test HMM annotaTION

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 39621c5..dfd120b 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -92,9 +92,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   FeaturesDisplayedI featuresDisplayed = null;
 
-  protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> historyList = new ArrayDeque<>();
 
-  protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> redoList = new ArrayDeque<>();
+  
 
   /**
    * alignment displayed in the viewport. Please use get/setter
@@ -609,7 +610,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean ignoreGapsInConsensusCalculation = false;
 
-  protected ResidueShaderI residueShading;
+  protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
+  protected ResidueShaderI residueShading = new ResidueShader();
 
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
@@ -696,6 +699,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected AlignmentAnnotation[] groupConservation;
 
+  protected AlignmentAnnotation hmmConsensus;
+
   /**
    * results of alignment consensus analysis for visible portion of view
    */
@@ -1113,7 +1118,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setHiddenColumns(HiddenColumns hidden)
   {
     this.alignment.setHiddenColumns(hidden);
-    // this.colSel = colsel;
   }
 
   @Override
@@ -1231,6 +1235,21 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   }
 
+  public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
+  {
+    ignoreBelowBackGroundFrequencyCalculation = b;
+    if (ap != null)
+    {
+      // updateConsensus(ap);
+      if (residueShading != null)
+      {
+        residueShading.setThreshold(residueShading.getThreshold(),
+                ignoreBelowBackGroundFrequencyCalculation);
+      }
+    }
+
+  }
+
   private long sgrouphash = -1, colselhash = -1;
 
   /**
@@ -1285,6 +1304,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ignoreGapsInConsensusCalculation;
   }
 
+  public boolean isIgnoreBelowBackground()
+  {
+    return ignoreBelowBackGroundFrequencyCalculation;
+  }
+
   // property change stuff
   // JBPNote Prolly only need this in the applet version.
   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
@@ -1298,7 +1322,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showOccupancy = true;
 
-  private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+  private Map<SequenceI, Color> sequenceColours = new HashMap<>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -1528,7 +1552,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+      hiddenRepSequences = new Hashtable<>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1736,7 +1760,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public List<int[]> getVisibleRegionBoundaries(int min, int max)
   {
-    ArrayList<int[]> regions = new ArrayList<int[]>();
+    ArrayList<int[]> regions = new ArrayList<>();
     int start = min;
     int end = max;
 
@@ -1779,7 +1803,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
           boolean selectedOnly)
   {
-    ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
     AlignmentAnnotation[] aa;
     if ((aa = alignment.getAlignmentAnnotation()) != null)
     {
@@ -1914,6 +1938,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
               MessageManager.getString("label.consensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
+
       initGapCounts();
 
       initComplementConsensus();
@@ -2133,7 +2158,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     // intersect alignment annotation with alignment groups
 
     AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
-    List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> oldrfs = new ArrayList<>();
     if (aan != null)
     {
       for (int an = 0; an < aan.length; an++)
@@ -2675,6 +2700,18 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setScaleProteinAsCdna(b);
   }
 
+  @Override
+  public boolean isProteinFontAsCdna()
+  {
+    return viewStyle.isProteinFontAsCdna();
+  }
+
+  @Override
+  public void setProteinFontAsCdna(boolean b)
+  {
+    viewStyle.setProteinFontAsCdna(b);
+  }
+
   /**
    * @return true if view should scroll to show the highlighted region of a
    *         sequence
@@ -2834,8 +2871,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionIsDefinedGroup = gps.contains(selectionGroup);
       }
     }
-    return selectionGroup.getContext() == alignment
-            || selectionIsDefinedGroup;
+    return selectionGroup.isDefined() || selectionIsDefinedGroup;
   }
 
   /**
@@ -2860,4 +2896,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return searchResults;
   }
+  
+
 }