JAL-2371 create a default ResidueShader when constructing the viewport

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index eefad4a..cdf0758 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -52,6 +52,7 @@ import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ComplementConsensusThread;
@@ -608,7 +609,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean ignoreGapsInConsensusCalculation = false;
 
-  protected ResidueShaderI residueShading;
+  protected ResidueShaderI residueShading = new ResidueShader();
 
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
@@ -832,7 +833,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
+    if (consensus == null || !autoCalculateConsensus)
     {
       return;
     }
@@ -1295,6 +1296,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showConsensus = true;
 
+  protected boolean showOccupancy = true;
+
   private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
@@ -1907,14 +1910,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         initRNAStructure();
       }
-      consensus = new AlignmentAnnotation("Consensus", "PID",
+      consensus = new AlignmentAnnotation("Consensus",
+              MessageManager.getString("label.consensus_descr"),
               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);
+      initGapCounts();
 
       initComplementConsensus();
     }
@@ -1948,7 +1948,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
         if (doConsensus)
         {
           complementConsensus = new AlignmentAnnotation("cDNA Consensus",
-                  "PID for cDNA", new Annotation[1], 0f, 100f,
+                  MessageManager
+                          .getString("label.complement_consensus_descr"),
+                  new Annotation[1], 0f, 100f,
                   AlignmentAnnotation.BAR_GRAPH);
           initConsensus(complementConsensus);
           return true;
@@ -1971,15 +1973,20 @@ 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)
+  private void initGapCounts()
   {
-    counts.hasText = false;
-    counts.autoCalculated = true;
-    counts.graph = AlignmentAnnotation.BAR_GRAPH;
-
-    if (showConsensus)
+    if (showOccupancy)
     {
-      alignment.addAnnotation(counts);
+      gapcounts = new AlignmentAnnotation("Occupancy",
+              MessageManager.getString("label.occupancy_descr"),
+              new Annotation[1], 0f,
+              alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+      gapcounts.hasText = true;
+      gapcounts.autoCalculated = true;
+      gapcounts.scaleColLabel = true;
+      gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+      alignment.addAnnotation(gapcounts);
     }
   }
 
@@ -1990,8 +1997,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       if (conservation == null)
       {
         conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than "
-                        + getConsPercGaps() + "% gaps", new Annotation[1],
+                MessageManager.formatMessage("label.conservation_descr",
+                        getConsPercGaps()), new Annotation[1],
                 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
@@ -2007,7 +2014,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       if (quality == null)
       {
         quality = new AlignmentAnnotation("Quality",
-                "Alignment Quality based on Blosum62 scores",
+                MessageManager.getString("label.quality_descr"),
                 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         quality.hasText = true;
         quality.autoCalculated = true;
@@ -2020,7 +2027,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (alignment.hasRNAStructure() && strucConsensus == null)
     {
-      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+      strucConsensus = new AlignmentAnnotation("StrucConsensus",
+              MessageManager.getString("label.strucconsensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       strucConsensus.hasText = true;
       strucConsensus.autoCalculated = true;
@@ -2667,6 +2675,18 @@ 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