X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=4c45aadce4485966d2ae6293b6038f5bce3c9eb9;hb=95de746a08351b07696a0c455ef37d866c8104d2;hp=be8af7bff60b7331a5670968b597d2cf2e6e6302;hpb=ffea8e06f34c1004671749a799722f64a83d8161;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index be8af7b..4c45aad 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -768,7 +768,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
-    showSeqFeatures.setSelected(av.showSequenceFeatures);
+    showSeqFeatures.setSelected(av.isShowSequenceFeatures());
     hiddenMarkers.setState(av.showHiddenMarkers);
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
@@ -1233,7 +1233,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // new HTMLOutput(alignPanel,
     // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
     // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
-    new HtmlSvgOutput(alignPanel);
+    new HtmlSvgOutput(null, alignPanel);
   }
 
   @Override
@@ -3092,7 +3092,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
             .isSelected());
-    if (viewport.getShowSequenceFeaturesHeight())
+    if (viewport.isShowSequenceFeaturesHeight())
     {
       // ensure we're actually displaying features
       viewport.setShowSequenceFeatures(true);
@@ -3325,6 +3325,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
+  public void annotationColumn_actionPerformed(ActionEvent e)
+  {
+    new AnnotationColumnChooser(viewport, alignPanel);
+  }
+
+  @Override
   public void rnahelicesColour_actionPerformed(ActionEvent e)
   {
     new RNAHelicesColourChooser(viewport, alignPanel);
@@ -4882,7 +4888,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       featuresFile = new FeaturesFile(file, type).parse(viewport
               .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
-              .getFeatureRenderer().featureColours, false,
+              .getFeatureRenderer().getFeatureColours(), false,
               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
     } catch (Exception ex)
     {
@@ -4891,7 +4897,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (featuresFile)
     {
-      viewport.showSequenceFeatures = true;
+      viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
       if (alignPanel.getSeqPanel().seqCanvas.fr != null)
       {