Merge branch 'bug/JAL-2811' into bug/JAL-2831

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 66739e0..4f01761 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -365,11 +365,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
             ranges.getStartRes(), ranges.getEndRes(),
             ranges.getStartSeq(), ranges.getEndSeq());
 
+    BufferedImage cursorImage = drawCursor(ranges.getStartRes(),
+            ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
+
     if ((img != null) && (fastPaint
             || (getVisibleRect().width != g.getClipBounds().width)
             || (getVisibleRect().height != g.getClipBounds().height)))
     {
-      BufferedImage lcimg = buildLocalImage(selectImage);
+      BufferedImage lcimg = buildLocalImage(selectImage, cursorImage);
       g.drawImage(lcimg, 0, 0, this);
       fastPaint = false;
     }
@@ -409,7 +412,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       }
 
       // lcimg is a local *copy* of img which we'll draw selectImage on top of
-      BufferedImage lcimg = buildLocalImage(selectImage);
+      BufferedImage lcimg = buildLocalImage(selectImage, cursorImage);
       g.drawImage(lcimg, 0, 0, this);
     }
   }
@@ -494,7 +497,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    * Make a local image by combining the cached image img
    * with any selection
    */
-  private BufferedImage buildLocalImage(BufferedImage selectImage)
+  private BufferedImage buildLocalImage(BufferedImage selectImage,
+          BufferedImage cursorImage)
   {
     // clone the cached image
     BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
@@ -509,6 +513,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
       g2d.drawImage(selectImage, 0, 0, this);
     }
+    // overlay cursor on lcimg
+    if (cursorImage != null)
+    {
+      g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+      g2d.drawImage(cursorImage, 0, 0, this);
+    }
     g2d.dispose();
 
     return lcimg;
@@ -1143,12 +1153,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         }
       }
 
-      if (av.cursorMode && cursorY == i && cursorX >= startRes
+      /*      if (av.cursorMode && cursorY == i && cursorX >= startRes
               && cursorX <= endRes)
       {
         seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
                 offset + ((i - startSeq) * charHeight));
-      }
+      }*/
     }
 
     if (av.getSelectionGroup() != null
@@ -1246,6 +1256,91 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     return selectionImage;
   }
 
+  /**
+   * Draw the cursor as a separate image and overlay
+   * 
+   * @param startRes
+   *          start residue of area to draw cursor in
+   * @param endRes
+   *          end residue of area to draw cursor in
+   * @param startSeq
+   *          start sequence of area to draw cursor in
+   * @param endSeq
+   *          end sequence of are to draw cursor in
+   * @return a transparent image of the same size as the sequence canvas, with
+   *         the cursor drawn on it, if any
+   */
+  private BufferedImage drawCursor(int startRes, int endRes, int startSeq,
+          int endSeq)
+  {
+    // define our cursor image
+    BufferedImage cursorImage = null;
+
+    // don't do work unless we have to
+    if (av.cursorMode && cursorY >= startSeq && cursorY <= endSeq)
+    {
+      int yoffset = 0;
+      int xoffset = 0;
+      int startx = startRes;
+      int endx = endRes;
+      if (av.getWrapAlignment())
+      {
+        // work out the correct offsets for the cursor
+        int charHeight = av.getCharHeight();
+        int charWidth = av.getCharWidth();
+        int canvasWidth = getWidth();
+        int canvasHeight = getHeight();
+
+        // height gap above each panel
+        int hgap = charHeight;
+        if (av.getScaleAboveWrapped())
+        {
+          hgap += charHeight;
+        }
+
+        int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+                / charWidth;
+        int cHeight = av.getAlignment().getHeight() * charHeight;
+
+        endx = startx + cWidth - 1;
+        int ypos = hgap; // vertical offset
+
+        // iterate down the wrapped panels
+        while ((ypos <= canvasHeight) && (endx < cursorX))
+        {
+          // update vertical offset
+          ypos += cHeight + getAnnotationHeight() + hgap;
+
+          // update horizontal offset
+          startx += cWidth;
+          endx = startx + cWidth - 1;
+        }
+        yoffset = ypos;
+        xoffset = labelWidthWest;
+      }
+
+      // now check if cursor is within range for x values
+      if (cursorX >= startx && cursorX <= endx)
+      {
+        // get a new image of the correct size
+        cursorImage = setupImage();
+        Graphics2D g = (Graphics2D) cursorImage.getGraphics();
+
+        // get the character the cursor is drawn at
+        SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
+        char s = seq.getCharAt(cursorX);
+
+        seqRdr.drawCursor(g, s,
+                xoffset + (cursorX - startx) * av.getCharWidth(),
+                yoffset + (cursorY - startSeq) * av.getCharHeight());
+        g.dispose();
+      }
+    }
+
+    return cursorImage;
+  }
+
+
   /*
    * Set up graphics for selection group
    */

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 0a1e8ef..81b394b 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -481,21 +481,30 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
   }
 
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  /**
+   * Draw a sequence canvas cursor
+   * 
+   * @param g
+   *          graphics context to draw on
+   * @param s
+   *          character to draw at cursor
+   * @param x1
+   *          x position of cursor in graphics context
+   * @param y1
+   *          y position of cursor in graphics context
+   */
+  public void drawCursor(Graphics g, char s, int x1, int y1)
   {
     int pady = av.getCharHeight() / 5;
     int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+    g.setColor(Color.black);
+    g.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
 
     if (av.isValidCharWidth())
     {
-      graphics.setColor(Color.white);
-
-      char s = seq.getCharAt(res);
-
+      g.setColor(Color.white);
       charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s), charOffset + x1,
+      g.drawString(String.valueOf(s), charOffset + x1,
               (y1 + av.getCharHeight()) - pady);
     }