JAL-3705 unit test and "fix" borrowing unused schema attribute

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ccd9ab0..1851be7 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -2547,63 +2547,61 @@ public class Jalview2XML
   private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
           SequenceI parentseq, SequenceI jds, boolean recurse)
   {
-    Mapping mp = null;
-    if (jmp.getMap() != null)
+    if (jmp.getMap() == null)
     {
-      mp = new Mapping();
+      return null;
+    }
+    Mapping mp = new Mapping();
+
+    if (jmp.getMappedFromId() != null)
+    {
+      mp.setMappingType(jmp.getMappedFromId());
+    }
+    
+    jalview.util.MapList mlst = jmp.getMap();
+    List<int[]> r = mlst.getFromRanges();
+    for (int[] range : r)
+    {
+      MapListFrom mfrom = new MapListFrom();
+      mfrom.setStart(range[0]);
+      mfrom.setEnd(range[1]);
+      mp.getMapListFrom().add(mfrom);
+    }
+    r = mlst.getToRanges();
+    for (int[] range : r)
+    {
+      MapListTo mto = new MapListTo();
+      mto.setStart(range[0]);
+      mto.setEnd(range[1]);
+      mp.getMapListTo().add(mto);
+    }
+    mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
+    mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
+    if (jmp.getTo() != null)
+    {
+      // check/create ID for the sequence referenced by getTo()
 
-      jalview.util.MapList mlst = jmp.getMap();
-      List<int[]> r = mlst.getFromRanges();
-      for (int[] range : r)
+      String jmpid = "";
+      SequenceI ps = null;
+      if (parentseq != jmp.getTo()
+              && parentseq.getDatasetSequence() != jmp.getTo())
       {
-        MapListFrom mfrom = new MapListFrom();
-        mfrom.setStart(range[0]);
-        mfrom.setEnd(range[1]);
-        // mp.addMapListFrom(mfrom);
-        mp.getMapListFrom().add(mfrom);
+        // chaining dbref rather than a handshaking one
+        jmpid = seqHash(ps = jmp.getTo());
       }
-      r = mlst.getToRanges();
-      for (int[] range : r)
+      else
       {
-        MapListTo mto = new MapListTo();
-        mto.setStart(range[0]);
-        mto.setEnd(range[1]);
-        // mp.addMapListTo(mto);
-        mp.getMapListTo().add(mto);
+        jmpid = seqHash(ps = parentseq);
       }
-      mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
-      mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
-      if (jmp.getTo() != null)
+      mp.setDseqFor(jmpid);
+      if (!seqRefIds.containsKey(jmpid))
       {
-        // MappingChoice mpc = new MappingChoice();
-
-        // check/create ID for the sequence referenced by getTo()
-
-        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);
-        mp.setDseqFor(jmpid);
-        if (!seqRefIds.containsKey(jmpid))
-        {
-          jalview.bin.Cache.log.debug("creatign new DseqFor ID");
-          seqRefIds.put(jmpid, ps);
-        }
-        else
-        {
-          jalview.bin.Cache.log.debug("reusing DseqFor ID");
-        }
-
-        // mp.setMappingChoice(mpc);
+        jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+        seqRefIds.put(jmpid, ps);
+      }
+      else
+      {
+        jalview.bin.Cache.log.debug("reusing DseqFor ID");
       }
     }
     return mp;
@@ -5637,6 +5635,8 @@ public class Jalview2XML
             fto, m.getMapFromUnit().intValue(),
             m.getMapToUnit().intValue());
 
+    jmap.setMappedFromId(m.getMappingType());
+    
     /*
      * (optional) choice of dseqFor or Sequence
      */