From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 19 Aug 2016 15:47:13 +0000 (+0100)
Subject: JAL-2154 - possible patch .. but leads to new stringify difference:
X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~28
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=355b140aeb3c249120a37f5251b537703a0b0938;p=jalview.git

JAL-2154 - possible patch .. but leads to new stringify difference:
expected to see below in dataset, but it doesn’t appear in recovered:
>ENSMUSP00000131873/1-222 ENSEMBL (Protein)
MASPLTRFLSLNLLLLGESIILGSGEAKPQAPELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSS
KLPQPTFVVYMASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVP
VLQKVNSTTTKPVLRTPSPVHPTGTSQPQRPEDCRPRGSVKGTGLDFACDIYIWAPLAGICVALLLSLIITL
ICYHSR

This is actually a duplicate sequence in dataset.. so difference may be due to normalisation when project file is written out
---

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 56b7255..c80f3de 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2824,7 +2824,7 @@ public class Jalview2XML
         } else {
           incompleteSeqs.remove(seqId);
         }
-        if (vamsasSeq[vi].getId().equals(seqId))
+        if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
         {
           // most likely we are reading a dataset XML document so
           // update from vamsasSeq section of XML for this sequence