @@ public class IdentifyFile
             // Is this a single line BLC file?
             String data1 = source.nextLine();
             String data2 = source.nextLine();
+            int c1;
             if (checkPIR)
             {
               starterm = (data1 != null && data1.indexOf("*") > -1)
                       || (data2 != null && data2.indexOf("*") > -1);
             }
-            if (data2 != null && data.indexOf("*") > -1)
+            if (data2 != null && (c1=data.indexOf("*")) > -1)
             {
-              if (data.indexOf("*") == data2.indexOf("*"))
+              if (c1==0 && c1 == data2.indexOf("*"))
               {
                 reply = "BLC";
+              } else {
+                reply = "FASTA"; // possibly a bad choice - may be recognised as PIR 
               }
               // otherwise can still possibly be a PIR file
             }