X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=6d6d4c3e7697568115263a70fd002a63ab1b5804;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hp=d3d1b2b4b990832721a42a548598edb0c7254786;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index d3d1b2b..6d6d4c3 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -51,6 +51,37 @@ public class AlignmentView
   private boolean isNa = false;
 
   /**
+   * reference to the complementary CDS/Protein alignment for this alignment, if available
+   */
+  private AlignmentView complementView=null;
+  
+  /**
+   * setter for 
+   * @param complementView
+   */
+  public void setComplement(AlignmentView complementView)
+  {
+    this.complementView = complementView;
+    
+  }
+  /**
+   * 
+   * @return true if a complement is available
+   */
+  public boolean hasComplementView()
+  {
+    return complementView!=null;
+  }
+  /**
+   * 
+   * @return the complement view or null
+   */
+  public AlignmentView getComplementView()
+  {
+    return complementView;
+  }
+  
+  /**
    * false if the view concerns peptides
    * 
    * @return
@@ -74,7 +105,7 @@ public class AlignmentView
 
     ScGroup()
     {
-      seqs = new ArrayList<SeqCigar>();
+      seqs = new ArrayList<>();
     }
 
     /**
@@ -160,7 +191,6 @@ public class AlignmentView
     SequenceI[] selseqs;
     if (selection != null && selection.getSize() > 0)
     {
-      List<SequenceI> sel = selection.getSequences(null);
       this.selected = new ScGroup();
       selseqs = selection.getSequencesInOrder(alignment,
               selectedRegionOnly);
@@ -170,9 +200,9 @@ public class AlignmentView
       selseqs = alignment.getSequencesArray();
     }
 
-    List<List<SequenceI>> seqsets = new ArrayList<List<SequenceI>>();
+    List<List<SequenceI>> seqsets = new ArrayList<>();
     // get the alignment's group list and make a copy
-    List<SequenceGroup> grps = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> grps = new ArrayList<>();
     List<SequenceGroup> gg = alignment.getGroups();
     grps.addAll(gg);
     ScGroup[] sgrps = null;
@@ -185,7 +215,7 @@ public class AlignmentView
         // strip out any groups that do not actually intersect with the
         // visible and selected region
         int ssel = selection.getStartRes(), esel = selection.getEndRes();
-        List<SequenceGroup> isg = new ArrayList<SequenceGroup>();
+        List<SequenceGroup> isg = new ArrayList<>();
         for (SequenceGroup sg : grps)
         {
           if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel))
@@ -245,7 +275,7 @@ public class AlignmentView
               {
                 if (scGroups == null)
                 {
-                  scGroups = new ArrayList<ScGroup>();
+                  scGroups = new ArrayList<>();
                 }
                 addedgps[sg] = true;
                 scGroups.add(sgrps[sg]);