From 355b140aeb3c249120a37f5251b537703a0b0938 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 19 Aug 2016 16:47:13 +0100 Subject: [PATCH] =?utf8?q?JAL-2154=20-=20possible=20patch=20..=20but=20leads?= =?utf8?q?=20to=20new=20stringify=20difference:=20expected=20to=20see=20belo?= =?utf8?q?w=20in=20dataset,=20but=20it=20doesn=E2=80=99t=20appear=20in=20rec?= =?utf8?q?overed:=20>ENSMUSP00000131873/1-222=20ENSEMBL=20(Protein)=20MASPLT?= =?utf8?q?RFLSLNLLLLGESIILGSGEAKPQAPELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSS?= =?utf8?q?=20KLPQPTFVVYMASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNS?= =?utf8?q?VMYFSSVVP=20VLQKVNSTTTKPVLRTPSPVHPTGTSQPQRPEDCRPRGSVKGTGLDFACDIYIW?= =?utf8?q?APLAGICVALLLSLIITL=20ICYHSR?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit This is actually a duplicate sequence in dataset.. so difference may be due to normalisation when project file is written out --- src/jalview/gui/Jalview2XML.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 -- 1.7.10.2