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JAL-2189 source formatting
[jalview.git]
/
src
/
jalview
/
gui
/
TreeCanvas.java
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
254d032
..
0e513f7
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-29,7
+29,6
@@
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
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 jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
import jalview.util.Format;
@@
-175,13
+174,13
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
tree.findHeight(tree.getTopNode());
// Now have to calculate longest name based on the leaves
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++)
{
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())
{
if (lf.isPlaceholder())
{
@@
-748,21
+747,27
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
/**
}
/**
- * DOCUMENT ME!
+ * Empty method to satisfy the MouseListener interface
*
* @param e
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent e)
{
*/
@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
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseEntered(MouseEvent e)
*/
@Override
public void mouseEntered(MouseEvent e)
@@
-770,10
+775,9
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
/**
}
/**
- * DOCUMENT ME!
+ * Empty method to satisfy the MouseListener interface
*
* @param e
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseExited(MouseEvent e)
*/
@Override
public void mouseExited(MouseEvent e)
@@
-781,10
+785,11
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
/**
}
/**
- * 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
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseClicked(MouseEvent evt)
*/
@Override
public void mouseClicked(MouseEvent evt)
@@
-794,15
+799,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
return;
}
return;
}
- /*
- * isPopupTrigger is set on mouseReleased /
- * mouseClicked on Windows
- */
- if (evt.isPopupTrigger())
- {
- chooseSubtreeColour();
- }
- else if (evt.getClickCount() > 1)
+ if (evt.getClickCount() > 1)
{
tree.swapNodes(highlightNode);
tree.reCount(tree.getTopNode());
{
tree.swapNodes(highlightNode);
tree.reCount(tree.getTopNode());
@@
-810,13
+807,11
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
else
{
}
else
{
- Vector leaves = new Vector();
- tree.findLeaves(highlightNode, leaves);
+ Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
for (int i = 0; i < leaves.size(); i++)
{
for (int i = 0; i < leaves.size(); i++)
{
- SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
- .element();
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
treeSelectionChanged(seq);
}
av.sendSelection();
treeSelectionChanged(seq);
}
av.sendSelection();
@@
-876,10
+871,12
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
/**
}
/**
- * 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
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mousePressed(MouseEvent e)
*/
@Override
public void mousePressed(MouseEvent e)
@@
-888,7
+885,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
/*
* isPopupTrigger is set for mousePressed (Mac)
/*
* isPopupTrigger is set for mousePressed (Mac)
- * or mouseReleased / mouseClicked (Windows)
+ * or mouseReleased (Windows)
*/
if (e.isPopupTrigger())
{
*/
if (e.isPopupTrigger())
{
@@
-901,8
+898,9
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
/*
* defer right-click handling on Windows to
/*
* defer right-click handling on Windows to
- * mouseClicked; this also matches Cmd-click on Mac
- * which should do nothing here
+ * mouseClicked; note isRightMouseButton
+ * also matches Cmd-click on Mac which should do
+ * nothing here
*/
if (SwingUtilities.isRightMouseButton(e))
{
*/
if (SwingUtilities.isRightMouseButton(e))
{
@@
-967,17
+965,16
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
{
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
{
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++)
{
for (int j = 0; j < l.size(); j++)
{
- SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
- .element();
+ SequenceI s1 = (SequenceI) l.elementAt(j).element();
if (!sequences.contains(s1))
{
if (!sequences.contains(s1))
{
@@
-1020,10
+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",
- 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);
c.calculate();
c.verdict(false, aps[a].av.getConsPercGaps());
sg.cs.setConservation(c);