From: James Procter <j.procter@dundee.ac.uk>
Date: Mon, 15 May 2023 13:54:24 +0000 (+0100)
Subject: JAL-4182 patch - map selection group onto sequence positions - fixes failing test..
X-Git-Tag: Release_2_11_3_0~14^2~3^2^2~28
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=571d610157d2c8ae01464b20d6d9c1ea935705d6;p=jalview.git

JAL-4182 patch - map selection group onto sequence positions - fixes failing test..
---

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 403991a..0fdabc8 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1539,8 +1539,9 @@ public class AlignmentUtils
         int endRes = ann.annotations.length;
         if (selectionGroup != null)
         {
-          startRes = selectionGroup.getStartRes();
-          endRes = selectionGroup.getEndRes();
+          startRes = -1+Math.min(seq.getEnd(), Math.max(seq.getStart(),seq.findPosition(selectionGroup.getStartRes())));
+          endRes = -1+Math.min(seq.getEnd(),seq.findPosition(selectionGroup.getEndRes()));
+          
         }
         copyAnn.restrict(startRes, endRes + 0);