Merge branch 'develop' into feature/JAL-2759

[jalview.git] / src / jalview / gui / ScalePanel.java

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 6b2f9c9..2310866 100755 (executable)
--- 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;
@@ -168,13 +169,13 @@ public class ScalePanel extends JPanel
         {
           av.showColumn(reveal[0]);
           reveal = null;
-          ap.paintAlignment(true);
+          ap.paintAlignment(true, true);
           av.sendSelection();
         }
       });
       pop.add(item);
 
-      if (av.getAlignment().getHiddenColumns().hasHiddenColumns())
+      if (av.getAlignment().getHiddenColumns().hasManyHiddenColumns())
       {
         item = new JMenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
@@ -184,7 +185,7 @@ public class ScalePanel extends JPanel
           {
             av.showAllHiddenColumns();
             reveal = null;
-            ap.paintAlignment(true);
+            ap.paintAlignment(true, true);
             av.sendSelection();
           }
         });
@@ -208,7 +209,7 @@ public class ScalePanel extends JPanel
             av.setSelectionGroup(null);
           }
 
-          ap.paintAlignment(true);
+          ap.paintAlignment(true, true);
           av.sendSelection();
         }
       });
@@ -260,7 +261,7 @@ public class ScalePanel extends JPanel
       sg.setEndRes(max);
     }
     av.setSelectionGroup(sg);
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -297,7 +298,7 @@ public class ScalePanel extends JPanel
       }
       else
       {
-        ap.paintAlignment(false);
+        ap.paintAlignment(false, false);
       }
       return;
     }
@@ -316,7 +317,7 @@ public class ScalePanel extends JPanel
       }
     }
     stretchingGroup = false;
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -346,7 +347,7 @@ public class ScalePanel extends JPanel
     {
       stretchingGroup = true;
       cs.stretchGroup(res, sg, min, max);
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -487,23 +488,18 @@ public class ScalePanel extends JPanel
 
       if (av.getShowHiddenMarkers())
       {
-        List<Integer> positions = hidden.findHiddenRegionPositions();
-        for (int pos : positions)
+        Iterator<Integer> it = hidden.getBoundedStartIterator(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);
         }
       }
     }
@@ -550,7 +546,8 @@ public class ScalePanel extends JPanel
     // paint, so scroll events are identified as changes to the horizontal or
     // vertical start value.
     if (evt.getPropertyName().equals(ViewportRanges.STARTRES)
-            || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
+            || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)
+            || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
     {
       // scroll event, repaint panel
       repaint();