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consistent percentage gaps filter for conservation calculation.
[jalview.git]
/
src
/
jalview
/
gui
/
TreeCanvas.java
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
9435716
..
600683f
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-27,7
+27,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
int offx = 20;
\r
int offy = 20;
\r
\r
int offx = 20;
\r
int offy = 20;
\r
\r
- int threshold;
\r
+ float threshold;
\r
\r
String longestName;
\r
int labelLength=-1;
\r
\r
String longestName;
\r
int labelLength=-1;
\r
@@
-342,8
+342,14
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
\r
if (threshold != 0)
\r
{
\r
\r
if (threshold != 0)
\r
{
\r
+ if(av.getCurrentTree() == tree)
\r
g.setColor(Color.red);
\r
g.setColor(Color.red);
\r
- g.drawLine(threshold,0,threshold,getHeight());
\r
+ else
\r
+ g.setColor(Color.gray);
\r
+
\r
+ int x = (int)( threshold * (float)(getWidth()-labelLength - 2*offx) +offx ) ;
\r
+
\r
+ g.drawLine(x,0,x,getHeight());
\r
}
\r
\r
scrollPane.revalidate();
\r
}
\r
\r
scrollPane.revalidate();
\r
@@
-381,6
+387,9
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
}
\r
\r
public void mousePressed(MouseEvent e) {
\r
}
\r
\r
public void mousePressed(MouseEvent e) {
\r
+
\r
+ av.setCurrentTree(tree);
\r
+
\r
int x = e.getX();
\r
int y = e.getY();
\r
\r
int x = e.getX();
\r
int y = e.getY();
\r
\r
@@
-401,10
+410,10
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
// Find threshold
\r
\r
if (tree.getMaxHeight() != 0) {
\r
// Find threshold
\r
\r
if (tree.getMaxHeight() != 0) {
\r
- float fthreshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);
\r
- this.threshold = x;
\r
+ threshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);
\r
+
\r
tree.getGroups().removeAllElements();
\r
tree.getGroups().removeAllElements();
\r
- tree.groupNodes(tree.getTopNode(),fthreshold);
\r
+ tree.groupNodes(tree.getTopNode(),threshold);
\r
setColor(tree.getTopNode(),Color.black);
\r
\r
av.setSelectionGroup(null);
\r
setColor(tree.getTopNode(),Color.black);
\r
\r
av.setSelectionGroup(null);
\r
@@
-438,7
+447,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
sg.getEndRes());
\r
\r
c.calculate();
\r
sg.getEndRes());
\r
\r
c.calculate();
\r
- c.verdict(false, 100);
\r
+ c.verdict(false, av.ConsPercGaps);
\r
ccs = new ConservationColourScheme(c, ccs.cs);
\r
\r
sg.cs = ccs;
\r
ccs = new ConservationColourScheme(c, ccs.cs);
\r
\r
sg.cs = ccs;
\r