From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 18 Jul 2016 13:01:49 +0000 (+0100)
Subject: Merge branch 'features/JAL-2068groovyAnnotationWorker' into develop
X-Git-Tag: Release_2_10_0~138^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c956ba7509e394cf70dbf049abe5fbc967222144;p=jalview.git

Merge branch 'features/JAL-2068groovyAnnotationWorker' into develop
minor conflicts in constructor/imports for unification of Graduated/FeatureColour
---

c956ba7509e394cf70dbf049abe5fbc967222144
diff --cc src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 5d3aa2d,8c6bc5e..b007365
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@@ -50,8 -51,16 +51,18 @@@ public class FeatureRenderer extends Fe
  
    boolean av_validCharWidth, av_isShowSeqFeatureHeight;
  
 +  private Integer currentColour;
 +
+   /**
+    * Constructor given a viewport
+    * 
+    * @param viewport
+    */
+   public FeatureRenderer(AlignViewportI viewport)
+   {
+     this.av = viewport;
+   }
+ 
    protected void updateAvConfig()
    {
      av_charHeight = av.getCharHeight();
diff --cc src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index a4e4348,ee0721d..d813fe2
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@@ -27,9 -27,7 +27,8 @@@ import jalview.datamodel.AlignmentI
  import jalview.datamodel.SequenceFeature;
  import jalview.datamodel.SequenceI;
  import jalview.renderer.seqfeatures.FeatureRenderer;
 -import jalview.schemes.GraduatedColor;
 +import jalview.schemes.FeatureColour;
 +import jalview.schemes.UserColourScheme;
- import jalview.viewmodel.AlignmentViewport;
  
  import java.awt.Color;
  import java.beans.PropertyChangeListener;
@@@ -64,8 -65,14 +63,8 @@@ public abstract class FeatureRendererMo
    protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
            this);
  
-   protected AlignmentViewport av;
+   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()
    {