X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=36ae6827bf689684bbdf29dac6806f5c2ce2489b;hb=2630344183a212a726d06d7d7749de39404018d9;hp=772459269f0e3f806a56b662dc1a2e685f7dfe3b;hpb=06f2d682b8b68f630596e5ffa503fe0a32388002;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 7724592..36ae682 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -411,6 +411,13 @@ 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);
       g.drawImage(lcimg, 0, 0, this);
+
+    }
+
+    if (av.cursorMode)
+    {
+      drawCursor(g, ranges.getStartRes(), ranges.getEndRes(),
+              ranges.getStartSeq(), ranges.getEndSeq());
     }
   }
   
@@ -509,6 +516,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
       g2d.drawImage(selectImage, 0, 0, this);
     }
+
     g2d.dispose();
 
     return lcimg;
@@ -1142,13 +1150,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           }
         }
       }
-
-      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 +1247,96 @@ 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 void drawCursor(Graphics g, int startRes, int endRes,
+          int startSeq,
+          int endSeq)
+  {
+    // convert the cursorY into a position on the visible alignment
+    int cursor_ypos = av.getAlignment().getHiddenSequences()
+            .findIndexWithoutHiddenSeqs(cursorY);
+
+    // don't do work unless we have to
+    if (!av.getAlignment().getHiddenSequences().isHidden(cursorY)
+            && cursor_ypos >= startSeq && cursor_ypos <= endSeq)
+    {
+      int yoffset = 0;
+      int xoffset = 0;
+      int startx = startRes;
+      int endx = endRes;
+
+      // convert the cursorX into a position on the visible alignment
+      int cursor_xpos = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(cursorX);
+
+      if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
+      {
+
+        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 < cursor_xpos))
+          {
+            // 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 (cursor_xpos >= startx && cursor_xpos <= endx)
+        {
+          // get the character the cursor is drawn at
+          SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
+          char s = seq.getCharAt(cursorX);
+
+          seqRdr.drawCursor(g, s,
+                  xoffset + (cursor_xpos - startx) * av.getCharWidth(),
+                  yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
+        }
+      }
+    }
+  }
+
+
   /*
    * Set up graphics for selection group
    */
@@ -1661,6 +1752,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       repaint();
       return;
     }
+    else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
+    {
+      fastPaint = false;
+      repaint();
+      return;
+    }
 
     int scrollX = 0;
     if (eventName.equals(ViewportRanges.STARTRES)
@@ -1712,7 +1809,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       }
       else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
       {
-        fastPaint(scrollX, 0);
+        if (av.getWrapAlignment())
+        {
+          fastPaintWrapped(scrollX);
+        }
+        else
+        {
+          fastPaint(scrollX, 0);
+        }
         // bizarrely, we only need to scroll on the x value here as fastpaint
         // copies the full height of the image anyway. Passing in the y value
         // causes nasty repaint artefacts, which only disappear on a full