Merge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609...

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index b447214..6972657 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -374,12 +374,10 @@ public class Preferences extends GPreferences
     /*
      * Set overview panel defaults
      */
-    gapColour.setBackground(
-            Cache.getDefaultColour(GAP_COLOUR,
-                    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
-    hiddenColour.setBackground(
-            Cache.getDefaultColour(HIDDEN_COLOUR,
-                    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+    gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+    hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
     gapLabel.setEnabled(!useLegacyGap.isSelected());
     gapColour.setEnabled(!useLegacyGap.isSelected());
@@ -402,7 +400,8 @@ public class Preferences extends GPreferences
      * set choice of structure viewer, and path if saved as a preference;
      * default to Jmol (first choice) if an unexpected value is found
      */
-    String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
+    String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
+            ViewerType.JMOL.name());
     structViewer.setSelectedItem(viewerType);
     String viewerPath = "";
     ViewerType type = null;
@@ -438,10 +437,11 @@ public class Preferences extends GPreferences
       {
         if (validateViewerPath())
         {
-          Cache.setProperty(structViewer.getSelectedItem()
-                  .equals(ViewerType.CHIMERAX.name())
-                  ? CHIMERAX_PATH
-                  : CHIMERA_PATH, structureViewerPath.getText());
+          Cache.setProperty(
+                  structViewer.getSelectedItem().equals(
+                          ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH
+                                  : CHIMERA_PATH,
+                  structureViewerPath.getText());
         }
       }
     });
@@ -611,6 +611,7 @@ public class Preferences extends GPreferences
     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
             : new String(Cache.proxyAuthPassword));
     setCustomProxyEnabled();
+    applyProxyButtonEnabled(false);
 
     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 
@@ -654,8 +655,7 @@ public class Preferences extends GPreferences
 
     annotations_actionPerformed(null); // update the display of the annotation
                                        // settings
-    
-    
+
     /*
      * Set Backups tab defaults
      */
@@ -675,7 +675,7 @@ public class Preferences extends GPreferences
     comboBox.addItem(promptEachTimeOpt);
     comboBox.addItem(lineArtOpt);
     comboBox.addItem(textOpt);
-    
+
     /*
      * JalviewJS doesn't support Lineart so force it to Text
      */
@@ -826,8 +826,7 @@ public class Preferences extends GPreferences
             Boolean.toString(structFromPdb.isSelected()));
     String viewer = structViewer.getSelectedItem().toString();
     String viewerPath = structureViewerPath.getText();
-    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
-            viewer);
+    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
     if (viewer.equals(ViewerType.CHIMERA.name()))
     {
       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
@@ -958,16 +957,16 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
             Boolean.toString(enableBackupFiles.isSelected()));
     int preset = getComboIntStringKey(backupfilesPresetsCombo);
-    Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+    Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
+            Integer.toString(preset));
 
     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
     {
       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
-      Cache.applicationProperties
-              .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
-                      customBFPE.toString());
+      Cache.applicationProperties.setProperty(
+              BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
     }
 
     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
@@ -1277,8 +1276,7 @@ public class Preferences extends GPreferences
     if (!useLegacyGap.isSelected())
     {
       JalviewColourChooser.showColourChooser(this,
-              MessageManager.getString("label.select_gap_colour"),
-              gap);
+              MessageManager.getString("label.select_gap_colour"), gap);
     }
   }
 
@@ -1286,8 +1284,7 @@ public class Preferences extends GPreferences
   public void hiddenColour_actionPerformed(JPanel hidden)
   {
     JalviewColourChooser.showColourChooser(this,
-            MessageManager.getString("label.select_hidden_colour"),
-            hidden);
+            MessageManager.getString("label.select_hidden_colour"), hidden);
   }
 
   @Override