JAL-2811 Made it work for hidden columns/seqs too

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 394a0b6..4aa7851 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1275,13 +1275,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     // define our cursor image
     BufferedImage cursorImage = null;
 
+    // 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 && cursorY >= startSeq && cursorY <= endSeq)
+    if (av.cursorMode && 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.getWrapAlignment())
       {
         // work out the correct offsets for the cursor
@@ -1305,7 +1314,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         int ypos = hgap; // vertical offset
 
         // iterate down the wrapped panels
-        while ((ypos <= canvasHeight) && (endx < cursorX))
+        while ((ypos <= canvasHeight) && (endx < cursor_xpos))
         {
           // update vertical offset
           ypos += cHeight + getAnnotationHeight() + hgap;
@@ -1319,7 +1328,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       }
 
       // now check if cursor is within range for x values
-      if (cursorX >= startx && cursorX <= endx)
+      if (cursor_xpos >= startx && cursor_xpos <= endx)
       {
         // get a new image of the correct size
         cursorImage = setupImage();
@@ -1330,8 +1339,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         char s = seq.getCharAt(cursorX);
 
         seqRdr.drawCursor(g, s,
-                xoffset + (cursorX - startx) * av.getCharWidth(),
-                yoffset + (cursorY - startSeq) * av.getCharHeight());
+                xoffset + (cursor_xpos - startx) * av.getCharWidth(),
+                yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
         g.dispose();
       }
     }