X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=c7e13324920417d097c6723c5881dbb1d6a964f9;hb=b44b99801b03025f1d769f20476bc90823d92499;hp=5cb6512739993215b3d1b7ee8eed5e3d9d6ff085;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 5cb6512..c7e1332 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.ws.sifts.SiftsSettings;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -313,6 +314,18 @@ 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
      */
@@ -384,6 +397,7 @@ public class Preferences extends GPreferences
    * 
    * @param e
    */
+  @Override
   public void ok_actionPerformed(ActionEvent e)
   {
     if (!validateSettings())
@@ -492,6 +506,9 @@ 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
@@ -647,6 +664,7 @@ public class Preferences extends GPreferences
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void startupFileTextfield_mouseClicked()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -676,6 +694,7 @@ public class Preferences extends GPreferences
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void cancel_actionPerformed(ActionEvent e)
   {
     try
@@ -694,6 +713,7 @@ public class Preferences extends GPreferences
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void annotations_actionPerformed(ActionEvent e)
   {
     conservation.setEnabled(annotations.isSelected());
@@ -707,6 +727,7 @@ public class Preferences extends GPreferences
             && (identity.isSelected() || showGroupConsensus.isSelected()));
   }
 
+  @Override
   public void newLink_actionPerformed(ActionEvent e)
   {
 
@@ -733,6 +754,7 @@ public class Preferences extends GPreferences
     }
   }
 
+  @Override
   public void editLink_actionPerformed(ActionEvent e)
   {
     GSequenceLink link = new GSequenceLink();
@@ -774,6 +796,7 @@ public class Preferences extends GPreferences
     }
   }
 
+  @Override
   public void deleteLink_actionPerformed(ActionEvent e)
   {
     int index = linkNameList.getSelectedIndex();
@@ -796,6 +819,7 @@ public class Preferences extends GPreferences
     linkURLList.setListData(urlLinks);
   }
 
+  @Override
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     JFileChooser chooser = new JFileChooser(".");
@@ -818,6 +842,7 @@ 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