JAL-3130 Some automatically fixed deprecated calls. Mostly constructors converted...

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

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index f580d85..d3f4a69 100755 (executable)
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -42,10 +42,11 @@ 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 implements MouseMotionListener,
-        MouseListener, ViewportListenerI
+public class ScalePanel extends Panel
+        implements MouseMotionListener, MouseListener, ViewportListenerI
 {
 
   protected int offy = 4;
@@ -86,7 +87,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
     if (av.hasHiddenColumns())
     {
-      res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x);
+      res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
     }
     else
     {
@@ -95,7 +96,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
     min = res;
     max = res;
-    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
       rightMouseButtonPressed(evt, res);
     }
@@ -140,7 +142,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       sg.setStartRes(min);
       sg.setEndRes(max);
     }
-    ap.paintAlignment(true);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -157,7 +159,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     PopupMenu pop = new PopupMenu();
     if (reveal != null)
     {
-      MenuItem item = new MenuItem(MessageManager.getString("label.reveal"));
+      MenuItem item = new MenuItem(
+              MessageManager.getString("label.reveal"));
       item.addActionListener(new ActionListener()
       {
         @Override
@@ -165,17 +168,13 @@ public class ScalePanel extends Panel implements MouseMotionListener,
         {
           av.showColumn(reveal[0]);
           reveal = null;
-          ap.paintAlignment(true);
-          if (ap.overviewPanel != null)
-          {
-            ap.overviewPanel.updateOverviewImage();
-          }
+          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()
@@ -185,11 +184,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
           {
             av.showAllHiddenColumns();
             reveal = null;
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
+            ap.paintAlignment(true, true);
             av.sendSelection();
           }
         });
@@ -208,18 +203,13 @@ public class ScalePanel extends Panel implements MouseMotionListener,
         public void actionPerformed(ActionEvent e)
         {
           av.hideColumns(res, res);
-          if (av.getSelectionGroup() != null
-                  && av.getSelectionGroup().getSize() == av.getAlignment()
-                          .getHeight())
+          if (av.getSelectionGroup() != null && av.getSelectionGroup()
+                  .getSize() == av.getAlignment().getHeight())
           {
             av.setSelectionGroup(null);
           }
 
-          ap.paintAlignment(true);
-          if (ap.overviewPanel != null)
-          {
-            ap.overviewPanel.updateOverviewImage();
-          }
+          ap.paintAlignment(true, true);
           av.sendSelection();
         }
       });
@@ -245,12 +235,12 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     if (!stretchingGroup)
     {
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
 
       return;
     }
@@ -267,7 +257,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     }
 
     stretchingGroup = false;
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -286,7 +276,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     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);
@@ -296,7 +286,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     {
       stretchingGroup = true;
       cs.stretchGroup(res, sg, min, max);
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -356,8 +346,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
      */
     if (!av.getWrapAlignment())
     {
-      drawScale(g, av.getRanges().getStartRes(),
-              av.getRanges().getEndRes(), getSize().width, getSize().height);
+      drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+              getSize().width, getSize().height);
     }
   }
 
@@ -388,7 +378,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
         {
           if (hidden.isVisible(sel))
           {
-            sel = hidden.findColumnPosition(sel);
+            sel = hidden.absoluteToVisibleColumn(sel);
           }
           else
           {
@@ -447,21 +437,17 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       if (av.getShowHiddenMarkers())
       {
         int widthx = 1 + endx - startx;
-        List<Integer> positions = hidden.findHiddenRegionPositions();
-        for (int pos : positions)
+        Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+                startx + widthx + 1);
+        while (it.hasNext())
         {
+          res = it.next() - startx;
 
-          res = pos - startx;
-
-          if (res < 0 || res > widthx)
-          {
-            continue;
-          }
-
-          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);
+          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);
         }
       }
     }
@@ -476,7 +462,9 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     // 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();