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JAL-98 JAL-1854 encapsulate 'magic number' threshold 3 in Conservation
[jalview.git]
/
src
/
jalview
/
gui
/
TreeCanvas.java
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
ef65b92
..
84fd82f
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-811,8
+811,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
for (int i = 0; i < leaves.size(); i++)
{
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();
treeSelectionChanged(seq);
}
av.sendSelection();
@@
-968,15
+967,14
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
(int) (Math.random() * 255), (int) (Math.random() * 255));
setColor(tree.getGroups().elementAt(i), col.brighter());
(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++)
{
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 (!sequences.contains(s1))
{
@@
-1019,8
+1017,8
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (aps[a].av.getGlobalColourScheme() != null
&& aps[a].av.getGlobalColourScheme().conservationApplied())
{
if (aps[a].av.getGlobalColourScheme() != null
&& aps[a].av.getGlobalColourScheme().conservationApplied())
{
- Conservation c = new Conservation("Group", 3,
- sg.getSequences(null), sg.getStartRes(), sg.getEndRes());
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
c.calculate();
c.verdict(false, aps[a].av.getConsPercGaps());
sg.cs.setConservation(c);
c.calculate();
c.verdict(false, aps[a].av.getConsPercGaps());
sg.cs.setConservation(c);