From 2f0ad8e5b9b1fbb89be632d19ba1ff78d34b9399 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 13 Nov 2017 16:42:20 +0000
Subject: [PATCH] JAl-2811 Working for wrapped panels too

---
 src/jalview/gui/SeqCanvas.java |   61 +++++++++++++++++++++++++++++-----------
 1 file changed, 44 insertions(+), 17 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index bd2862a..2d040a3 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1275,8 +1275,48 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     // define our cursor image
     BufferedImage cursorImage = null;
 
+    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;
+    }
+
     if (av.cursorMode && cursorY >= startSeq && cursorY <= endSeq
-            && cursorX >= startRes && cursorX <= endRes)
+            && cursorX >= startx && cursorX <= endx)
     {
       // get a new image of the correct size
       cursorImage = setupImage();
@@ -1286,29 +1326,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
       char s = seq.getCharAt(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))
-        {
-          offset += wrappedRepeatHeightPx;
-          currentWidth++;
-        }
-      }
-
       seqRdr.drawCursor(g, s,
-              (cursorX - startRes) * av.getCharWidth(),
-              offset + ((cursorY - startSeq) * av.getCharHeight()));
+              xoffset + (cursorX - startx) * av.getCharWidth(),
+              yoffset + (cursorY - startSeq) * av.getCharHeight());
       g.dispose();
     }
 
     return cursorImage;
   }
 
+
   /*
    * Set up graphics for selection group
    */
-- 
1.7.10.2