JAL-3446 reorganized JalviewJSApp (accidentally put that in jalview/api)

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index dc274e9..4030afa 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -781,16 +781,16 @@ public class Preferences extends GPreferences
             protColour.getSelectedItem().toString());
     Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
             nucColour.getSelectedItem().toString());
-    Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+    Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MIN",
             minColour.getBackground());
-    Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+    Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MAX",
             maxColour.getBackground());
 
     /*
      * Save Overview settings
      */
-    Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
-    Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+    Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground());
+    Cache.setColourPropertyNoSave(HIDDEN_COLOUR, hiddenColour.getBackground());
     Cache.setPropertyNoSave(USE_LEGACY_GAP,
             Boolean.toString(useLegacyGap.isSelected()));
     Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
@@ -809,8 +809,8 @@ public class Preferences extends GPreferences
             Boolean.toString(structFromPdb.isSelected()));
     if (!Platform.isJS())
     {
-    Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
-            structViewer.getSelectedItem().toString());
+      Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
+              structViewer.getSelectedItem().toString());
     }
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
     Cache.setPropertyNoSave("MAP_WITH_SIFTS",
@@ -963,7 +963,7 @@ public class Preferences extends GPreferences
             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 
     Cache.saveProperties();
-    Desktop.instance.doConfigureStructurePrefs();
+    Desktop.getInstance().doConfigureStructurePrefs();
     try
     {
       frame.setClosed(true);
@@ -1110,7 +1110,7 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
               MessageManager.getString("label.new_sequence_url_link"),
               JvOptionPane.OK_CANCEL_OPTION, -1,
               null) == JvOptionPane.OK_OPTION)
@@ -1162,7 +1162,7 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
               MessageManager.getString("label.edit_sequence_url_link"),
               JvOptionPane.OK_CANCEL_OPTION, -1,
               null) == JvOptionPane.OK_OPTION)
@@ -1335,7 +1335,7 @@ public class Preferences extends GPreferences
     } catch (NumberFormatException x)
     {
       userIdWidth.setText("");
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
               MessageManager
                       .getString("warn.user_defined_width_requirements"),
               MessageManager.getString("label.invalid_id_column_width"),
@@ -1361,7 +1361,7 @@ public class Preferences extends GPreferences
       File f = new File(chimeraPath.getText());
       if (!f.canExecute())
       {
-        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+        JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                 MessageManager.getString("label.invalid_chimera_path"),
                 MessageManager.getString("label.invalid_name"),
                 JvOptionPane.ERROR_MESSAGE);
@@ -1400,7 +1400,7 @@ public class Preferences extends GPreferences
     if (!found)
     {
       String[] options = { "OK", "Help" };
-      int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+      int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,