JAL-653 (experimental) 'realise' dummy sequences in add alignment

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 92c6355..5944b80 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -482,6 +482,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getGapCharacter()
   {
     return getAlignment().getGapCharacter();
@@ -506,6 +507,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return colSel;
@@ -617,6 +619,7 @@ public class AlignViewport extends AlignmentViewport implements
   /**
    * Send the current selection to be broadcast to any selection listeners.
    */
+  @Override
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
@@ -736,6 +739,7 @@ public class AlignViewport extends AlignmentViewport implements
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
 
+  @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -750,6 +754,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return true if alignment characters should be displayed
    */
+  @Override
   public boolean isValidCharWidth()
   {
     return validCharWidth;
@@ -825,10 +830,10 @@ public class AlignViewport extends AlignmentViewport implements
    * may give the user the option to open a new frame, or split panel, with cDNA
    * and protein linked.
    * 
-   * @param al
+   * @param toAdd
    * @param title
    */
-  public void addAlignment(AlignmentI al, String title)
+  public void addAlignment(AlignmentI toAdd, String title)
   {
     // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
 
@@ -841,25 +846,37 @@ public class AlignViewport extends AlignmentViewport implements
     // TODO: create undo object for this JAL-1101
 
     /*
-     * If any cDNA/protein mappings can be made between the alignments, offer to
-     * open a linked alignment with split frame option.
+     * Ensure datasets are created for the new alignment as
+     * mappings operate on dataset sequences
+     */
+    toAdd.setDataset(null);
+
+    /*
+     * Check if any added sequence could be the object of a mapping or
+     * cross-reference; if so, make the mapping explicit 
+     */
+    realiseMappings(getAlignment(), toAdd);
+
+    /*
+     * If any cDNA/protein mappings exist or can be made between the alignments, 
+     * offer to open a split frame with linked alignments
      */
     if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
     {
-      if (al.getDataset() == null)
-      {
-        // need to create ds seqs
-        for (SequenceI sq : al.getSequences())
-        {
-          if (sq.getDatasetSequence() == null)
-          {
-            sq.createDatasetSequence();
-          }
-        }
-      }
-      if (AlignmentUtils.isMappable(al, getAlignment()))
+      // if (toAdd.getDataset() == null)
+      // {
+      // // need to create ds seqs
+      // for (SequenceI sq : toAdd.getSequences())
+      // {
+      // if (sq.getDatasetSequence() == null)
+      // {
+      // sq.createDatasetSequence();
+      // }
+      // }
+      // }
+      if (AlignmentUtils.isMappable(toAdd, getAlignment()))
       {
-        if (openLinkedAlignment(al, title))
+        if (openLinkedAlignment(toAdd, title))
         {
           return;
         }
@@ -872,9 +889,9 @@ public class AlignViewport extends AlignmentViewport implements
     // TODO: JAL-407 regardless of above - identical sequences (based on ID and
     // provenance) should share the same dataset sequence
 
-    for (int i = 0; i < al.getHeight(); i++)
+    for (int i = 0; i < toAdd.getHeight(); i++)
     {
-      getAlignment().addSequence(al.getSequenceAt(i));
+      getAlignment().addSequence(toAdd.getSequenceAt(i));
     }
 
     setEndSeq(getAlignment().getHeight());
@@ -882,6 +899,54 @@ public class AlignViewport extends AlignmentViewport implements
   }
 
   /**
+   * Check if any added sequence could be the object of a mapping or
+   * cross-reference; if so, make the mapping explicit. Returns the count of
+   * mappings updated.
+   * 
+   * @param al
+   * @param toAdd
+   */
+  protected int realiseMappings(AlignmentI al, AlignmentI toAdd)
+  {
+    // TODO this is proof of concept
+    // we might want to give the user some choice here
+    int count = 0;
+    for (SequenceI seq : toAdd.getSequences())
+    {
+      count += realiseMappingsTo(al, seq);
+    }
+    return count;
+  }
+
+  /**
+   * If the alignment holds any mappings to a dummy (placeholder) sequence that
+   * matches the given sequence, then update the mapping to point to the
+   * sequence. Returns the number of mappings updated.
+   * 
+   * @param al
+   * @param seq
+   * @return
+   */
+  protected int realiseMappingsTo(AlignmentI al, SequenceI seq)
+  {
+    int count = 0;
+    Set<AlignedCodonFrame> mappings = al.getDataset().getCodonFrames();
+    // TODO are mappings on alignment or alignment dataset?!?
+    for (AlignedCodonFrame mapping : mappings)
+    {
+      /*
+       * TODO could just go straight to realiseWith() here unless we want
+       * to give the user some choice before going ahead
+       */
+      if (mapping.isRealisableWith(seq))
+      {
+        count += mapping.realiseWith(seq);
+      }
+    }
+    return count;
+  }
+
+  /**
    * Show a dialog with the option to open and link (cDNA <-> protein) as a new
    * alignment, either as a standalone alignment or in a split frame. Returns
    * true if the new alignment was opened, false if not, because the user