Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / src / jalview / viewmodel / seqfeatures / FeatureRendererModel.java

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index d813fe2..9733081 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -27,8 +27,10 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.schemes.Colour;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
 
 import java.awt.Color;
 import java.beans.PropertyChangeListener;
@@ -65,6 +67,12 @@ public abstract class FeatureRendererModel implements
 
   protected AlignViewportI av;
 
+  /*
+   * map holds per feature type, {{min, max}, {min, max}} feature score
+   * values for positional and non-positional features respectively
+   */
+  private Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+
   @Override
   public AlignViewportI getViewport()
   {
@@ -191,8 +199,6 @@ public abstract class FeatureRendererModel implements
     renderOrder = neworder;
   }
 
-  protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
-
   public Map<String, float[][]> getMinMax()
   {
     return minmax;
@@ -539,7 +545,7 @@ public abstract class FeatureRendererModel implements
     if (fc == null)
     {
       Color col = UserColourScheme.createColourFromName(featureType);
-      fc = new FeatureColour(col);
+      fc = new FeatureColour(new Colour(col));
       featureColours.put(featureType, fc);
     }
     return fc;
@@ -555,7 +561,7 @@ public abstract class FeatureRendererModel implements
   public Color getColour(SequenceFeature feature)
   {
     FeatureColourI fc = getFeatureStyle(feature.getType());
-    return fc.getColor(feature);
+    return ColorUtils.getColor(fc.getColor(feature));
   }
 
   protected boolean showFeature(SequenceFeature sequenceFeature)
@@ -759,9 +765,6 @@ public abstract class FeatureRendererModel implements
     return renderOrder != null;
   }
 
-  /**
-   * Returns feature types in ordering of rendering, where last means on top
-   */
   public List<String> getRenderOrder()
   {
     if (renderOrder == null)
@@ -811,7 +814,7 @@ public abstract class FeatureRendererModel implements
    * @return list of groups
    */
   @Override
-  public List getGroups(boolean visible)
+  public List<String> getGroups(boolean visible)
   {
     if (featureGroups != null)
     {
@@ -882,10 +885,6 @@ public abstract class FeatureRendererModel implements
     return av.getFeaturesDisplayed();
   }
 
-  /**
-   * Returns a (possibly empty) list of visible feature types, in render order
-   * (last is on top)
-   */
   @Override
   public List<String> getDisplayedFeatureTypes()
   {