JAL-1541 minor code clean up, and added test for BioJsHTMLOutput

[jalview.git] / src / jalview / io / JSONFile.java

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index fcedb2b..28b8ed2 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -37,8 +37,6 @@ public class JSONFile extends AlignFile
 {
   private ColourSchemeI colourScheme;
 
-  // private static boolean seqFeaturesEnabled;
-
   private String jalviewVersion;
 
   private String webStartLaunchServletUrl;
@@ -55,8 +53,6 @@ public class JSONFile extends AlignFile
 
   private FeaturesDisplayedI displayedFeatures;
 
-  // private AlignViewportI viewport;
-
   private FeatureRenderer fr;
 
   private JSONExportSettings jsonExportSettings;
@@ -112,7 +108,6 @@ public class JSONFile extends AlignFile
         setDisplayedFeatures(getViewport().getFeaturesDisplayed());
         showSeqFeatures = getViewport().isShowSequenceFeatures();
         fr = getViewport().getFeatureRenderer();
-        // setSeqFeaturesEnabled(viewport.isShowSequenceFeatures());
       }
 
       int count = 0;
@@ -298,7 +293,6 @@ public class JSONFile extends AlignFile
         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
                 "showSeqFeatures").toString());
         setColourScheme(getJalviewColorScheme(jsColourScheme));
-        // JSONFile.setSeqFeaturesEnabled(showFeatures);
         setShowSeqFeatures(showFeatures);
       }
 
@@ -467,7 +461,7 @@ public class JSONFile extends AlignFile
     return jalviewColor;
   }
 
-  public void LoadAlignmentFeatures(AlignFrame af)
+  public void applySettingsToAlignFrame(AlignFrame af)
   {
     af.setShowSeqFeatures(isShowSeqFeatures());
     af.changeColour(getColourScheme());