Merge branch 'bug/JAL-3072scrollThread' into merge/JAL-3072_3073

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

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 2310866..0f2b765 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -23,7 +23,6 @@ package jalview.gui;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.MessageManager;
@@ -35,6 +34,7 @@ import java.awt.Color;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
+import java.awt.Point;
 import java.awt.RenderingHints;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -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())
@@ -158,7 +158,12 @@ public class ScalePanel extends JPanel
   protected void rightMouseButtonPressed(MouseEvent evt, final int res)
   {
     JPopupMenu pop = new JPopupMenu();
-    if (reveal != null)
+
+    /*
+     * grab the hidden range in case mouseMoved nulls it
+     */
+    final int[] hiddenRange = reveal;
+    if (hiddenRange != null)
     {
       JMenuItem item = new JMenuItem(
               MessageManager.getString("label.reveal"));
@@ -167,15 +172,16 @@ public class ScalePanel extends JPanel
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          av.showColumn(reveal[0]);
+          av.showColumn(hiddenRange[0]);
           reveal = null;
+          ap.updateLayout();
           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()
@@ -185,6 +191,7 @@ public class ScalePanel extends JPanel
           {
             av.showAllHiddenColumns();
             reveal = null;
+            ap.updateLayout();
             ap.paintAlignment(true, true);
             av.sendSelection();
           }
@@ -209,6 +216,7 @@ public class ScalePanel extends JPanel
             av.setSelectionGroup(null);
           }
 
+          ap.updateLayout();
           ap.paintAlignment(true, true);
           av.sendSelection();
         }
@@ -237,15 +245,7 @@ public class ScalePanel extends JPanel
     }
 
     av.getColumnSelection().addElement(res);
-    SequenceGroup sg = new SequenceGroup();
-    // try to be as quick as possible
-    SequenceI[] iVec = av.getAlignment().getSequencesArray();
-    for (int i = 0; i < iVec.length; i++)
-    {
-      sg.addSequence(iVec[i], false);
-      iVec[i] = null;
-    }
-    iVec = null;
+    SequenceGroup sg = new SequenceGroup(av.getAlignment().getSequences());
     sg.setStartRes(res);
     sg.setEndRes(res);
 
@@ -266,29 +266,26 @@ public class ScalePanel extends JPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on mouseUp is to set the limit of the current selection group (if
+   * there is one) and broadcast the selection
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseReleased(MouseEvent evt)
   {
     mouseDragging = false;
+    ap.getSeqPanel().stopScrolling();
 
-    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);
-    }
-
-    if (res >= av.getAlignment().getWidth())
-    {
-      res = av.getAlignment().getWidth() - 1;
+              .visibleToAbsoluteColumn(res);
     }
+    res = Math.min(res, av.getAlignment().getWidth() - 1);
 
     if (!stretchingGroup)
     {
@@ -318,12 +315,17 @@ public class ScalePanel extends JPanel
     }
     stretchingGroup = false;
     ap.paintAlignment(false, false);
+    av.isSelectionGroupChanged(true);
+    av.isColSelChanged(true);
     av.sendSelection();
   }
 
   /**
    * Action on dragging the mouse in the scale panel is to expand or shrink the
-   * selection group range (including any hidden columns that it spans)
+   * selection group range (including any hidden columns that it spans). Note
+   * that the selection is only broadcast at the start of the drag (on
+   * mousePressed) and at the end (on mouseReleased), to avoid overload
+   * redrawing of other views.
    * 
    * @param evt
    */
@@ -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);
@@ -356,16 +358,22 @@ public class ScalePanel extends JPanel
   {
     if (mouseDragging)
     {
-      ap.getSeqPanel().scrollCanvas(null);
+      ap.getSeqPanel().stopScrolling();
     }
   }
 
+  /**
+   * Action on leaving the panel bounds with mouse drag in progress is to start
+   * scrolling the alignment in the direction of the mouse. To restrict
+   * scrolling to left-right (not up-down), the y-value of the mouse position is
+   * replaced with zero.
+   */
   @Override
   public void mouseExited(MouseEvent evt)
   {
     if (mouseDragging)
     {
-      ap.getSeqPanel().scrollCanvas(evt);
+      ap.getSeqPanel().startScrolling(new Point(evt.getX(), 0));
     }
   }
 
@@ -393,7 +401,7 @@ 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 +418,8 @@ 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 +468,7 @@ public class ScalePanel extends JPanel
         {
           if (hidden.isVisible(sel))
           {
-            sel = hidden.findColumnPosition(sel);
+            sel = hidden.absoluteToVisibleColumn(sel);
           }
           else
           {
@@ -488,7 +498,7 @@ 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())
         {
@@ -550,7 +560,11 @@ 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();
     }
   }