From b718dc55184e25f610ba7cf8cfb26b84c179fbfd Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 29 Jul 2016 15:01:07 +0100
Subject: [PATCH] JAL-2154 only include mappings in dbref/alcodon in dataset
 XML

---
 src/jalview/gui/Jalview2XML.java |  112 +++++++++++++++++++++-----------------
 1 file changed, 62 insertions(+), 50 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3bf73df..094fa7a 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1001,7 +1001,8 @@ public class Jalview2XML
       jal = av.getAlignment();
     }
     // SAVE MAPPINGS
-    if (jal.getCodonFrames() != null)
+    // FOR DATASET
+    if (storeDS && jal.getCodonFrames() != null)
     {
       List<AlignedCodonFrame> jac = jal.getCodonFrames();
       for (AlignedCodonFrame acf : jac)
@@ -2049,16 +2050,17 @@ public class Jalview2XML
     if (jds.getDatasetSequence() != null)
     {
       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
-      if (jds.getDatasetSequence().getDBRefs() != null)
-      {
-        dbrefs = jds.getDatasetSequence().getDBRefs();
-      }
     }
     else
     {
-      vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
+      // seqId==dsseqid so we can tell which sequences really are
       // dataset sequences only
+      vamsasSeq.setDsseqid(id);
       dbrefs = jds.getDBRefs();
+      if (parentseq == null)
+      {
+        parentseq = jds;
+      }
     }
     if (dbrefs != null)
     {
@@ -2110,38 +2112,32 @@ public class Jalview2XML
       if (jmp.getTo() != null)
       {
         MappingChoice mpc = new MappingChoice();
-        if (recurse
-                && (parentseq != jmp.getTo() || parentseq
-                        .getDatasetSequence() != jmp.getTo()))
+
+        // check/create ID for the sequence referenced by getTo()
+
+        String jmpid = "";
+        SequenceI ps = null;
+        if (parentseq != jmp.getTo()
+                && parentseq.getDatasetSequence() != jmp.getTo())
         {
-          mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
-                  jmp.getTo(), jds));
+          // chaining dbref rather than a handshaking one
+          jmpid = seqHash(ps = jmp.getTo());
         }
         else
         {
-          String jmpid = "";
-          SequenceI ps = null;
-          if (parentseq != jmp.getTo()
-                  && parentseq.getDatasetSequence() != jmp.getTo())
-          {
-            // chaining dbref rather than a handshaking one
-            jmpid = seqHash(ps = jmp.getTo());
-          }
-          else
-          {
-            jmpid = seqHash(ps = parentseq);
-          }
-          mpc.setDseqFor(jmpid);
-          if (!seqRefIds.containsKey(mpc.getDseqFor()))
-          {
-            jalview.bin.Cache.log.debug("creatign new DseqFor ID");
-            seqRefIds.put(mpc.getDseqFor(), ps);
-          }
-          else
-          {
-            jalview.bin.Cache.log.debug("reusing DseqFor ID");
-          }
+          jmpid = seqHash(ps = parentseq);
+        }
+        mpc.setDseqFor(jmpid);
+        if (!seqRefIds.containsKey(mpc.getDseqFor()))
+        {
+          jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+          seqRefIds.put(mpc.getDseqFor(), ps);
         }
+        else
+        {
+          jalview.bin.Cache.log.debug("reusing DseqFor ID");
+        }
+
         mp.setMappingChoice(mpc);
       }
     }
@@ -2837,7 +2833,39 @@ public class Jalview2XML
     SequenceI[] orderedSeqs = tmpseqs
             .toArray(new SequenceI[tmpseqs.size()]);
 
-    AlignmentI al = new Alignment(orderedSeqs);
+    AlignmentI al = null;
+    // so we must create or recover the dataset alignment before going further
+    // ///////////////////////////////
+    if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
+    {
+      // older jalview projects do not have a dataset - so creat alignment and
+      // dataset
+      al = new Alignment(orderedSeqs);
+      al.setDataset(null);
+    }
+    else
+    {
+      boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0;
+      if (isdsal)
+      {
+        // we are importing a dataset record, so
+        // recover reference to an alignment already materialsed as dataset
+        al = getDatasetFor(vamsasSet.getDatasetId());
+      }
+      if (al == null)
+      {
+        // materialse the alignment
+        al = new Alignment(orderedSeqs);
+      }
+      if (isdsal)
+      {
+        addDatasetRef(vamsasSet.getDatasetId(), al);
+      }
+
+      // finally, verify all data in vamsasSet is actually present in al
+      // passing on flag indicating if it is actually a stored dataset
+      recoverDatasetFor(vamsasSet, al, isdsal);
+    }
 
     if (referenceseqForView != null)
     {
@@ -2850,22 +2878,6 @@ public class Jalview2XML
       al.setProperty(ssp.getKey(), ssp.getValue());
     }
 
-    // /
-    // SequenceFeatures are added to the DatasetSequence,
-    // so we must create or recover the dataset before loading features
-    // ///////////////////////////////
-    if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
-    {
-      // older jalview projects do not have a dataset id.
-      al.setDataset(null);
-    }
-    else
-    {
-      // recover dataset - passing on flag indicating if this a 'viewless'
-      // sequence set (a.k.a. a stored dataset for the project)
-      recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
-              .getViewportCount() == 0);
-    }
     // ///////////////////////////////
 
     Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
-- 
1.7.10.2