/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
break;
}
-
+
if ((data.indexOf("<") > -1))
{
reply = "RNAML";
-
+
break;
}
break;
}
-
-
+
else if (data.indexOf(">") > -1)
{
// FASTA, PIR file or BLC file
// 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
public static void main(String[] args)
{
-
for (int i = 0; args != null && i < args.length; i++)
{
IdentifyFile ider = new IdentifyFile();