/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
super.initData();\r
}\r
\r
- public void parse() throws IOException\r
+ public void parse()\r
+ throws IOException\r
{\r
int i = 0;\r
String line;\r
.length();\r
}\r
\r
-\r
Sequence newSeq = parseId(headers.elementAt(i).toString());\r
- newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString());\r
+ newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).\r
+ toString());\r
seqs.addElement(newSeq);\r
- }\r
+ }\r
else\r
{\r
System.err.println("PFAM File reader: Can't find sequence for " +\r
\r
while ( (j < s.length) && (s[j] != null))\r
{\r
- out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));\r
+ out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));\r
\r
out.append(s[j].getSequenceAsString() + "\n");\r
j++;\r