X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=d7d9ccb7a801a31ac07fc87b4f758ef76c604710;hb=8de672a19aa66c59e84511da1961dd35397c02cb;hp=4861bd5640311d0a2d5fa28ab3af2ff1af5fae4e;hpb=adf7ce928faa801045db27cb7fb998821b5eb5f1;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 4861bd5..d7d9ccb 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -151,7 +151,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     for (ScaleMark mark : marks)
     {
       int mpos = mark.column; // (i - startx - 1)
-//      System.out.println("n " + mpos +  " "  + ypos);
       if (mpos < 0)
       {
         continue;
@@ -199,9 +198,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     int startX = startx;
     int endX = endx;
     
-    //System.out.println("v " + startx +  " "  + endx + " " + ypos);
-
-
     if (av.hasHiddenColumns())
     {
       HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
@@ -237,6 +233,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
         }
       }
 
+      
       /*
        * white fill the space for the scale
        */
@@ -245,7 +242,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       // fillRect origin is top left of rectangle
       g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast,
               charHeight + 1);
- 
+
       if (value != -1)
       {
         /*
@@ -259,11 +256,9 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
         int xOffset = labelSpace - labelLength;
         g.setColor(Color.black);
         g.drawString(valueAsString, xOffset, y);
-        
-        //System.out.println("v " + valueAsString + " " + xOffset +  " "  + y);
-
       }
     }
+
   }
 
   /**
@@ -770,7 +765,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
    * @param endColumn
    * @param canvasHeight
    */
-  protected void drawWrappedWidth(Graphics g, int ypos, int startColumn,
+  protected void drawWrappedWidth(Graphics gg, int ypos, int startColumn,
           int endColumn, int canvasHeight)
   {
     ViewportRanges ranges = av.getRanges();
@@ -787,12 +782,23 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     int xOffset = labelWidthWest
             + ((startColumn - ranges.getStartRes()) % viewportWidth)
             * charWidth;
+
+    // BH 2018 note: I have switched to using Graphics.create() here because it is 
+    // more reliable (and simpler) to reset. The difference seems to be that SwingJS 
+    // automatically sets a clipping region on an image to be the image dimensions, whereas
+    // Java sets no clip for an image. (A bug? Go figure!)
+    // Since we are using an off-screen BufferedImage here, the result is that g.getClip()
+    // returns non-null in JavaScript but not Java. 
+    //
+    // Anyway, this works and, I suggest, is better design anyway. 
+    // 
+    Graphics g = gg.create();
+
     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);
@@ -803,6 +809,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
               viewportWidth * charWidth, (int) clip.getBounds().getHeight());
     }
 
+
     /*
      * white fill the region to be drawn (so incremental fast paint doesn't
      * scribble over an existing image)
@@ -828,8 +835,9 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
               startColumn, endx + 1);
       g.translate(0, -cHeight - ypos - 3);
     }
-    g.setClip(clip);
-    g.translate(-xOffset, 0);
+    g.dispose();
+//    g.translate(-xOffset, 0);
+//    g.setClip(clip);
   }
 
   /**
@@ -844,6 +852,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     int charWidth = av.getCharWidth();
 
     g.setFont(av.getFont());
+
     g.setColor(Color.black);
 
     int ypos = wrappedSpaceAboveAlignment;
@@ -866,7 +875,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       {
         int x = labelWidthWest + viewportWidth * charWidth;
         
-        //System.out.println("shifting " + x);
         g.translate(x, 0);
         drawVerticalScale(g, startCol, endColumn, ypos, false);
         g.translate(-x, 0);
@@ -1567,20 +1575,42 @@ public class SeqCanvas extends JPanel 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)
     {
@@ -1589,7 +1619,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     boolean wrapped = av.getWrapAlignment();
     try
     {
-      fastPaint = !noFastPaint;
+      fastPaint = doFastPaint;
       fastpainting = fastPaint;
 
       /*