Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop

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

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 605cc5c..6abee08 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -113,7 +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())
@@ -169,13 +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().hasManyHiddenColumns())
+      if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
       {
         item = new JMenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
@@ -185,7 +185,7 @@ public class ScalePanel extends JPanel
           {
             av.showAllHiddenColumns();
             reveal = null;
-            ap.paintAlignment(true);
+            ap.paintAlignment(true, true);
             av.sendSelection();
           }
         });
@@ -209,7 +209,7 @@ public class ScalePanel extends JPanel
             av.setSelectionGroup(null);
           }
 
-          ap.paintAlignment(true);
+          ap.paintAlignment(true, true);
           av.sendSelection();
         }
       });
@@ -261,7 +261,7 @@ public class ScalePanel extends JPanel
       sg.setEndRes(max);
     }
     av.setSelectionGroup(sg);
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -276,13 +276,15 @@ public class ScalePanel extends JPanel
   {
     mouseDragging = false;
 
-    int res = (evt.getX() / av.getCharWidth())
+    int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
+
+    int res = (xCords / av.getCharWidth())
             + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     if (res >= av.getAlignment().getWidth())
@@ -298,7 +300,7 @@ public class ScalePanel extends JPanel
       }
       else
       {
-        ap.paintAlignment(false);
+        ap.paintAlignment(false, false);
       }
       return;
     }
@@ -317,7 +319,7 @@ public class ScalePanel extends JPanel
       }
     }
     stretchingGroup = false;
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -337,7 +339,7 @@ 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);
@@ -347,7 +349,7 @@ public class ScalePanel extends JPanel
     {
       stretchingGroup = true;
       cs.stretchGroup(res, sg, min, max);
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -393,7 +395,7 @@ 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(
@@ -410,6 +412,8 @@ 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
@@ -458,7 +462,7 @@ public class ScalePanel extends JPanel
         {
           if (hidden.isVisible(sel))
           {
-            sel = hidden.findColumnPosition(sel);
+            sel = hidden.absoluteToVisibleColumn(sel);
           }
           else
           {
@@ -488,7 +492,7 @@ public class ScalePanel extends JPanel
 
       if (av.getShowHiddenMarkers())
       {
-        Iterator<Integer> it = hidden.getBoundedStartIterator(startx,
+        Iterator<Integer> it = hidden.getStartRegionIterator(startx,
                 startx + widthx + 1);
         while (it.hasNext())
         {
@@ -545,10 +549,16 @@ public class ScalePanel extends JPanel
     // 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();
+       
+       // 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();
     }
   }