Merge branch 'develop' into JAL-1483_featureBasedTreeCalc

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 460748a..4b7f2f8 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -765,7 +765,7 @@ 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());
@@ -3086,7 +3086,7 @@ 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);
@@ -4872,7 +4872,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       featuresFile = new FeaturesFile(file, type).parse(viewport
               .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
-              .getFeatureRenderer().featureColours, false,
+              .getFeatureRenderer().getFeatureColours(), false,
               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
     } catch (Exception ex)
     {
@@ -4881,7 +4881,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (featuresFile)
     {
-      viewport.showSequenceFeatures = true;
+      viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
       if (alignPanel.seqPanel.seqCanvas.fr != null)
       {