From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 14 Nov 2017 10:33:33 +0000 (+0000)
Subject: JAL-2831 deal with hidden cols and seqs in new cursor code
X-Git-Tag: Release_2_10_3b1~28^2~9
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=24eed665b66cab524acc09a392af9189c4b51706;p=jalview.git

JAL-2831 deal with hidden cols and seqs in new cursor code
---

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 9a1e13c..0e7b431 100644
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -625,12 +625,17 @@ public class ViewportRanges extends ViewportProperties
   {
     // if (x,y) is already visible don't do anything
     boolean changedLocation = false;
-    if (startRes > x || x > endRes || startSeq > y && y > endSeq)
+
+    int vis_x = al.getHiddenColumns().findColumnPosition(x);
+    int vis_y = al.getHiddenSequences().findIndexWithoutHiddenSeqs(y);
+
+    if (startRes > vis_x || vis_x > endRes
+            || startSeq > vis_y && vis_y > endSeq)
     {
       int width = getViewportWidth();
-      int[] oldresvalues = updateStartEndRes(x, x + width - 1);
+      int[] oldresvalues = updateStartEndRes(vis_x, vis_x + width - 1);
 
-      int startseq = y;
+      int startseq = vis_y;
       int height = getViewportHeight();
       if (startseq + height - 1 > getVisibleAlignmentHeight() - 1)
       {