Merge branch 'features/JAL-2295setChimeraAttributes' into

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 544835d..94d0dd1 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,6 +20,17 @@
  */
 package jalview.viewmodel;
 
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
@@ -57,17 +68,6 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -597,7 +597,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean ignoreGapsInConsensusCalculation = false;
 
-  protected ResidueShaderI globalColourScheme;
+  protected ResidueShaderI residueShading;
 
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
@@ -615,25 +615,22 @@ public abstract class AlignmentViewport implements AlignViewportI,
      * this means that any conservation or PID threshold settings
      * persist when the alignment colour scheme is changed
      */
-    if (globalColourScheme == null)
+    if (residueShading == null)
     {
-      globalColourScheme = new ResidueShader(viewStyle);
+      residueShading = new ResidueShader(viewStyle);
     }
-    globalColourScheme.setColourScheme(cs);
+    residueShading.setColourScheme(cs);
 
     // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
     // ...problem: groups need these, but do not currently have a ViewStyle
 
     if (cs != null)
     {
-      // if (getConservationSelected() || getAbovePIDThreshold()
-      // || cs instanceof PIDColourScheme
-      // || cs instanceof Blosum62ColourScheme)
       if (getConservationSelected())
       {
-        globalColourScheme.setConservation(hconservation);
+        residueShading.setConservation(hconservation);
       }
-      globalColourScheme.alignmentChanged(alignment, hiddenRepSequences);
+      residueShading.alignmentChanged(alignment, hiddenRepSequences);
     }
 
     /*
@@ -661,20 +658,22 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public ColourSchemeI getGlobalColourScheme()
   {
-    return globalColourScheme == null ? null : globalColourScheme
+    return residueShading == null ? null : residueShading
             .getColourScheme();
   }
 
   @Override
-  public ResidueShaderI getViewportColourScheme()
+  public ResidueShaderI getResidueShading()
   {
-    return globalColourScheme;
+    return residueShading;
   }
 
   protected AlignmentAnnotation consensus;
 
   protected AlignmentAnnotation complementConsensus;
 
+  protected AlignmentAnnotation gapcounts;
+
   protected AlignmentAnnotation strucConsensus;
 
   protected AlignmentAnnotation conservation;
@@ -777,6 +776,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
+  public AlignmentAnnotation getAlignmentGapAnnotation()
+  {
+    return gapcounts;
+  }
+
+  @Override
   public AlignmentAnnotation getComplementConsensusAnnotation()
   {
     return complementConsensus;
@@ -816,7 +821,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (consensus == null || !autoCalculateConsensus)
+    if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
     {
       return;
     }
@@ -928,7 +933,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     hconsensus = null;
     hcomplementConsensus = null;
     // colour scheme may hold reference to consensus
-    globalColourScheme = null;
+    residueShading = null;
     // TODO remove listeners from changeSupport?
     changeSupport = null;
     setAlignment(null);
@@ -1076,7 +1081,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
-   * Set the selection group for this window.
+   * Set the selection group for this window. Also sets the current alignment as
+   * the context for the group, if it does not already have one.
    * 
    * @param sg
    *          - group holding references to sequences in this alignment view
@@ -1086,6 +1092,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setSelectionGroup(SequenceGroup sg)
   {
     selectionGroup = sg;
+    if (sg != null && sg.getContext() == null)
+    {
+      sg.setContext(alignment);
+    }
   }
 
   public void setHiddenColumns(ColumnSelection colsel)
@@ -1198,9 +1208,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
     if (ap != null)
     {
       updateConsensus(ap);
-      if (globalColourScheme != null)
+      if (residueShading != null)
       {
-        globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+        residueShading.setThreshold(residueShading.getThreshold(),
                 ignoreGapsInConsensusCalculation);
       }
     }
@@ -1846,7 +1856,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   void updateAllColourSchemes()
   {
-    ResidueShaderI rs = globalColourScheme;
+    ResidueShaderI rs = residueShading;
     if (rs != null)
     {
       rs.alignmentChanged(alignment, hiddenRepSequences);
@@ -1890,6 +1900,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
       consensus = new AlignmentAnnotation("Consensus", "PID",
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
+      gapcounts = new AlignmentAnnotation("Occupancy",
+              "Number of aligned positions",
+              new Annotation[1], 0f, alignment.getHeight(),
+              AlignmentAnnotation.BAR_GRAPH);
+      initGapCounts(gapcounts);
 
       initComplementConsensus();
     }
@@ -1942,6 +1957,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
+  // these should be extracted from the view model - style and settings for
+  // derived annotation
+  private void initGapCounts(AlignmentAnnotation counts)
+  {
+    counts.hasText = false;
+    counts.autoCalculated = true;
+    counts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+    if (showConsensus)
+    {
+      alignment.addAnnotation(counts);
+    }
+  }
+
   private void initConservation()
   {
     if (showConservation)
@@ -2428,6 +2457,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setViewStyle(ViewStyleI settingsForView)
   {
     viewStyle = new ViewStyle(settingsForView);
+    if (residueShading != null)
+    {
+      residueShading.setConservationApplied(settingsForView
+              .isConservationColourSelected());
+    }
   }
 
   @Override
@@ -2812,7 +2846,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean selectionIsDefinedGroup = false;
 
-
   @Override
   public boolean isSelectionDefinedGroup()
   {