JAL-845 code/refactoring/tests related to linking DNA and protein

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index ed63e0f..7145f7b 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -37,6 +37,7 @@ import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
+import jalview.util.MappingUtils;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
@@ -60,9 +61,10 @@ import java.util.Vector;
 public abstract class AlignmentViewport implements AlignViewportI
 {
   /*
-   * A viewport that is a slave of (driven by) this one in some sense.
+   * A viewport that hosts the cDna view of this (protein), or vice versa (if
+   * set).
    */
-  AlignViewportI slave = null;
+  AlignViewportI codingComplement = null;
 
   /**
    * alignment displayed in the viewport. Please use get/setter
@@ -963,6 +965,17 @@ public abstract class AlignmentViewport implements AlignViewportI
 
     hideSequence(seqs);
 
+    AlignViewportI peer = getCodingComplement();
+    if (peer != null)
+    {
+      SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(
+              selectionGroup, this, peer);
+      ((AlignmentViewport) peer).hideSequence(mappedGroup
+              .getSequencesInOrder(peer.getAlignment()));
+      peer.setSelectionGroup(null);
+
+    }
+
     setSelectionGroup(null);
   }
 
@@ -1650,21 +1663,36 @@ public abstract class AlignmentViewport implements AlignViewportI
   };
 
   @Override
-  public AlignViewportI getSlave()
+  public AlignViewportI getCodingComplement()
   {
-    return this.slave;
+    return this.codingComplement;
   }
 
+  /**
+   * Set this as the (cDna/protein) complement of the given viewport. Also
+   * ensures the reverse relationship is set on the given viewport.
+   */
   @Override
-  public void setSlave(AlignViewportI sl)
+  public void setCodingComplement(AlignViewportI av)
   {
-    if (this == sl.getSlave())
+    if (this == av)
     {
-      System.err.println("Ignoring recursive setSlave request");
+      System.err.println("Ignoring recursive setCodingComplement request");
     }
     else
     {
-      this.slave = sl;
+      this.codingComplement = av;
+      // avoid infinite recursion!
+      if (av.getCodingComplement() != this)
+      {
+        av.setCodingComplement(this);
+      }
     }
   }
+
+  @Override
+  public boolean isNucleotide()
+  {
+    return getAlignment() == null ? false : getAlignment().isNucleotide();
+  }
 }