JAL-3171 resolve dataset for imported projects via the alignment’s SequenceSetId

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index edadf75..5cd8f9a 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -169,6 +169,12 @@ public class Jalview2XML
 
   private static final String UTF_8 = "UTF-8";
 
+  /**
+   * prefix for recovering datasets for alignments with multiple views where
+   * non-existent dataset IDs were written for some views
+   */
+  private static final String UNIQSEQSETID = "uniqueSeqSetId.";
+
   // use this with nextCounter() to make unique names for entities
   private int counter = 0;
 
@@ -2868,6 +2874,28 @@ public class Jalview2XML
             : null;
 
     // ////////////////////////////////
+    // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
+    //
+    //
+    // If we just load in the same jar file again, the sequenceSetId
+    // will be the same, and we end up with multiple references
+    // to the same sequenceSet. We must modify this id on load
+    // so that each load of the file gives a unique id
+
+    /**
+     * used to resolve correct alignment dataset for alignments with multiple
+     * views
+     */
+    String uniqueSeqSetId = null;
+    String viewId = null;
+    if (view != null)
+    {
+      uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
+      viewId = (view.getId() == null ? null
+              : view.getId() + uniqueSetSuffix);
+    }
+
+    // ////////////////////////////////
     // LOAD SEQUENCES
 
     List<SequenceI> hiddenSeqs = null;
@@ -2985,7 +3013,7 @@ public class Jalview2XML
 
       // 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);
+      recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
     }
 
     if (referenceseqForView != null)
@@ -3533,13 +3561,6 @@ public class Jalview2XML
     // ///////////////////////////////
     // LOAD VIEWPORT
 
-    // If we just load in the same jar file again, the sequenceSetId
-    // will be the same, and we end up with multiple references
-    // to the same sequenceSet. We must modify this id on load
-    // so that each load of the file gives a unique id
-    String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
-    String viewId = (view.getId() == null ? null
-            : view.getId() + uniqueSetSuffix);
     AlignFrame af = null;
     AlignViewport av = null;
     // now check to see if we really need to create a new viewport.
@@ -5083,13 +5104,25 @@ public class Jalview2XML
   }
 
   private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
-          boolean ignoreUnrefed)
+          boolean ignoreUnrefed, String uniqueSeqSetId)
   {
     jalview.datamodel.AlignmentI ds = getDatasetFor(
             vamsasSet.getDatasetId());
     Vector dseqs = null;
     if (ds == null)
     {
+      if (!ignoreUnrefed)
+      {
+        // try to resolve the dataset via uniqueSeqSetId
+        ds = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
+        if (ds != null)
+        {
+          addDatasetRef(vamsasSet.getDatasetId(), ds);
+        }
+      }
+    }
+    if (ds == null)
+    {
       // create a list of new dataset sequences
       dseqs = new Vector();
     }
@@ -5112,6 +5145,8 @@ public class Jalview2XML
     if (al.getDataset() == null && !ignoreUnrefed)
     {
       al.setDataset(ds);
+      // register dataset for the alignment's uniqueSeqSetId for legacy projects
+      addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
     }
   }
 

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index c461210..8c3175f 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -192,6 +192,12 @@ public class Jalview2XML
 
   private static final String UTF_8 = "UTF-8";
 
+  /**
+   * prefix for recovering datasets for alignments with multiple views where
+   * non-existent dataset IDs were written for some views
+   */
+  private static final String UNIQSEQSETID = "uniqueSeqSetId.";
+
   // use this with nextCounter() to make unique names for entities
   private int counter = 0;
 
@@ -3030,6 +3036,28 @@ public class Jalview2XML
             : null;
 
     // ////////////////////////////////
+    // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
+    //
+    //
+    // If we just load in the same jar file again, the sequenceSetId
+    // will be the same, and we end up with multiple references
+    // to the same sequenceSet. We must modify this id on load
+    // so that each load of the file gives a unique id
+
+    /**
+     * used to resolve correct alignment dataset for alignments with multiple
+     * views
+     */
+    String uniqueSeqSetId = null;
+    String viewId = null;
+    if (view != null)
+    {
+      uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
+      viewId = (view.getId() == null ? null
+              : view.getId() + uniqueSetSuffix);
+    }
+
+    // ////////////////////////////////
     // LOAD SEQUENCES
 
     List<SequenceI> hiddenSeqs = null;
@@ -3150,7 +3178,7 @@ public class Jalview2XML
 
       // 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);
+      recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
     }
 
     if (referenceseqForView != null)
@@ -3690,13 +3718,6 @@ public class Jalview2XML
     // ///////////////////////////////
     // LOAD VIEWPORT
 
-    // If we just load in the same jar file again, the sequenceSetId
-    // will be the same, and we end up with multiple references
-    // to the same sequenceSet. We must modify this id on load
-    // so that each load of the file gives a unique id
-    String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
-    String viewId = (view.getId() == null ? null
-            : view.getId() + uniqueSetSuffix);
     AlignFrame af = null;
     AlignViewport av = null;
     // now check to see if we really need to create a new viewport.
@@ -5195,13 +5216,25 @@ public class Jalview2XML
   }
 
   private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
-          boolean ignoreUnrefed)
+          boolean ignoreUnrefed, String uniqueSeqSetId)
   {
     jalview.datamodel.AlignmentI ds = getDatasetFor(
             vamsasSet.getDatasetId());
     Vector dseqs = null;
     if (ds == null)
     {
+      if (!ignoreUnrefed)
+      {
+        // try to resolve the dataset via uniqueSeqSetId
+        ds = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
+        if (ds != null)
+        {
+          addDatasetRef(vamsasSet.getDatasetId(), ds);
+        }
+      }
+    }
+    if (ds == null)
+    {
       // create a list of new dataset sequences
       dseqs = new Vector();
     }
@@ -5224,6 +5257,8 @@ public class Jalview2XML
     if (al.getDataset() == null && !ignoreUnrefed)
     {
       al.setDataset(ds);
+      // register dataset for the alignment's uniqueSeqSetId for legacy projects
+      addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
     }
   }