Merge branch 'bug/JAL-689' into develop

diff --combined .classpath
index 69a49b0,f87dd26..1529545
--- 1/.classpath
--- 2/.classpath
+++ b/.classpath
@@@ -45,7 -45,6 +45,7 @@@
        <classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
        <classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
        <classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
 +      <classpathentry kind="lib" path="lib/jsoup-1.8.1.jar"/>
        <classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
        <classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
        <classpathentry kind="lib" path="lib/VARNAv3-91.jar"/>
@@@ -56,6 -55,5 +56,5 @@@
        <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
        <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
-       <classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
        <classpathentry kind="output" path="classes"/>
  </classpath>

diff --combined src/jalview/gui/AlignViewport.java
index 0b3fa70,d24f6c4..632d2b2
--- 1/src/jalview/gui/AlignViewport.java
--- 2/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@@ -43,9 -43,7 +43,7 @@@ import jalview.analysis.NJTree
  import jalview.api.AlignViewportI;
  import jalview.bin.Cache;
  import jalview.commands.CommandI;
- import jalview.datamodel.AlignmentAnnotation;
  import jalview.datamodel.AlignmentI;
- import jalview.datamodel.Annotation;
  import jalview.datamodel.ColumnSelection;
  import jalview.datamodel.PDBEntry;
  import jalview.datamodel.Sequence;
@@@ -131,7 -129,7 +129,7 @@@ public class AlignViewport extends Alig
     * Keys are the feature types which are currently visible. Note: Values are
     * not used!
     */
 -  Hashtable featuresDisplayed = null;
 +  private Hashtable featuresDisplayed = null;
  
    boolean antiAlias = false;
  
@@@ -338,10 -336,6 +336,6 @@@
                false);
        showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
        showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
-       consensus = new AlignmentAnnotation("Consensus", "PID",
-               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-       consensus.hasText = true;
-       consensus.autoCalculated = true;
      }
      initAutoAnnotation();
      if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
@@@ -1280,16 -1274,6 +1274,16 @@@
      }
    }
  
 +
 +  public Hashtable getFeaturesDisplayed()
 +  {
 +    return featuresDisplayed;
 +  }
 +
 +  public void setFeaturesDisplayed(Hashtable featuresDisplayed)
 +  {
 +    this.featuresDisplayed = featuresDisplayed;
 +  }
    protected SequenceAnnotationOrder getSortAnnotationsBy()
    {
      return sortAnnotationsBy;