JAL-1421 type parameter added to some collections

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 5cb6512..6b2d3c4 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -30,6 +30,8 @@ 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;
 import java.awt.Color;
@@ -39,7 +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;
@@ -95,7 +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
@@ -105,14 +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
     {
@@ -151,10 +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;
 
@@ -175,7 +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;
@@ -313,11 +316,23 @@ public class Preferences extends GPreferences
       }
     });
 
+    if (Cache.getDefault("MAP_WITH_SIFTS", false))
+    {
+      siftsMapping.setSelected(true);
+    }
+    else
+    {
+      nwMapping.setSelected(true);
+    }
+
+    SiftsSettings
+            .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
     /*
      * 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();
@@ -384,6 +399,7 @@ public class Preferences extends GPreferences
    * 
    * @param e
    */
+  @Override
   public void ok_actionPerformed(ActionEvent e)
   {
     if (!validateSettings())
@@ -492,6 +508,9 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
             .getSelectedItem().toString());
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+    Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+            Boolean.toString(siftsMapping.isSelected()));
+    SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 
     /*
      * Save Output settings
@@ -516,7 +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) + "|"
@@ -647,6 +666,7 @@ public class Preferences extends GPreferences
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void startupFileTextfield_mouseClicked()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -676,6 +696,7 @@ public class Preferences extends GPreferences
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void cancel_actionPerformed(ActionEvent e)
   {
     try
@@ -694,6 +715,7 @@ public class Preferences extends GPreferences
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void annotations_actionPerformed(ActionEvent e)
   {
     conservation.setEnabled(annotations.isSelected());
@@ -707,6 +729,7 @@ public class Preferences extends GPreferences
             && (identity.isSelected() || showGroupConsensus.isSelected()));
   }
 
+  @Override
   public void newLink_actionPerformed(ActionEvent e)
   {
 
@@ -733,6 +756,7 @@ public class Preferences extends GPreferences
     }
   }
 
+  @Override
   public void editLink_actionPerformed(ActionEvent e)
   {
     GSequenceLink link = new GSequenceLink();
@@ -774,6 +798,7 @@ public class Preferences extends GPreferences
     }
   }
 
+  @Override
   public void deleteLink_actionPerformed(ActionEvent e)
   {
     int index = linkNameList.getSelectedIndex();
@@ -796,6 +821,7 @@ public class Preferences extends GPreferences
     linkURLList.setListData(urlLinks);
   }
 
+  @Override
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     JFileChooser chooser = new JFileChooser(".");
@@ -818,13 +844,14 @@ public class Preferences extends GPreferences
    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   protected void showunconserved_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
     super.showunconserved_actionPerformed(e);
   }
 
-  public static Collection getGroupURLLinks()
+  public static List<String> getGroupURLLinks()
   {
     return groupURLLinks;
   }