From 3be19c1e81d0960f7e7f03e600abdc912890c761 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 4 Feb 2016 14:02:16 +0000
Subject: [PATCH] JAL-599 bug fixed so array of visible types is populated

---
 src/jalview/controller/AlignViewController.java |   14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 06b1e4c..6a7e222 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -333,20 +333,20 @@ public class AlignViewController implements AlignViewControllerI
     gps = fr == null ? null : fr.getDisplayedFeatureGroups();
     if (typ != null)
     {
-      ArrayList types = new ArrayList();
-      for (int i = 0; i < typ.length; i++)
+      List<String> types = new ArrayList<String>();
+      for (String displayed : typ)
       {
-        if (typ[i] != null)
+        if (displayed != null)
         {
-          types.add(typ[i]);
+          types.add(displayed);
         }
-        typ = new String[types.size()];
-        types.toArray(typ);
       }
+      typ = new String[types.size()];
+      types.toArray(typ);
     }
     if (gps != null)
     {
-      ArrayList grps = new ArrayList();
+      List<String> grps = new ArrayList<String>();
 
       for (int i = 0; i < gps.length; i++)
       {
-- 
1.7.10.2