/*
- * 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.
// TODO: JBPNote - decide if this is always an error
// (eg. not when a tree is associated to another alignment which has more
// sequences)
- if (tmp.size() < nSeq)
+ if (tmp.size() != nSeq)
{
addStrays(align, tmp);
}
if (tmp.size() != nSeq)
{
- System.err.println("ERROR: tmp.size()=" + tmp.size() + " != nseq="
- + nSeq + " in getOrderByTree");
+ System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+ + nSeq + " in getOrderByTree - tree contains sequences not in alignment");
}
}
{
if (node.element() instanceof SequenceI)
{
- if (!tmp.contains(node.element()))
+ if (!tmp.contains(node.element())) // && (seqset==null || seqset.size()==0 || seqset.contains(tmp)))
{
tmp.addElement((SequenceI) node.element());
}
// filter for selection criteria
if (
// ignore features outwith alignment start-stop positions.
- (sf[f].end < sstart || sf[f].begin > sstop)
- ||
- // or ignore based on selection criteria
+ (sf[f].end < sstart || sf[f].begin > sstop) ||
+ // or ignore based on selection criteria
(featureLabels != null && !AlignmentSorter
.containsIgnoreCase(sf[f].type, featureLabels))
|| (groupLabels != null