/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.SequenceNode;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
import jalview.util.Format;
for (int i = 0; i < leaves.size(); i++)
{
- SequenceI seq = (SequenceI) leaves.elementAt(i)
- .element();
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
treeSelectionChanged(seq);
}
av.sendSelection();
(int) (Math.random() * 255), (int) (Math.random() * 255));
setColor(tree.getGroups().elementAt(i), col.brighter());
- Vector<SequenceNode> l = tree.findLeaves(tree
- .getGroups().elementAt(i));
+ Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
+ .elementAt(i));
Vector<SequenceI> sequences = new Vector<SequenceI>();
for (int j = 0; j < l.size(); j++)
{
- SequenceI s1 = (SequenceI) l.elementAt(j)
- .element();
+ SequenceI s1 = (SequenceI) l.elementAt(j).element();
if (!sequences.contains(s1))
{
if (aps[a].av.getGlobalColourScheme() != null
&& aps[a].av.getGlobalColourScheme().conservationApplied())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes());
-
+ Conservation c = new Conservation("Group", 3,
+ sg.getSequences(null), sg.getStartRes(), sg.getEndRes());
c.calculate();
c.verdict(false, aps[a].av.getConsPercGaps());
sg.cs.setConservation(c);