Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 06b1e4c..be84bbf 100644 (file)
--- 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++)
       {
@@ -393,7 +393,7 @@ public class AlignViewController implements AlignViewControllerI
     boolean featuresFile = false;
     try
     {
-      featuresFile = new FeaturesFile(file, protocol).parse(viewport
+      featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
               .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
               .getFeatureColours(), false, relaxedIdMatching);
     } catch (Exception ex)