JAL-2431 show cDNA consensus after New View in split frame

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 544835d..6dcf26d 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -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);
     }
 
     /*
@@ -661,14 +658,14 @@ 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;
@@ -928,7 +925,7 @@ 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 +1073,8 @@ 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 +1084,10 @@ 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 +1200,9 @@ 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 +1848,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   void updateAllColourSchemes()
   {
-    ResidueShaderI rs = globalColourScheme;
+    ResidueShaderI rs = residueShading;
     if (rs != null)
     {
       rs.alignmentChanged(alignment, hiddenRepSequences);
@@ -1896,10 +1898,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
-   * If this is a protein alignment and there are mappings to cDNA, add the cDNA
-   * consensus annotation.
+   * If this is a protein alignment and there are mappings to cDNA, adds the
+   * cDNA consensus annotation and returns true, else returns false.
    */
-  public void initComplementConsensus()
+  public boolean initComplementConsensus()
   {
     if (!alignment.isNucleotide())
     {
@@ -1926,9 +1928,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
                   "PID for cDNA", new Annotation[1], 0f, 100f,
                   AlignmentAnnotation.BAR_GRAPH);
           initConsensus(complementConsensus);
+          return true;
         }
       }
     }
+    return false;
   }
 
   private void initConsensus(AlignmentAnnotation aa)
@@ -2428,6 +2432,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setViewStyle(ViewStyleI settingsForView)
   {
     viewStyle = new ViewStyle(settingsForView);
+    if (residueShading != null)
+    {
+      residueShading.setConservationApplied(settingsForView
+              .isConservationColourSelected());
+    }
   }
 
   @Override