Merge branch 'features/JAL-1767pcaInProject' into bug/JAL-3171_maintain_datasets_acro...

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 689261c..42760f3 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -194,6 +194,12 @@ 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;
 
@@ -1127,13 +1133,13 @@ public class Jalview2XML
           {
             TreePanel tp = (TreePanel) frames[t];
 
-            if (tp.treeCanvas.av.getAlignment() == jal)
+            if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
             {
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
               tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
               tree.setNewick(tp.getTree().print());
-              tree.setThreshold(tp.treeCanvas.threshold);
+              tree.setThreshold(tp.getTreeCanvas().getThreshold());
 
               tree.setFitToWindow(tp.fitToWindow.getState());
               tree.setFontName(tp.getTreeFont().getName());
@@ -1291,7 +1297,7 @@ public class Jalview2XML
       {
         view.setComplementId(av.getCodingComplement().getViewId());
       }
-      view.setViewName(av.viewName);
+      view.setViewName(av.getViewName());
       view.setGatheredViews(av.isGatherViewsHere());
 
       Rectangle size = ap.av.getExplodedGeometry();
@@ -3071,6 +3077,28 @@ 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;
@@ -3188,7 +3216,7 @@ 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)
@@ -3736,13 +3764,6 @@ 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.
@@ -3967,10 +3988,11 @@ public class Jalview2XML
           tp.setTitle(tree.getTitle());
           tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
                   tree.getWidth(), tree.getHeight()));
-          tp.av = av;
-          tp.treeCanvas.av = av; // af.viewport;
-          tp.treeCanvas.ap = ap; // af.alignPanel;
-
+          tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all
+          // views'
+          // works still
+          tp.getTreeCanvas().setViewport(av); // af.viewport;
+          tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
         }
         if (tp == null)
         {
@@ -3997,7 +4019,7 @@ public class Jalview2XML
         tp.showBootstrap(tree.getShowBootstrap());
         tp.showDistances(tree.getShowDistances());
 
-        tp.treeCanvas.threshold = tree.getThreshold();
+        tp.getTreeCanvas().setThreshold(tree.getThreshold());
         tp.treeCanvas.applyToAllViews = tree.isLinkToAllViews();
 
         if (tree.getCurrentTree())
@@ -4731,7 +4753,7 @@ public class Jalview2XML
 
     if (view.getViewName() != null)
     {
-      af.viewport.viewName = view.getViewName();
+      af.viewport.setViewName(view.getViewName());
       af.setInitialTabVisible();
     }
     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
@@ -5286,13 +5308,25 @@ 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();
     }
@@ -5315,6 +5349,8 @@ 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);
     }
   }
 
@@ -5656,6 +5692,9 @@ public class Jalview2XML
     initSeqRefs();
     JalviewModel jm = saveState(ap, null, null, null);
 
+    addDatasetRef(jm.getVamsasModel().getSequenceSet()[0].getDatasetId(),
+            ap.getAlignment().getDataset());
+
     uniqueSetSuffix = "";
     jm.getJalviewModelSequence().getViewport(0).setId(null);
     // we don't overwrite the view we just copied