/*
- * 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
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)
// 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
{
// 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)
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(",")) // &&