From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 29 Jun 2023 14:38:22 +0000 (+0100)
Subject: JAL-4216 compute size of annotation using start/end of sequence and given length... 
X-Git-Tag: Release_2_11_4_0~258
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f3c0a009ab04c4e92d00cb72abbea5cbac3baeb1;p=jalview.git

JAL-4216 compute size of annotation using start/end of sequence and given length. This might not work...
---

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index c64dac1..57b406e 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -488,7 +488,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   {
     int length = sq.getLength();
     boolean ssFound = false;
-    Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+    Annotation asecstr[] = new Annotation[length + (firstResNum-sq.getStart())];
     for (int p = 0; p < length; p++)
     {
       if (secstr[p] >= 'A' && secstr[p] <= 'z')