X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=08d4dca897efd371f81db835f045e782354280b1;hb=ad5029edaf36ceaafb4e269f2e00b0e1e0d7ffc4;hp=d30ed202e8ad00ef01e8bd49914cf5e8a7211036;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index d30ed20..08d4dca 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,24 +1,26 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import java.io.*;
-import java.net.*;
/**
* DOCUMENT ME!
@@ -133,6 +135,13 @@ public class IdentifyFile
break;
}
+ if ((data.indexOf("<") > -1))
+ {
+ reply = "RNAML";
+
+ break;
+ }
+
if ((data.length() < 1) || (data.indexOf("#") == 0))
{
lineswereskipped = true;
@@ -160,6 +169,7 @@ public class IdentifyFile
break;
}
+
else if (data.indexOf(">") > -1)
{
// FASTA, PIR file or BLC file
@@ -182,17 +192,23 @@ 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
}
else