JAL-845 - portability patch - workaround for lastToken failing for '\'

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3a40a16..67db6fc 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -30,6 +30,7 @@ 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;
@@ -47,10 +48,10 @@ 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;
-import java.util.Vector;
 
 /**
  * base class holding visualization and analysis attributes and common logic for
@@ -63,8 +64,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
         ViewStyleI
 {
   protected ViewStyleI viewStyle = new ViewStyle();
-  
-  
+
+  /**
+   * A viewport that hosts the cDna view of this (protein), or vice versa (if
+   * set).
+   */
+  AlignViewportI codingComplement = null;
+
   /**
    * @param name
    * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
@@ -1127,7 +1133,7 @@ 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
@@ -1364,9 +1370,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public abstract void sendSelection();
-
-  @Override
   public void invertColumnSelection()
   {
     colSel.invertColumnSelection(0, alignment.getWidth());
@@ -1420,10 +1423,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
 
   @Override
-  public jalview.datamodel.CigarArray getViewAsCigars(
+  public CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
-    return new jalview.datamodel.CigarArray(alignment, colSel,
+    return new CigarArray(alignment, colSel,
             (selectedRegionOnly ? selectionGroup : null));
   }
 
@@ -1485,9 +1488,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
 
   @Override
-  public int[][] getVisibleRegionBoundaries(int min, int max)
+  public List<int[]> getVisibleRegionBoundaries(int min, int max)
   {
-    Vector regions = new Vector();
+    ArrayList<int[]> regions = new ArrayList<int[]>();
     int start = min;
     int end = max;
 
@@ -1511,7 +1514,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         }
       }
 
-      regions.addElement(new int[]
+      regions.add(new int[]
       { start, end });
 
       if (colSel != null && colSel.hasHiddenColumns())
@@ -1523,10 +1526,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     int[][] startEnd = new int[regions.size()][2];
 
-    regions.copyInto(startEnd);
-
-    return startEnd;
-
+    return regions;
   }
 
   @Override
@@ -1877,35 +1877,22 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
   }
 
+  @Override
   public boolean isColourByReferenceSeq()
   {
     return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
   }
 
-
   @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);
@@ -1919,10 +1906,6 @@ 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)
@@ -1938,9 +1921,43 @@ 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
@@ -2081,7 +2098,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return viewStyle.isShowColourText();
   }
-
   /**
    * @return
    * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight()