/*
- * 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.
- *
+ *
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
*/
public AlignFile()
{
+ // Shouldn't we init data structures (JBPNote: not sure - initData is for initialising the structures used for reading from a datasource, and the bare constructor hasn't got any datasource)
+ initData();
}
/**
initData();
parse();
// sets the index of each sequence in the alignment
- for( int i=0,c=seqs.size(); i<c; i++ ) {
- seqs.get(i).setIndex(i);
+ for (int i = 0, c = seqs.size(); i < c; i++)
+ {
+ seqs.get(i).setIndex(i);
}
}
initData();
parse();
// sets the index of each sequence in the alignment
- for( int i=0,c=seqs.size(); i<c; i++ ) {
- seqs.get(i).setIndex(i);
+ for (int i = 0, c = seqs.size(); i < c; i++)
+ {
+ seqs.get(i).setIndex(i);
}
}