X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=68245b6be5925b13d885e3c32a5def8370bd484d;hb=0f40a8334651302a74a223ecd3e583451302bb42;hp=3bf73df1d77775ad5d51e6e725e11c08758253f8;hpb=9de1722b93793d379233e4680afc2700c5659eea;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3bf73df..68245b6 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);
       }
     }
@@ -2353,6 +2349,7 @@ public class Jalview2XML
       initSeqRefs();
     }
     AlignFrame af = null, _af = null;
+    IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
     Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
     final String file = jprovider.getFilename();
     try
@@ -2380,13 +2377,24 @@ public class Jalview2XML
           if (true) // !skipViewport(object))
           {
             _af = loadFromObject(object, file, true, jprovider);
-            if (object.getJalviewModelSequence().getViewportCount() > 0)
+            if (_af != null
+                    && object.getJalviewModelSequence().getViewportCount() > 0)
             {
-              af = _af;
-              if (af.viewport.isGatherViewsHere())
+              if (af == null)
+              {
+                // store a reference to the first view
+                af = _af;
+              }
+              if (_af.viewport.isGatherViewsHere())
               {
-                gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+                // if this is a gathered view, keep its reference since
+                // after gathering views, only this frame will remain
+                af = _af;
+                gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
               }
+              // Save dataset to register mappings once all resolved
+              importedDatasets.put(af.viewport.getAlignment().getDataset(),
+                      af.viewport.getAlignment().getDataset());
             }
           }
           entryCount++;
@@ -2442,11 +2450,6 @@ public class Jalview2XML
       e.printStackTrace();
     }
 
-    if (Desktop.instance != null)
-    {
-      Desktop.instance.stopLoading();
-    }
-
     /*
      * Regather multiple views (with the same sequence set id) to the frame (if
      * any) that is flagged as the one to gather to, i.e. convert them to tabbed
@@ -2460,11 +2463,24 @@ public class Jalview2XML
     }
 
     restoreSplitFrames();
-
+    for (AlignmentI ds : importedDatasets.keySet())
+    {
+      if (ds.getCodonFrames() != null)
+      {
+        StructureSelectionManager.getStructureSelectionManager(
+                Desktop.instance).registerMappings(ds.getCodonFrames());
+      }
+    }
     if (errorMessage != null)
     {
       reportErrors();
     }
+
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
+
     return af;
   }
 
@@ -2837,7 +2853,39 @@ 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 +2898,6 @@ 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??