From: Jim Procter Date: Sat, 23 Jul 2016 10:09:48 +0000 (+0100) Subject: JAL-2154 patch the hack (Jalview2XML tests pass) X-Git-Tag: Release_2_10_0~125^2~8 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7c25229cd1f73806388e1d08f3f67f05cd332133;p=jalview.git JAL-2154 patch the hack (Jalview2XML tests pass) --- diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 3f38082..1a82a68 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -2666,7 +2666,7 @@ public class Jalview2XML // LOAD SEQUENCES List hiddenSeqs = null; - jalview.datamodel.Sequence jseq; + List tmpseqs = new ArrayList(); @@ -2688,14 +2688,14 @@ public class Jalview2XML } else { - jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(), + tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(), vamsasSeq[vi].getSequence()); - jseq.setDescription(vamsasSeq[vi].getDescription()); - jseq.setStart(jseqs[i].getStart()); - jseq.setEnd(jseqs[i].getEnd()); - jseq.setVamsasId(uniqueSetSuffix + seqId); - seqRefIds.put(vamsasSeq[vi].getId(), jseq); - tmpseqs.add(jseq); + tmpSeq.setDescription(vamsasSeq[vi].getDescription()); + tmpSeq.setStart(jseqs[i].getStart()); + tmpSeq.setEnd(jseqs[i].getEnd()); + tmpSeq.setVamsasId(uniqueSetSuffix + seqId); + seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq); + tmpseqs.add(tmpSeq); vi++; }