X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FScalePanel.java;h=c91449ffec53d7f3b34e1b48528361e32a959fe5;hb=782db63cc15bc2261c398a87da13fd729da7a18d;hp=e00db7c3e2a0f2c778c76e1b155f291c6181126a;hpb=5e92df41fe4f6fa8b50c3a65000bdb8ddcdc901f;p=jalview.git

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index e00db7c..c91449f 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/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;
 
 public class ScalePanel extends Panel
@@ -86,7 +87,7 @@ public class ScalePanel extends Panel
 
     if (av.hasHiddenColumns())
     {
-      res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x);
+      res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
     }
     else
     {
@@ -141,7 +142,7 @@ public class ScalePanel extends Panel
       sg.setStartRes(min);
       sg.setEndRes(max);
     }
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -167,13 +168,13 @@ public class ScalePanel extends Panel
         {
           av.showColumn(reveal[0]);
           reveal = null;
-          ap.paintAlignment(true);
+          ap.paintAlignment(true, true);
           av.sendSelection();
         }
       });
       pop.add(item);
 
-      if (av.getAlignment().getHiddenColumns().hasManyHiddenColumns())
+      if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
       {
         item = new MenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
@@ -183,7 +184,7 @@ public class ScalePanel extends Panel
           {
             av.showAllHiddenColumns();
             reveal = null;
-            ap.paintAlignment(true);
+            ap.paintAlignment(true, true);
             av.sendSelection();
           }
         });
@@ -208,7 +209,7 @@ public class ScalePanel extends Panel
             av.setSelectionGroup(null);
           }
 
-          ap.paintAlignment(true);
+          ap.paintAlignment(true, true);
           av.sendSelection();
         }
       });
@@ -234,12 +235,12 @@ public class ScalePanel extends Panel
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     if (!stretchingGroup)
     {
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
 
       return;
     }
@@ -256,7 +257,7 @@ public class ScalePanel extends Panel
     }
 
     stretchingGroup = false;
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -275,7 +276,7 @@ public class ScalePanel extends Panel
     int res = (evt.getX() / av.getCharWidth())
             + av.getRanges().getStartRes();
     res = Math.max(0, res);
-    res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
+    res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
     res = Math.min(res, av.getAlignment().getWidth() - 1);
     min = Math.min(res, min);
     max = Math.max(res, max);
@@ -285,7 +286,7 @@ public class ScalePanel extends Panel
     {
       stretchingGroup = true;
       cs.stretchGroup(res, sg, min, max);
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -377,7 +378,7 @@ public class ScalePanel extends Panel
         {
           if (hidden.isVisible(sel))
           {
-            sel = hidden.findColumnPosition(sel);
+            sel = hidden.absoluteToVisibleColumn(sel);
           }
           else
           {
@@ -436,19 +437,17 @@ public class ScalePanel extends Panel
       if (av.getShowHiddenMarkers())
       {
         int widthx = 1 + endx - startx;
-        List<Integer> positions = hidden.findHiddenRegionPositions(startx,
+        Iterator<Integer> it = hidden.getStartRegionIterator(startx,
                 startx + widthx + 1);
-        for (int pos : positions)
+        while (it.hasNext())
         {
-          res = pos - startx;
+          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);
         }
       }
     }
@@ -463,7 +462,9 @@ public class ScalePanel extends Panel
     // Here we only want to fastpaint on a scroll, with resize using a normal
     // paint, so scroll events are identified as changes to the horizontal or
     // vertical start value.
-    if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
+    if (evt.getPropertyName().equals(ViewportRanges.STARTRES)
+            || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)
+            || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
     {
       // scroll event, repaint panel
       repaint();