JAL-653 realise virtual mappings and align when adding sequences

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 8378f30..06dc4c4 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -72,7 +72,6 @@ import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
@@ -461,7 +460,7 @@ public class AlignViewport extends AlignmentViewport implements
     AlignmentI al = getAlignment();
     if (al != null)
     {
-      Set<AlignedCodonFrame> mappings = al.getCodonFrames();
+      List<AlignedCodonFrame> mappings = al.getCodonFrames();
       if (mappings != null)
       {
         StructureSelectionManager ssm = StructureSelectionManager
@@ -482,6 +481,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getGapCharacter()
   {
     return getAlignment().getGapCharacter();
@@ -506,6 +506,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return colSel;
@@ -617,6 +618,7 @@ 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 +738,7 @@ public class AlignViewport extends AlignmentViewport implements
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
 
+  @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -750,6 +753,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return true if alignment characters should be displayed
    */
+  @Override
   public boolean isValidCharWidth()
   {
     return validCharWidth;
@@ -825,10 +829,10 @@ 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 +845,26 @@ 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 
+     */
+    getAlignment().realiseMappings(toAdd.getSequences());
+
+    /*
+     * 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 (AlignmentUtils.isMappable(toAdd, getAlignment()))
       {
-        if (openLinkedAlignment(al, title))
+        if (openLinkedAlignment(toAdd, title))
         {
           return;
         }
@@ -872,9 +877,22 @@ 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++)
+    AlignmentI al = getAlignment();
+    String gap = String.valueOf(al.getGapCharacter());
+    for (int i = 0; i < toAdd.getHeight(); i++)
     {
-      getAlignment().addSequence(al.getSequenceAt(i));
+      SequenceI seq = toAdd.getSequenceAt(i);
+      /*
+       * experimental!
+       * - 'align' any mapped sequences as per existing 
+       *    e.g. cdna to genome, domain hit to protein sequence
+       * very experimental! (need a separate menu option for this)
+       * - only add mapped sequences ('select targets from a dataset')
+       */
+      if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
+      {
+        al.addSequence(seq);
+      }
     }
 
     setEndSeq(getAlignment().getHeight());
@@ -926,7 +944,7 @@ public class AlignViewport extends AlignmentViewport implements
      * is a pre-requisite for building mappings.
      */
     al.setDataset(null);
-    AlignmentUtils.mapProteinToCdna(protein, cdna);
+    AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
 
     /*
      * Create the AlignFrame for the added alignment. If it is protein, mappings
@@ -1072,7 +1090,7 @@ public class AlignViewport extends AlignmentViewport implements
       // TODO would like next line without cast but needs more refactoring...
       final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
               .getAlignPanel();
-      complementPanel.setFollowingComplementScroll(true);
+      complementPanel.setDontScrollComplement(true);
       complementPanel.scrollToCentre(sr, verticalOffset);
     }
   }