/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* 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
}
/**
- * create sequences with each seuqence string replaced with the one given in
+ * create sequences with each sequence string replaced with the one given in
* omitHiddenCOlumns
*
* @param seqs
{
if (omitHidden != null)
{
- //
- Alignment alv = new Alignment(replaceStrings(alignment
- .getSequencesArray(), omitHidden));
+ // TODO consider using AlignmentView to prune to visible region
+ // TODO prune sequence annotation and groups to visible region
+ Alignment alv = new Alignment(replaceStrings(
+ alignment.getSequencesArray(), omitHidden));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
if (ala != null)
{
AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
if (selgp != null)
{
- colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
- .getEndRes(), na);
+ colSel.makeVisibleAnnotation(selgp.getStartRes(),
+ selgp.getEndRes(), na);
}
else
{