From 39d2bb916a37d0530b77c5d6d8bed98272069759 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 14 Apr 2016 12:17:28 +0100
Subject: [PATCH] JAL-1421 type parameter added to some collections

---
 src/jalview/gui/Preferences.java |   24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index c7e1332..6b2d3c4 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -30,6 +30,7 @@ import jalview.jbgui.GPreferences;
 import jalview.jbgui.GSequenceLink;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.BorderLayout;
@@ -40,7 +41,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.io.File;
-import java.util.Collection;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
@@ -96,7 +97,7 @@ public class Preferences extends GPreferences
    * Holds name and link separated with | character. Sequence ID must be
    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
    */
-  public static Vector sequenceURLLinks;
+  public static Vector<String> sequenceURLLinks;
 
   /**
    * Holds name and link separated with | character. Sequence IDS and Sequences
@@ -106,14 +107,14 @@ public class Preferences extends GPreferences
    * (TODO: proper escape for using | to separate ids or sequences
    */
 
-  public static Vector groupURLLinks;
+  public static List<String> groupURLLinks;
   static
   {
     String string = Cache
             .getDefault(
                     "SEQUENCE_LINKS",
                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
-    sequenceURLLinks = new Vector();
+    sequenceURLLinks = new Vector<String>();
 
     try
     {
@@ -152,10 +153,10 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new Vector();
+    groupURLLinks = new ArrayList<String>();
   }
 
-  Vector nameLinks, urlLinks;
+  Vector<String> nameLinks, urlLinks;
 
   JInternalFrame frame;
 
@@ -176,7 +177,8 @@ public class Preferences extends GPreferences
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
     int width = 500, height = 450;
-    if (new jalview.util.Platform().isAMac())
+    new jalview.util.Platform();
+    if (Platform.isAMac())
     {
       width = 570;
       height = 480;
@@ -329,8 +331,8 @@ public class Preferences extends GPreferences
     /*
      * Set Connections tab defaults
      */
-    nameLinks = new Vector();
-    urlLinks = new Vector();
+    nameLinks = new Vector<String>();
+    urlLinks = new Vector<String>();
     for (int i = 0; i < sequenceURLLinks.size(); i++)
     {
       String link = sequenceURLLinks.elementAt(i).toString();
@@ -533,7 +535,7 @@ public class Preferences extends GPreferences
     if (nameLinks.size() > 0)
     {
       StringBuffer links = new StringBuffer();
-      sequenceURLLinks = new Vector();
+      sequenceURLLinks = new Vector<String>();
       for (int i = 0; i < nameLinks.size(); i++)
       {
         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
@@ -849,7 +851,7 @@ public class Preferences extends GPreferences
     super.showunconserved_actionPerformed(e);
   }
 
-  public static Collection getGroupURLLinks()
+  public static List<String> getGroupURLLinks()
   {
     return groupURLLinks;
   }
-- 
1.7.10.2