From f47cbc54ccc008c3e4eefd4b0e514036b7ace708 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 21 Jun 2016 10:21:23 +0100
Subject: [PATCH] =?utf8?q?JAL-1369=20ensure=20*real*=20alignment=E2=80=99s=20?=
 =?utf8?q?metadata=20written=20in=20Jalview2XML=20when=20view=20contains=20h?=
 =?utf8?q?idden=20sequences?=
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---
 src/jalview/gui/Jalview2XML.java |   24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a3604d6..5fb8e62 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -634,11 +634,15 @@ public class Jalview2XML
     object.setVersion(jalview.bin.Cache.getDefault("VERSION",
             "Development Build"));
 
-    jalview.datamodel.AlignmentI jal = av.getAlignment();
+    /**
+     * rjal is full height alignment, jal is actual alignment with full metadata
+     * but excludes hidden sequences.
+     */
+    jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
 
     if (av.hasHiddenRows())
     {
-      jal = jal.getHiddenSequences().getFullAlignment();
+      rjal = jal.getHiddenSequences().getFullAlignment();
     }
 
     SequenceSet vamsasSet = new SequenceSet();
@@ -655,6 +659,7 @@ public class Jalview2XML
       {
         // switch jal and the dataset
         jal = jal.getDataset();
+        rjal = jal;
       }
     }
     if (jal.getProperties() != null)
@@ -674,9 +679,9 @@ public class Jalview2XML
     Set<String> calcIdSet = new HashSet<String>();
 
     // SAVE SEQUENCES
-    for (int i = 0; i < jal.getHeight(); i++)
+    for (int i = 0; i < rjal.getHeight(); i++)
     {
-      final SequenceI jds = jal.getSequenceAt(i);
+      final SequenceI jds = rjal.getSequenceAt(i);
       final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
               : jds.getDatasetSequence();
       String id = seqHash(jds);
@@ -715,20 +720,21 @@ public class Jalview2XML
         // Store any sequences this sequence represents
         if (av.hasHiddenRows())
         {
+          // use rjal, contains the full height alignment
           jseq.setHidden(av.getAlignment().getHiddenSequences()
                   .isHidden(jds));
 
-          if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
+          if (av.isHiddenRepSequence(rjal.getSequenceAt(i)))
           {
             jalview.datamodel.SequenceI[] reps = av
-                    .getRepresentedSequences(jal.getSequenceAt(i))
-                    .getSequencesInOrder(jal);
+                    .getRepresentedSequences(rjal.getSequenceAt(i))
+                    .getSequencesInOrder(rjal);
 
             for (int h = 0; h < reps.length; h++)
             {
-              if (reps[h] != jal.getSequenceAt(i))
+              if (reps[h] != rjal.getSequenceAt(i))
               {
-                jseq.addHiddenSequences(jal.findIndex(reps[h]));
+                jseq.addHiddenSequences(rjal.findIndex(reps[h]));
               }
             }
           }
-- 
1.7.10.2