X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=2139b6b78814830eeaed2742911a6142f2f70b6a;hb=b8196b19d8f419759df704d0f016de59b0c6ead0;hp=795faffd3f0705eec5c09b2395c4bf2bf31e2804;hpb=3cdfc5e46776dbb8127f0a5b64df3545b988e3d9;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 795faff..2139b6b 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -39,13 +39,12 @@ import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.RenderingHints;
-import java.awt.Shape;
 import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
 import java.util.Iterator;
 import java.util.List;
 
-import javax.swing.JComponent;
+import javax.swing.JPanel;
 
 /**
  * The Swing component on which the alignment sequences, and annotations (if
@@ -53,7 +52,7 @@ import javax.swing.JComponent;
  * Wrapped mode, but not the scale above in Unwrapped mode.
  * 
  */
-public class SeqCanvas extends JComponent implements ViewportListenerI
+public class SeqCanvas extends JPanel implements ViewportListenerI
 {
   /*
    * pixels gap between sequences and annotations when in wrapped mode
@@ -93,7 +92,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
   private int wrappedVisibleWidths; // number of wrapped widths displayed
 
-  private Graphics2D gg;
+  // Don't do this! Graphics handles are supposed to be transient
+  //private Graphics2D gg;
 
   /**
    * Creates a new SeqCanvas object.
@@ -114,7 +114,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
   public SequenceRenderer getSequenceRenderer()
   {
-    return seqRdr;
+    return seqRdr; 
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -200,7 +200,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int yPos = ypos + charHeight;
     int startX = startx;
     int endX = endx;
-
+    
     if (av.hasHiddenColumns())
     {
       HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
@@ -236,6 +236,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         }
       }
 
+      
       /*
        * white fill the space for the scale
        */
@@ -260,6 +261,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         g.drawString(valueAsString, xOffset, y);
       }
     }
+
   }
 
   /**
@@ -282,7 +284,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    */
   public void fastPaint(int horizontal, int vertical)
   {
-    if (fastpainting || gg == null || img == null)
+    if (fastpainting  || img == null)
     {
       return;
     }
@@ -302,6 +304,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       int transX = 0;
       int transY = 0;
       
+      Graphics gg = img.getGraphics();
       gg.copyArea(horizontal * charWidth, vertical * charHeight,
               img.getWidth(), img.getHeight(), -horizontal * charWidth,
               -vertical * charHeight);
@@ -342,7 +345,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       gg.translate(transX, transY);
       drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
       gg.translate(-transX, -transY);
-
+      gg.dispose();
+      
       // 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.
@@ -356,18 +360,19 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   @Override
   public void paintComponent(Graphics g)
   {
-    super.paintComponent(g);    
-    
+    //super.paintComponent(g); // BH 2019
+
     int charHeight = av.getCharHeight();
     int charWidth = av.getCharWidth();
-    
+
     ViewportRanges ranges = av.getRanges();
-    
+
     int width = getWidth();
     int height = getHeight();
-    
+
     width -= (width % charWidth);
     height -= (height % charHeight);
+
     
     if ((img != null) && (fastPaint
             || (getVisibleRect().width != g.getClipBounds().width)
@@ -390,19 +395,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               || height != img.getHeight())
       {
         img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
-        gg = (Graphics2D) img.getGraphics();
-        gg.setFont(av.getFont());
       }
-    
+      
+      Graphics2D gg = (Graphics2D) img.getGraphics();
+      gg.setFont(av.getFont());
+
       if (av.antiAlias)
       {
         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                 RenderingHints.VALUE_ANTIALIAS_ON);
       }
-    
+
       gg.setColor(Color.white);
       gg.fillRect(0, 0, img.getWidth(), img.getHeight());
-    
+
       if (av.getWrapAlignment())
       {
         drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
@@ -417,6 +423,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
 
       g.drawImage(img, 0, 0, this);
+      gg.dispose();
     }
 
     if (av.cursorMode)
@@ -500,9 +507,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
 
-    System.out.println(Thread.currentThread().getName()
-            + " " + System.currentTimeMillis() + " labelWidthWest: "
-            + labelWidthWest);
     return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
   }
 
@@ -691,21 +695,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int xOffset = labelWidthWest
             + ((startColumn - ranges.getStartRes()) % viewportWidth)
             * charWidth;
-    g.translate(xOffset, 0);
-
-    // When printing we have an extra clipped region,
-    // the Printable page which we need to account for here
-    Shape clip = g.getClip();
 
-    if (clip == null)
-    {
-      g.setClip(0, 0, viewportWidth * charWidth, canvasHeight);
-    }
-    else
-    {
-      g.setClip(0, (int) clip.getBounds().getY(),
-              viewportWidth * charWidth, (int) clip.getBounds().getHeight());
-    }
+    g.translate(xOffset, 0);
 
     /*
      * white fill the region to be drawn (so incremental fast paint doesn't
@@ -733,7 +724,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               startColumn, endx + 1);
       g.translate(0, -yShift);
     }
-    g.setClip(clip);
     g.translate(-xOffset, 0);
   }
 
@@ -749,6 +739,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int charWidth = av.getCharWidth();
 
     g.setFont(av.getFont());
+
     g.setColor(Color.black);
 
     int ypos = wrappedSpaceAboveAlignment;
@@ -770,6 +761,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       if (av.getScaleRightWrapped())
       {
         int x = labelWidthWest + viewportWidth * charWidth;
+        
         g.translate(x, 0);
         drawVerticalScale(g, startCol, endColumn, ypos, false);
         g.translate(-x, 0);
@@ -1102,23 +1094,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       do
       {
         g.setColor(group.getOutlineColour());
-
         drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
                 endSeq, offset);
 
         groupIndex++;
-
         if (groupIndex >= av.getAlignment().getGroups().size())
         {
           break;
         }
-
         group = av.getAlignment().getGroups().get(groupIndex);
-
       } while (groupIndex < av.getAlignment().getGroups().size());
-
     }
-
   }
 
   /**
@@ -1464,20 +1450,42 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    * Highlights search results in the visible region by rendering as white text
    * on a black background. Any previous highlighting is removed. Answers true
    * if any highlight was left on the visible alignment (so status bar should be
+   * set to match), else false. This method does _not_ set the 'fastPaint' flag,
+   * so allows the next repaint to update the whole display.
+   * 
+   * @param results
+   * @return
+   */
+  public boolean highlightSearchResults(SearchResultsI results)
+  {
+    return highlightSearchResults(results, false);
+
+  }
+  
+  /**
+   * Highlights search results in the visible region by rendering as white text
+   * on a black background. Any previous highlighting is removed. Answers true
+   * if any highlight was left on the visible alignment (so status bar should be
    * set to match), else false.
    * <p>
-   * Currently fastPaint is not implemented for wrapped alignments. If a wrapped
-   * alignment had to be scrolled to show the highlighted region, then it should
-   * be fully redrawn, otherwise a fast paint can be performed. This argument
-   * could be removed if fast paint of scrolled wrapped alignment is coded in
-   * future (JAL-2609).
+   * Optionally, set the 'fastPaint' flag for a faster redraw if only the
+   * highlighted regions are modified. This speeds up highlighting across linked
+   * alignments.
+   * <p>
+   * Currently fastPaint is not implemented for scrolled wrapped alignments. If
+   * a wrapped alignment had to be scrolled to show the highlighted region, then
+   * it should be fully redrawn, otherwise a fast paint can be performed. This
+   * argument could be removed if fast paint of scrolled wrapped alignment is
+   * coded in future (JAL-2609).
    * 
    * @param results
-   * @param noFastPaint
+   * @param doFastPaint
+   *          if true, sets a flag so the next repaint only redraws the modified
+   *          image
    * @return
    */
   public boolean highlightSearchResults(SearchResultsI results,
-          boolean noFastPaint)
+          boolean doFastPaint)
   {
     if (fastpainting)
     {
@@ -1486,7 +1494,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     boolean wrapped = av.getWrapAlignment();
     try
     {
-      fastPaint = !noFastPaint;
+      fastPaint = doFastPaint;
       fastpainting = fastPaint;
 
       /*
@@ -1543,7 +1551,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    */
   protected boolean drawMappedPositions(SearchResultsI results)
   {
-    if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
+    if ((results == null) || (img == null)) // JAL-2784 check gg is not null
     {
       return false;
     }
@@ -1615,9 +1623,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       }
       int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
       int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
+      Graphics gg = img.getGraphics();
       gg.translate(transX, transY);
       drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
       gg.translate(-transX, -transY);
+      gg.dispose();
     }
 
     return matchFound;
@@ -1738,7 +1748,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       return;
     }
 
-    if (fastpainting || gg == null)
+    if (fastpainting || img == null)
     {
       return;
     }
@@ -1748,6 +1758,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     try
     {
+      
+      Graphics gg = img.getGraphics();
+      
       calculateWrappedGeometry(getWidth(), getHeight());
 
       /*
@@ -1776,6 +1789,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
        */
       drawWrappedDecorators(gg, ranges.getStartRes());
 
+      gg.dispose();
+      
       repaint();
     } finally
     {
@@ -1799,6 +1814,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       return;
     }
 
+    Graphics gg = img.getGraphics();
+    
     ViewportRanges ranges = av.getRanges();
     int viewportWidth = ranges.getViewportWidth();
     int charWidth = av.getCharWidth();
@@ -1825,6 +1842,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       /*
        * white fill first to erase annotations
        */
+      
+      
       gg.translate(xOffset, 0);
       gg.setColor(Color.white);
       gg.fillRect(labelWidthWest, ypos,
@@ -1832,6 +1851,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       gg.translate(-xOffset, 0);
 
       drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
+      
     }
 
     /*
@@ -1875,7 +1895,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       gg.setColor(Color.white);
       gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow);
     }
-  }
+    gg.dispose();
+ }
 
   /**
    * Shifts the visible alignment by the specified number of columns - left if
@@ -1891,6 +1912,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     {
       return;
     }
+
+    Graphics gg = img.getGraphics();
+
     int charWidth = av.getCharWidth();
 
     int canvasHeight = getHeight();
@@ -1964,11 +1988,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
                   * charWidth, heightToCopy, widthToCopy,
                   -wrappedRepeatHeightPx);
         }
-
         y += wrappedRepeatHeightPx;
         xpos += viewportWidth;
       }
     }
+    gg.dispose();
   }
 
   
@@ -1984,7 +2008,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    */
   protected boolean drawMappedPositionsWrapped(SearchResultsI results)
   {
-    if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
+    if ((results == null) || (img == null)) // JAL-2784 check gg is not null
     {
       return false;
     }
@@ -2019,6 +2043,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
 
+    
+    Graphics gg = img.getGraphics();
+
     for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
             .getEndSeq(); seqNo++)
     {
@@ -2089,6 +2116,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       }
     }
   
+    gg.dispose();
+
     return matchFound;
   }