From fa7207f0bc89596989ad270a7d92bc8fba91aea8 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 19 Aug 2016 11:18:56 +0100
Subject: [PATCH] JAL-2154 reorder the dataset sequences according to the
 dataset XML doc (which, perversely, is read after all
 views)

---
 src/jalview/gui/Jalview2XML.java |   44 ++++++++++++++++++++++++++++++++++++--
 1 file changed, 42 insertions(+), 2 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3125cba..56b7255 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -4940,7 +4940,7 @@ public class Jalview2XML
     for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
     {
       Sequence vamsasSeq = vamsasSet.getSequence(i);
-      ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
+      ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
     }
     // create a new dataset
     if (ds == null)
@@ -4967,18 +4967,29 @@ public class Jalview2XML
    *          dataset alignment
    * @param dseqs
    *          vector to add new dataset sequence to
+   * @param ignoreUnrefed
+   *          - when true, don't create new sequences from vamsasSeq if it's id
+   *          doesn't already have an asssociated Jalview sequence.
+   * @param vseqpos
+   *          - used to reorder the sequence in the alignment according to the
+   *          vamsasSeq array ordering, to preserve ordering of dataset
    */
   private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
-          AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
+          AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
   {
     // JBP TODO: Check this is called for AlCodonFrames to support recovery of
     // xRef Codon Maps
     SequenceI sq = seqRefIds.get(vamsasSeq.getId());
+    boolean reorder = false;
     SequenceI dsq = null;
     if (sq != null && sq.getDatasetSequence() != null)
     {
       dsq = sq.getDatasetSequence();
     }
+    else
+    {
+      reorder = true;
+    }
     if (sq == null && ignoreUnrefed)
     {
       return;
@@ -5074,6 +5085,35 @@ public class Jalview2XML
         // + (post ? "appended" : ""));
       }
     }
+    else
+    {
+      // sequence refs are identical. We may need to update the existing dataset
+      // alignment with this one, though.
+      if (ds != null && dseqs == null)
+      {
+        int opos = ds.findIndex(dsq);
+        SequenceI tseq = null;
+        if (opos != -1 && vseqpos != opos)
+        {
+          // remove from old position
+          ds.deleteSequence(dsq);
+        }
+        if (vseqpos < ds.getHeight())
+        {
+          if (vseqpos != opos)
+          {
+            // save sequence at destination position
+            tseq = ds.getSequenceAt(vseqpos);
+            ds.replaceSequenceAt(vseqpos, dsq);
+            ds.addSequence(tseq);
+          }
+        }
+        else
+        {
+          ds.addSequence(dsq);
+        }
+      }
+    }
   }
 
   /*
-- 
1.7.10.2