Faster JTable processing; fixes Annotation painting issues (?)

diff --git a/.gitignore b/.gitignore
index 116f2f1..e80a2b1 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,4 @@ TESTNG
 *.class
 /site1/
 /site2/
+/site3/

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 61b4565..a120403 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -228,7 +228,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
             new Dimension(10, av.getCharHeight() + fm.getDescent()));
     idwidthAdjuster.invalidate();
     scalePanelHolder.invalidate();
-    getIdPanel().getIdCanvas().gg = null;
+    // BH 2018 getIdPanel().getIdCanvas().gg = null;
     getSeqPanel().seqCanvas.img = null;
     getAnnotationPanel().adjustPanelHeight();
 
@@ -858,6 +858,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      */
     ViewportRanges ranges = av.getRanges();
     setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
+    super.paintComponent(g);
   }
 
   /**

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 5f4e9fa..1fc5734 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -113,7 +113,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   public volatile BufferedImage fadedImage;
 
-  Graphics2D gg;
+  // private Graphics2D gg;
 
   public FontMetrics fm;
 
@@ -971,6 +971,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   private volatile boolean imageFresh = false;
+  private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle();
 
   /**
    * DOCUMENT ME!
@@ -981,17 +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;
       }
@@ -1002,6 +1013,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       return;
     }
+    Graphics2D gg;
     if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
@@ -1037,10 +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);
   }
@@ -1058,7 +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())
@@ -1071,6 +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);
 
@@ -1090,6 +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
@@ -1233,7 +1253,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     ap = null;
     image = null;
     fadedImage = null;
-    gg = null;
+//    gg = null;
     _mwl = null;
 
     /*

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index cf88c90..5540c72 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -55,7 +55,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
   BufferedImage image;
 
-  Graphics2D gg;
+//  Graphics2D gg;
 
   int imgHeight = 0;
 
@@ -155,7 +155,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     /*
      * for now, not attempting fast paint of wrapped ids...
      */
-    if (gg == null || av.getWrapAlignment())
+    if (image == null || av.getWrapAlignment())
     {
       repaint();
 
@@ -164,6 +164,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     ViewportRanges ranges = av.getRanges();
 
+    Graphics2D gg = image.createGraphics();
     gg.copyArea(0, 0, getWidth(), imgHeight, 0,
             -vertical * av.getCharHeight());
 
@@ -200,6 +201,8 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     gg.translate(0, -transY);
 
+    gg.dispose();
+    
     fastPaint = true;
 
     // Call repaint on alignment panel so that repaints from other alignment
@@ -246,13 +249,15 @@ public class IdCanvas extends JPanel implements ViewportListenerI
                 BufferedImage.TYPE_INT_RGB);
     }
     
-    gg = (Graphics2D) image.getGraphics();
+    Graphics2D gg = image.createGraphics();
     
     // Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
     
     drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults);
+
+    gg.dispose();
     
     g.drawImage(image, 0, 0, this);
   }

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 641365d..6325e61 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -109,7 +109,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
 
   public SequenceRenderer getSequenceRenderer()
   {
-    return seqRdr;
+    return seqRdr; 
   }
 
   public FeatureRenderer getFeatureRenderer()

diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index bee9d83..4612acd 100644 (file)
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ

diff --git a/swingjs/timestamp b/swingjs/timestamp
index 00a8235..fe7ed5a 100644 (file)
--- a/swingjs/timestamp
+++ b/swingjs/timestamp
@@ -1 +1 @@
-20181204022550 
+20181210013635 

diff --git a/swingjs/ver/3.2.4/SwingJS-site.zip b/swingjs/ver/3.2.4/SwingJS-site.zip
index bee9d83..4612acd 100644 (file)
Binary files a/swingjs/ver/3.2.4/SwingJS-site.zip and b/swingjs/ver/3.2.4/SwingJS-site.zip differ

diff --git a/swingjs/ver/3.2.4/timestamp b/swingjs/ver/3.2.4/timestamp
index 00a8235..fe7ed5a 100644 (file)
--- a/swingjs/ver/3.2.4/timestamp
+++ b/swingjs/ver/3.2.4/timestamp
@@ -1 +1 @@
-20181204022550 
+20181210013635