Faster JTable processing; fixes Annotation painting issues (?)

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 1460985..1fc5734 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -31,6 +31,7 @@ import jalview.renderer.AwtRenderPanelI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
 
@@ -112,7 +113,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   public volatile BufferedImage fadedImage;
 
-  Graphics2D gg;
+  // private Graphics2D gg;
 
   public FontMetrics fm;
 
@@ -211,7 +212,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public Dimension getPreferredScrollableViewportSize()
   {
-    return getPreferredSize();
+    Dimension ps = getPreferredSize();
+    return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
   }
 
   @Override
@@ -312,7 +314,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (action.equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, LABEL);
-      String label = JvOptionPane.showInputDialog(this,
+      String label = JvOptionPane.showInputDialog(
               MessageManager.getString("label.enter_label"), exMesg);
 
       if (label == null)
@@ -808,7 +810,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else
     {
       this.setToolTipText(null);
-      ap.alignFrame.statusBar.setText(" ");
+      ap.alignFrame.setStatus(" ");
     }
   }
 
@@ -927,7 +929,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
     }
 
-    ap.alignFrame.statusBar.setText(text.toString());
+    ap.alignFrame.setStatus(text.toString());
   }
 
   /**
@@ -969,6 +971,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   private volatile boolean imageFresh = false;
+  private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle();
 
   /**
    * DOCUMENT ME!
@@ -979,17 +982,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void paintComponent(Graphics g)
   {
-    super.paintComponent(g);
-
+         
+         // BH: note that this method is generally recommended to 
+         // call super.paintComponent(g). Otherwise, the children of this
+         // component will not be rendered. That is not needed here 
+         // because AnnotationPanel does not have any children. It is
+         // just a JPanel contained in a JViewPort. 
+
+    computeVisibleRect(visibleRect);
+    
     g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
+    g.fillRect(0, 0, visibleRect.width, visibleRect.height);
 
     if (image != null)
     {
-      if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
-              || (getVisibleRect().height != g.getClipBounds().height))
+       // BH 2018 optimizing generation of new Rectangle().
+      if (fastPaint || (visibleRect.width != (clipBounds = g.getClipBounds(clipBounds)).width)
+            || (visibleRect.height != clipBounds.height))
       {
-        g.drawImage(image, 0, 0, this);
+
+         
+         g.drawImage(image, 0, 0, this);
         fastPaint = false;
         return;
       }
@@ -1000,6 +1013,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       return;
     }
+    Graphics2D gg;
     if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
@@ -1035,10 +1049,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       gg.setColor(Color.white);
       gg.fillRect(0, 0, imgWidth, image.getHeight());
       imageFresh = true;
+    } else {
+        gg = (Graphics2D) image.getGraphics();
+
     }
     
     drawComponent(gg, av.getRanges().getStartRes(),
             av.getRanges().getEndRes() + 1);
+    gg.dispose();
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
@@ -1056,7 +1074,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public void fastPaint(int horizontal)
   {
-    if ((horizontal == 0) || gg == null
+    if ((horizontal == 0) || image == null
             || av.getAlignment().getAlignmentAnnotation() == null
             || av.getAlignment().getAlignmentAnnotation().length < 1
             || av.isCalcInProgress())
@@ -1069,6 +1087,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
 
+    Graphics2D gg = (Graphics2D) image.getGraphics();
+
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
 
@@ -1088,6 +1108,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     gg.translate(-transX, 0);
 
+    gg.dispose();
+    
     fastPaint = true;
 
     // Call repaint on alignment panel so that repaints from other alignment
@@ -1231,7 +1253,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     ap = null;
     image = null;
     fadedImage = null;
-    gg = null;
+//    gg = null;
     _mwl = null;
 
     /*
@@ -1266,4 +1288,49 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       repaint();
     }
   }
+
+  /**
+   * computes the visible height of the annotation panel
+   * 
+   * @param adjustPanelHeight
+   *          - when false, just adjust existing height according to other
+   *          windows
+   * @param annotationHeight
+   * @return height to use for the ScrollerPreferredVisibleSize
+   */
+  public int adjustForAlignFrame(boolean adjustPanelHeight,
+          int annotationHeight)
+  {
+    /*
+     * Estimate available height in the AlignFrame for alignment +
+     * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+     * hscroll, status bar, insets. 
+     */
+    int stuff = (ap.getViewName() != null ? 30 : 0)
+            + (Platform.isAMac() ? 120 : 140);
+    int availableHeight = ap.alignFrame.getHeight() - stuff;
+    int rowHeight = av.getCharHeight();
+
+    if (adjustPanelHeight)
+    {
+      int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+      /*
+       * If not enough vertical space, maximize annotation height while keeping
+       * at least two rows of alignment visible
+       */
+      if (annotationHeight + alignmentHeight > availableHeight)
+      {
+        annotationHeight = Math.min(annotationHeight,
+                availableHeight - 2 * rowHeight);
+      }
+    }
+    else
+    {
+      // maintain same window layout whilst updating sliders
+      annotationHeight = Math.min(ap.annotationScroller.getSize().height,
+              availableHeight - 2 * rowHeight);
+    }
+    return annotationHeight;
+  }
 }