Merge branch 'develop' into feature_29/JAL-1372_referenceseq

diff --combined resources/lang/Messages.properties
index 7adae2a,5c1de0b..d944b5b
--- 1/resources/lang/Messages.properties
--- 2/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -57,10 -57,8 +57,10 @@@ action.by_pairwise_id = by Pairwise Ide
  action.by_id = by Id
  action.by_length = by Length
  action.by_group = by Group
 +action.unmark_as_reference = Unmark as Reference 
 +action.set_as_reference = Set as Reference 
  action.remove = Remove
 -action.remove_redundancy = Remove Redundancy
 +action.remove_redundancy = Remove Redundancy...
  action.pairwise_alignment = Pairwise Alignments...
  action.by_rna_helixes = by RNA Helices
  action.user_defined = User Defined...
@@@ -478,8 -476,8 +478,8 @@@ label.settings_for_type = Settings for 
  label.view_full_application = View in Full Application
  label.load_associated_tree = Load Associated Tree ...
  label.load_features_annotations = Load Features/Annotations ...
 -label.export_features = Export Features
 -label.export_annotations = Export Annotations
 +label.export_features = Export Features ...
 +label.export_annotations = Export Annotations ...
  label.jalview_copy = Copy (Jalview Only)
  label.jalview_cut = Cut (Jalview Only)
  label.to_upper_case = To Upper Case
@@@ -597,7 -595,7 +597,7 @@@ label.figure_id_column_width = Figure I
  label.use_modeller_output = Use Modeller Output
  label.wrap_alignment = Wrap Alignment
  label.right_align_ids = Right Align Ids
 -label.sequence_name_italics = Seq Name Italics
 +label.sequence_name_italics = Sequence Name Italics
  label.open_overview = Open Overview
  label.default_colour_scheme_for_alignment = Default Colour Scheme for alignment
  label.annotation_shading_default = Annotation Shading Default
@@@ -1178,3 -1176,16 +1178,16 @@@ label.show_logo = Show Log
  label.normalise_logo = Normalise Logo
  label.no_colour_selection_in_scheme = Please, make a colour selection before to apply colour scheme
  label.no_colour_selection_warn = Error saving colour scheme
+ label.select_by_annotation = Select By Annotation
+ action.select_by_annotation = Select by annotation...
+ label.threshold_filter =  Threshold Filter
+ action.hide = Hide
+ action.select = Select
+ label.alpha_helix = Alpha Helix
+ label.beta_strand = Beta Strand
+ label.turn = Turn
+ label.select_all = Select All
+ label.structures_filter = Structures Filter
+ label.search_filter = Search Filter
+ label.display_name = Display Label
+ label.description = Description

diff --combined src/jalview/gui/AlignFrame.java
index 5c42418,4c45aad..0206c46
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -3325,6 -3325,12 +3325,12 @@@ public class AlignFrame extends GAlignF
    }
  
    @Override
+   public void annotationColumn_actionPerformed(ActionEvent e)
+   {
+     new AnnotationColumnChooser(viewport, alignPanel);
+   }
+ 
+   @Override
    public void rnahelicesColour_actionPerformed(ActionEvent e)
    {
      new RNAHelicesColourChooser(viewport, alignPanel);
@@@ -5148,7 -5154,7 +5154,7 @@@
        // try to parse as annotation.
        boolean isAnnotation = (format == null || format
                .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
 -              .readAnnotationFile(viewport.getAlignment(), file, protocol)
 +              .annotateAlignmentView(viewport, file, protocol)
                : false;
  
        if (!isAnnotation)
@@@ -5753,16 -5759,6 +5759,16 @@@
        alignPanel.paintAlignment(true);
      }
    }
 +  public void clearAlignmentSeqRep()
 +  {
 +    // TODO refactor alignmentseqrep to controller
 +    if (viewport.getAlignment().hasSeqrep()) {
 +      viewport.getAlignment().setSeqrep(null);
 +      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
 +      alignPanel.updateAnnotation();
 +      alignPanel.paintAlignment(true);
 +    }
 +  }
  
    @Override
    protected void createGroup_actionPerformed(ActionEvent e)