Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a48c910..364222e 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;
@@ -45,6 +46,7 @@ import jalview.workers.StrucConsensusThread;
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.BitSet;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -59,6 +61,12 @@ import java.util.Vector;
  */
 public abstract class AlignmentViewport implements AlignViewportI
 {
+  /*
+   * A viewport that hosts the cDna view of this (protein), or vice versa (if
+   * set).
+   */
+  AlignViewportI codingComplement = null;
+
   /**
    * alignment displayed in the viewport. Please use get/setter
    */
@@ -637,10 +645,6 @@ public abstract class AlignmentViewport implements AlignViewportI
   public void setHiddenColumns(ColumnSelection colsel)
   {
     this.colSel = colsel;
-    if (colSel.getHiddenColumns() != null)
-    {
-      hasHiddenColumns = true;
-    }
   }
 
   @Override
@@ -676,15 +680,22 @@ public abstract class AlignmentViewport implements AlignViewportI
     this.hiddenRepSequences = hiddenRepSequences;
   }
 
-  protected boolean hasHiddenColumns = false;
+  @Override
+  public boolean hasHiddenColumns()
+  {
+    return colSel != null && colSel.hasHiddenColumns();
+  }
 
   public void updateHiddenColumns()
   {
-    hasHiddenColumns = colSel.hasHiddenColumns();
+    // this method doesn't really do anything now. But - it could, since a
+    // column Selection could be in the process of modification
+    // hasHiddenColumns = colSel.hasHiddenColumns();
   }
 
   protected boolean hasHiddenRows = false;
 
+  @Override
   public boolean hasHiddenRows()
   {
     return hasHiddenRows;
@@ -810,7 +821,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   protected boolean showConsensus = true;
 
-  Hashtable sequenceColours;
+  private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
 
   /**
    * Property change listener for changes in alignment
@@ -864,7 +875,6 @@ public abstract class AlignmentViewport implements AlignViewportI
     colSel.hideSelectedColumns();
     setSelectionGroup(null);
 
-    hasHiddenColumns = true;
   }
 
   public void hideColumns(int start, int end)
@@ -877,23 +887,17 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       colSel.hideColumns(start, end);
     }
-
-    hasHiddenColumns = true;
   }
 
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
-    if (colSel.getHiddenColumns() == null)
-    {
-      hasHiddenColumns = false;
-    }
+
   }
 
   public void showAllHiddenColumns()
   {
     colSel.revealAllHiddenColumns();
-    hasHiddenColumns = false;
   }
 
   // common hide/show seq stuff
@@ -1054,9 +1058,6 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   @Override
-  public abstract void sendSelection();
-
-  @Override
   public void invertColumnSelection()
   {
     colSel.invertColumnSelection(0, alignment.getWidth());
@@ -1110,11 +1111,10 @@ public abstract class AlignmentViewport implements AlignViewportI
 
 
   @Override
-  public jalview.datamodel.CigarArray getViewAsCigars(
+  public CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
-    return new jalview.datamodel.CigarArray(alignment,
-            (hasHiddenColumns ? colSel : null),
+    return new CigarArray(alignment, colSel,
             (selectedRegionOnly ? selectionGroup : null));
   }
 
@@ -1132,7 +1132,8 @@ public abstract class AlignmentViewport implements AlignViewportI
           boolean selectedOnly, boolean markGroups)
   {
     return new AlignmentView(alignment, colSel, selectionGroup,
-            hasHiddenColumns, selectedOnly, markGroups);
+            colSel != null && colSel.hasHiddenColumns(), selectedOnly,
+            markGroups);
   }
 
 
@@ -1158,7 +1159,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     }
 
     selection = new String[iSize];
-    if (hasHiddenColumns)
+    if (colSel != null && colSel.hasHiddenColumns())
     {
       selection = colSel.getVisibleSequenceStrings(start, end, seqs);
     }
@@ -1183,7 +1184,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
     do
     {
-      if (hasHiddenColumns)
+      if (colSel != null && colSel.hasHiddenColumns())
       {
         if (start == 0)
         {
@@ -1204,7 +1205,7 @@ public abstract class AlignmentViewport implements AlignViewportI
       regions.addElement(new int[]
       { start, end });
 
-      if (hasHiddenColumns)
+      if (colSel != null && colSel.hasHiddenColumns())
       {
         start = colSel.adjustForHiddenColumns(end);
         start = colSel.getHiddenBoundaryLeft(start) + 1;
@@ -1576,11 +1577,13 @@ public abstract class AlignmentViewport implements AlignViewportI
     this.displayReferenceSeq = displayReferenceSeq;
   }
 
+  @Override
   public boolean isColourByReferenceSeq()
   {
     return alignment.hasSeqrep() && colourByReferenceSeq;
   }
 
+  @Override
   public void setColourByReferenceSeq(boolean colourByReferenceSeq)
   {
     this.colourByReferenceSeq = colourByReferenceSeq;
@@ -1589,26 +1592,13 @@ public abstract class AlignmentViewport implements AlignViewportI
   @Override
   public Color getSequenceColour(SequenceI seq)
   {
-    Color sqc = Color.white;
-    if (sequenceColours != null)
-    {
-      sqc = (Color) sequenceColours.get(seq);
-      if (sqc == null)
-      {
-        sqc = Color.white;
-      }
-    }
-    return sqc;
+    Color sqc = sequenceColours.get(seq);
+    return (sqc == null ? Color.white : sqc);
   }
 
   @Override
   public void setSequenceColour(SequenceI seq, Color col)
   {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-
     if (col == null)
     {
       sequenceColours.remove(seq);
@@ -1622,10 +1612,6 @@ public abstract class AlignmentViewport implements AlignViewportI
   @Override
   public void updateSequenceIdColours()
   {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
     for (SequenceGroup sg : alignment.getGroups())
     {
       if (sg.idColour != null)
@@ -1641,9 +1627,43 @@ public abstract class AlignmentViewport implements AlignViewportI
   @Override
   public void clearSequenceColours()
   {
-    sequenceColours = null;
+    sequenceColours.clear();
   };
 
+  @Override
+  public AlignViewportI getCodingComplement()
+  {
+    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 setCodingComplement(AlignViewportI av)
+  {
+    if (this == av)
+    {
+      System.err.println("Ignoring recursive setCodingComplement request");
+    }
+    else
+    {
+      this.codingComplement = av;
+      // avoid infinite recursion!
+      if (av.getCodingComplement() != this)
+      {
+        av.setCodingComplement(this);
+      }
+    }
+  }
+
+  @Override
+  public boolean isNucleotide()
+  {
+    return getAlignment() == null ? false : getAlignment().isNucleotide();
+  }
+
   FeaturesDisplayedI featuresDisplayed = null;
 
   @Override
@@ -1728,5 +1748,4 @@ public abstract class AlignmentViewport implements AlignViewportI
   {
     this.rightAlignIds = rightAlignIds;
   }
-
 }