/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
{
if (omitHidden != null)
{
- //
- Alignment alv = new Alignment(replaceStrings(alignment
- .getSequencesArray(), omitHidden));
+ //
+ Alignment alv = new Alignment(replaceStrings(
+ alignment.getSequencesArray(), omitHidden));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
- for (int i = 0; i < ala.length; i++)
+ if (ala != null)
{
- AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
- if (selgp != null)
+ for (int i = 0; i < ala.length; i++)
{
- colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
- .getEndRes(), na);
+ AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
+ if (selgp != null)
+ {
+ colSel.makeVisibleAnnotation(selgp.getStartRes(),
+ selgp.getEndRes(), na);
+ }
+ else
+ {
+ colSel.makeVisibleAnnotation(na);
+ }
+ alv.addAnnotation(na);
}
- else
- {
- colSel.makeVisibleAnnotation(na);
- }
- alv.addAnnotation(na);
}
return this.formatSequences(format, alv, suffix);
}