X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=4aa7851c44782deba0a0e513c2071de817e6fb51;hb=8fb1345b723e9104cab28c80b352a882e502b1ed;hp=bd2862a3b8affddc0858182222080e86f83011fd;hpb=875193c17720b95fa13a38703b1dd63949e12ca9;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index bd2862a..4aa7851 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1275,40 +1275,80 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     // define our cursor image
     BufferedImage cursorImage = null;
 
-    if (av.cursorMode && cursorY >= startSeq && cursorY <= endSeq
-            && cursorX >= startRes && cursorX <= endRes)
+    // convert the cursorY into a position on the visible alignment
+    int cursor_ypos = av.getAlignment().getHiddenColumns()
+            .findColumnPosition(cursorY);
+
+    // don't do work unless we have to
+    if (av.cursorMode && cursor_ypos >= startSeq && cursor_ypos <= endSeq)
     {
-      // get a new image of the correct size
-      cursorImage = setupImage();
-      Graphics2D g = (Graphics2D) cursorImage.getGraphics();
+      int yoffset = 0;
+      int xoffset = 0;
+      int startx = startRes;
+      int endx = endRes;
 
-      // get the character the cursor is drawn at
-      SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
-      char s = seq.getCharAt(cursorX);
+      // convert the cursorX into a position on the visible alignment
+      int cursor_xpos = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(cursorX);
 
-      int offset = 0;
       if (av.getWrapAlignment())
       {
-        // work out the correct offset for the cursor
-        offset = wrappedSpaceAboveAlignment;
-        int currentWidth = 0;
-        while ((currentWidth < wrappedVisibleWidths)
-                && (currentWidth < cursorX))
+        // 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))
         {
-          offset += wrappedRepeatHeightPx;
-          currentWidth++;
+          // update vertical offset
+          ypos += cHeight + getAnnotationHeight() + hgap;
+
+          // update horizontal offset
+          startx += cWidth;
+          endx = startx + cWidth - 1;
         }
+        yoffset = ypos;
+        xoffset = labelWidthWest;
       }
 
-      seqRdr.drawCursor(g, s,
-              (cursorX - startRes) * av.getCharWidth(),
-              offset + ((cursorY - startSeq) * av.getCharHeight()));
-      g.dispose();
+      // now check if cursor is within range for x values
+      if (cursor_xpos >= startx && cursor_xpos <= 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 + (cursor_xpos - startx) * av.getCharWidth(),
+                yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
+        g.dispose();
+      }
     }
 
     return cursorImage;
   }
 
+
   /*
    * Set up graphics for selection group
    */