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 threshold;\r
+  float threshold;\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
+      if(av.getCurrentTree() == tree)\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
@@ -381,6 +387,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
   }\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
@@ -401,10 +410,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
           // 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.groupNodes(tree.getTopNode(),fthreshold);\r
+              tree.groupNodes(tree.getTopNode(),threshold);\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
-                    c.verdict(false, 100);\r
+                    c.verdict(false, av.ConsPercGaps);\r
                     ccs = new ConservationColourScheme(c, ccs.cs);\r
 \r
                     sg.cs = ccs;\r