X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;fp=src%2Fjalview%2Fgui%2FScalePanel.java;h=e6bba0249677a351fda2ba24b41333f521e95b11;hb=04a4d60a50394d846d0479c442facebe360b5b9c;hp=798c833735b18a6358ffc642fbae0feebe61ce21;hpb=653e250e0a2a5dd455ae4c52794c4ce0de340418;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 798c833..e6bba02 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -42,6 +42,7 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.JMenuItem;
@@ -112,7 +113,7 @@ public class ScalePanel extends JPanel
 
     if (av.hasHiddenColumns())
     {
-      x = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x);
+      x = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
     }
 
     if (x >= av.getAlignment().getWidth())
@@ -174,7 +175,7 @@ public class ScalePanel extends JPanel
       });
       pop.add(item);
 
-      if (av.getAlignment().getHiddenColumns().hasHiddenColumns())
+      if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
       {
         item = new JMenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
@@ -281,7 +282,7 @@ public class ScalePanel extends JPanel
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     if (res >= av.getAlignment().getWidth())
@@ -336,7 +337,7 @@ public class ScalePanel extends JPanel
     int res = (evt.getX() / av.getCharWidth())
             + av.getRanges().getStartRes();
     res = Math.max(0, res);
-    res = hidden.adjustForHiddenColumns(res);
+    res = hidden.visibleToAbsoluteColumn(res);
     res = Math.min(res, av.getAlignment().getWidth() - 1);
     min = Math.min(res, min);
     max = Math.max(res, max);
@@ -392,7 +393,7 @@ public class ScalePanel extends JPanel
     reveal = av.getAlignment().getHiddenColumns()
             .getRegionWithEdgeAtRes(res);
 
-    res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
+    res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
 
     ToolTipManager.sharedInstance().registerComponent(this);
     this.setToolTipText(
@@ -409,6 +410,8 @@ public class ScalePanel extends JPanel
   @Override
   public void paintComponent(Graphics g)
   {
+    super.paintComponent(g);
+
     /*
      * shouldn't get called in wrapped mode as the scale above is
      * drawn instead by SeqCanvas.drawNorthScale
@@ -457,7 +460,7 @@ public class ScalePanel extends JPanel
         {
           if (hidden.isVisible(sel))
           {
-            sel = hidden.findColumnPosition(sel);
+            sel = hidden.absoluteToVisibleColumn(sel);
           }
           else
           {
@@ -487,23 +490,18 @@ public class ScalePanel extends JPanel
 
       if (av.getShowHiddenMarkers())
       {
-        List<Integer> positions = hidden.findHiddenRegionPositions();
-        for (int pos : positions)
+        Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+                startx + widthx + 1);
+        while (it.hasNext())
         {
-          res = pos - startx;
-
-          if (res < 0 || res > widthx)
-          {
-            continue;
-          }
+          res = it.next() - startx;
 
           gg.fillPolygon(
                   new int[]
-                  { -1 + res * avCharWidth - avCharHeight / 4,
-                      -1 + res * avCharWidth + avCharHeight / 4,
-                      -1 + res * avCharWidth },
-                  new int[]
-                  { y, y, y + 2 * yOf }, 3);
+          { -1 + res * avCharWidth - avCharHeight / 4,
+              -1 + res * avCharWidth + avCharHeight / 4,
+              -1 + res * avCharWidth }, new int[]
+          { y, y, y + 2 * yOf }, 3);
         }
       }
     }
@@ -554,7 +552,11 @@ public class ScalePanel extends JPanel
             || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
     {
       // scroll event, repaint panel
-      repaint();
+    	
+  	// Call repaint on alignment panel so that repaints from other alignment
+    // panel components can be aggregated. Otherwise performance of the overview
+    // window and others may be adversely affected.
+      av.getAlignPanel().repaint();
     }
   }