From 2630344183a212a726d06d7d7749de39404018d9 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 15 Nov 2017 16:22:21 +0000
Subject: [PATCH] JAL-2831 Don't show cursor if position in hidden region

---
 src/jalview/gui/SeqCanvas.java |   79 +++++++++++++++++++++-------------------
 src/jalview/gui/SeqPanel.java  |    8 +++-
 2 files changed, 49 insertions(+), 38 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 8d9e537..36ae682 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1270,7 +1270,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
             .findIndexWithoutHiddenSeqs(cursorY);
 
     // don't do work unless we have to
-    if (cursor_ypos >= startSeq && cursor_ypos <= endSeq)
+    if (!av.getAlignment().getHiddenSequences().isHidden(cursorY)
+            && cursor_ypos >= startSeq && cursor_ypos <= endSeq)
     {
       int yoffset = 0;
       int xoffset = 0;
@@ -1281,52 +1282,56 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       int cursor_xpos = av.getAlignment().getHiddenColumns()
               .findColumnPosition(cursorX);
 
-      if (av.getWrapAlignment())
+      if (av.getAlignment().getHiddenColumns().isVisible(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())
+        if (av.getWrapAlignment())
         {
-          hgap += charHeight;
-        }
+          // 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;
+          int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+                  / charWidth;
+          int cHeight = av.getAlignment().getHeight() * charHeight;
 
-        endx = startx + cWidth - 1;
-        int ypos = hgap; // vertical offset
+          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;
+          // 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;
+            // update horizontal offset
+            startx += cWidth;
+            endx = startx + cWidth - 1;
+          }
+          yoffset = ypos;
+          xoffset = labelWidthWest;
         }
-        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);
+        // 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());
+          seqRdr.drawCursor(g, s,
+                  xoffset + (cursor_xpos - startx) * av.getCharWidth(),
+                  yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
+        }
       }
     }
   }
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 9a5f6c6..2958f9d 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -427,8 +427,14 @@ public class SeqPanel extends JPanel
                 seqCanvas.cursorY);
       }
     }
-    setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
+
+    if (!av.getAlignment().getHiddenSequences().isHidden(seqCanvas.cursorY)
+            && av.getAlignment().getHiddenColumns()
+                    .isVisible(seqCanvas.cursorX))
+    {
+      setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
+    }
 
     if (repaintNeeded)
     {
-- 
1.7.10.2