From c2128745577234fbee1f276f3db96776e1533d9e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 20 Feb 2014 15:18:28 +0000 Subject: [PATCH] JAL-1447 patch to correctly recognise FASTA files containing '*' --- src/jalview/io/IdentifyFile.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) 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 } -- 1.7.10.2