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 (file)
--- 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