/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
}
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- for (int i = 0; i < len; i++)
+ List<SequenceI> asq;
+ synchronized (asq = align.getSequences())
{
- // SequenceI tmp = seqs[i];
- align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
- align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
+ for (int i = 0; i < len; i++)
+ {
+ // SequenceI tmp = seqs[i];
+ asq.set(i, seqs[nSeq - i - 1]);
+ asq.set(nSeq - i - 1, seqs[i]);
+ }
}
}
public static void setOrder(AlignmentI align, SequenceI[] seqs)
{
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- Vector algn = align.getSequences();
- Vector tmp = new Vector();
-
- for (int i = 0; i < seqs.length; i++)
+ List<SequenceI> algn;
+ synchronized (algn = align.getSequences())
{
- if (algn.contains(seqs[i]))
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
+
+ for (int i = 0; i < seqs.length; i++)
{
- tmp.addElement(seqs[i]);
+ if (algn.contains(seqs[i]))
+ {
+ tmp.add(seqs[i]);
+ }
}
- }
- algn.removeAllElements();
- // User may have hidden seqs, then clicked undo or redo
- for (int i = 0; i < tmp.size(); i++)
- {
- algn.addElement(tmp.elementAt(i));
+ algn.clear();
+ // User may have hidden seqs, then clicked undo or redo
+ for (int i = 0; i < tmp.size(); i++)
+ {
+ algn.add(tmp.get(i));
+ }
}
-
}
/**
// SORTS GROUPS BY SIZE
// ////////////////////
- for (int i = 0; i < align.getGroups().size(); i++)
+ for (SequenceGroup sg:align.getGroups())
{
- SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
-
for (int j = 0; j < groups.size(); j++)
{
SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
}
/**
- * DOCUMENT ME!
- *
+ * Select sequences in order from tmp that is present in mask, and any
+ * remaining seqeunces in mask not in tmp
+ *
* @param tmp
- * DOCUMENT ME!
+ * thread safe collection of sequences
* @param mask
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * thread safe collection of sequences
+ *
+ * @return intersect(tmp,mask)+intersect(complement(tmp),mask)
*/
- private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+ private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
+ List<SequenceI> mask)
{
- Vector seqs = new Vector();
+ ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
int i, idx;
boolean[] tmask = new boolean[mask.size()];
for (i = 0; i < tmp.size(); i++)
{
- Object sq = tmp.elementAt(i);
+ SequenceI sq = tmp.get(i);
idx = mask.indexOf(sq);
if (idx > -1 && tmask[idx])
{
tmask[idx] = false;
- seqs.addElement(sq);
+ seqs.add(sq);
}
}
{
if (tmask[i])
{
- seqs.addElement(mask.elementAt(i));
+ seqs.add(mask.get(i));
}
}
- return vectorToArray(seqs);
+ return seqs.toArray(new SequenceI[seqs.size()]);
}
/**
* @return DOCUMENT ME!
*/
private static Vector _sortByTree(SequenceNode node, Vector tmp,
- Vector seqset)
+ List<SequenceI> seqset)
{
if (node == null)
{