Merge branch 'Release_2_8_2_Branch' into JAL-1483_featureBasedTreeCalc

diff --cc src/jalview/analysis/Conservation.java
Simple merge

diff --cc src/jalview/analysis/Finder.java
Simple merge

diff --cc src/jalview/analysis/SequenceIdMatcher.java
Simple merge

diff --cc src/jalview/api/AlignmentViewPanel.java
Simple merge

diff --cc src/jalview/api/FeatureRenderer.java
Simple merge

diff --cc src/jalview/appletgui/AlignmentPanel.java
Simple merge

diff --cc src/jalview/appletgui/FeatureRenderer.java
Simple merge

diff --cc src/jalview/gui/AlignmentPanel.java
Simple merge

diff --cc src/jalview/gui/AppJmolBinding.java
Simple merge

diff --cc src/jalview/gui/FeatureRenderer.java
index 5c7f32a,eb64dee..d36105a
--- 1/src/jalview/gui/FeatureRenderer.java
--- 2/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@@ -170,13 -172,15 +172,16 @@@ public class FeatureRenderer extends ja
      this.transparency = fr.transparency;
      this.featureOrder = fr.featureOrder;
    }
+ 
    /**
     * update from another feature renderer
-    * @param fr settings to copy
+    * 
+    * @param fr
+    *          settings to copy
     */
 -  public void transferSettings(FeatureRenderer fr)
 +  public void transferSettings(jalview.api.FeatureRenderer _fr)
    {
 +    FeatureRenderer fr = (FeatureRenderer) _fr;
      FeatureRendererSettings frs = new FeatureRendererSettings(fr);
      this.renderOrder = frs.renderOrder;
      this.featureGroups = frs.featureGroups;

diff --cc src/jalview/schemes/AnnotationColourGradient.java
Simple merge

diff --cc src/jalview/ws/jws2/AADisorderClient.java
Simple merge