JAL-4290 incorrect usage of main()

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index ece573d..a72da0d 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -179,8 +179,7 @@ public class Commands
 
     if (argParser.getBoolean(Arg.QUIT))
     {
-      Jalview.getInstance().exit(
-              "Exiting due to " + Arg.QUIT.argString() + " argument.",
+      Jalview.exit("Exiting due to " + Arg.QUIT.argString() + " argument.",
               ExitCode.OK);
       return true;
     }
@@ -908,7 +907,8 @@ public class Commands
           boolean showSSAnnotations, boolean showAnnotations,
           boolean hideTFrows)
   {
-    af.setAnnotationsVisibility(true, showSSAnnotations, showAnnotations);
+    af.setAnnotationsVisibility(showSSAnnotations, true, false);
+    af.setAnnotationsVisibility(showAnnotations, false, true);
 
     // show temperature factor annotations?
     if (hideTFrows)