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;
import javax.swing.JColorChooser;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
/**
tree.findHeight(tree.getTopNode());
// Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+ Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
boolean has_placeholders = false;
longestName = "";
for (int i = 0; i < leaves.size(); i++)
{
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+ SequenceNode lf = leaves.elementAt(i);
if (lf.isPlaceholder())
{
}
/**
- * DOCUMENT ME!
+ * Empty method to satisfy the MouseListener interface
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent e)
{
+ /*
+ * isPopupTrigger is set on mouseReleased on Windows
+ */
+ if (e.isPopupTrigger())
+ {
+ chooseSubtreeColour();
+ e.consume(); // prevent mouseClicked happening
+ }
}
/**
- * DOCUMENT ME!
+ * Empty method to satisfy the MouseListener interface
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseEntered(MouseEvent e)
}
/**
- * DOCUMENT ME!
+ * Empty method to satisfy the MouseListener interface
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseExited(MouseEvent e)
}
/**
- * DOCUMENT ME!
+ * Handles a mouse click on a tree node (clicks elsewhere are handled in
+ * mousePressed). Click selects the sub-tree, double-click swaps leaf nodes
+ * order, right-click opens a dialogue to choose colour for the sub-tree.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseClicked(MouseEvent evt)
{
return;
}
- if (evt.isPopupTrigger())
- {
- chooseSubtreeColour();
- }
- else if (evt.getClickCount() > 1)
+
+ if (evt.getClickCount() > 1)
{
tree.swapNodes(highlightNode);
tree.reCount(tree.getTopNode());
}
else
{
- Vector leaves = new Vector();
- tree.findLeaves(highlightNode, leaves);
+ Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
for (int i = 0; i < leaves.size(); i++)
{
- SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
+ SequenceI seq = (SequenceI) leaves.elementAt(i)
.element();
treeSelectionChanged(seq);
}
}
/**
- * DOCUMENT ME!
+ * Handles a mouse press on a sequence name or the tree background canvas
+ * (click on a node is handled in mouseClicked). The action is to create
+ * groups by partitioning the tree at the mouse position. Colours for the
+ * groups (and sequence names) are generated randomly.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mousePressed(MouseEvent e)
{
av.setCurrentTree(tree);
- if (highlightNode != null && e.isPopupTrigger())
+
+ /*
+ * isPopupTrigger is set for mousePressed (Mac)
+ * or mouseReleased (Windows)
+ */
+ if (e.isPopupTrigger())
+ {
+ if (highlightNode != null)
+ {
+ chooseSubtreeColour();
+ }
+ return;
+ }
+
+ /*
+ * defer right-click handling on Windows to
+ * mouseClicked; note isRightMouseButton
+ * also matches Cmd-click on Mac which should do
+ * nothing here
+ */
+ if (SwingUtilities.isRightMouseButton(e))
{
- chooseSubtreeColour();
return;
}
{
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
- setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+ setColor(tree.getGroups().elementAt(i), col.brighter());
- Vector l = tree.findLeaves(
- (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+ Vector<SequenceNode> l = tree.findLeaves(tree
+ .getGroups().elementAt(i));
- Vector sequences = new Vector();
+ Vector<SequenceI> sequences = new Vector<SequenceI>();
for (int j = 0; j < l.size(); j++)
{
- SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
+ 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);