Merge branch 'develop' into developtomchmmer

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 296c4bf..a0a7511 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -25,6 +25,8 @@ import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.hmmer.HmmerCommand;
+import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
 import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -86,6 +88,9 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  */
 public class Preferences extends GPreferences
 {
+  // suggested list delimiter character
+  public static final String COMMA = ",";
+
   public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
 
   public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
@@ -118,8 +123,6 @@ public class Preferences extends GPreferences
 
   public static final String CYGWIN_PATH = "CYGWIN_PATH";
 
-  public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
-
   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
@@ -187,8 +190,6 @@ public class Preferences extends GPreferences
 
   JInternalFrame frame;
 
-  DasSourceBrowser dasSource;
-
   private WsPreferences wsPrefs;
 
   private OptionsParam promptEachTimeOpt = new OptionsParam(
@@ -209,8 +210,6 @@ public class Preferences extends GPreferences
     super();
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    dasSource = new DasSourceBrowser();
-    dasTab.add(dasSource, BorderLayout.CENTER);
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
     int width = 500, height = 450;
@@ -258,7 +257,12 @@ public class Preferences extends GPreferences
     });
     if (cygwinPath != null)
     {
-      cygwinPath.setText(Cache.getProperty(CYGWIN_PATH));
+      String path = Cache.getProperty(CYGWIN_PATH);
+      if (path == null)
+      {
+        path = FileUtils.getPathTo("bash");
+      }
+      cygwinPath.setText(path);
       cygwinPath.addActionListener(new ActionListener()
       {
         @Override
@@ -403,7 +407,7 @@ public class Preferences extends GPreferences
     gapLabel.setEnabled(!useLegacyGap.isSelected());
     gapColour.setEnabled(!useLegacyGap.isSelected());
     showHiddenAtStart
-            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
+            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 
     /*
      * Set Structure tab defaults.
@@ -624,6 +628,12 @@ public class Preferences extends GPreferences
 
     annotations_actionPerformed(null); // update the display of the annotation
                                        // settings
+    
+    
+    /*
+     * Set Backups tab defaults
+     */
+    loadLastSavedBackupsOptions();
   }
 
   /**
@@ -911,8 +921,31 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
-    dasSource.saveProperties(Cache.applicationProperties);
     wsPrefs.updateAndRefreshWsMenuConfig(false);
+
+    /*
+     * Save Backups settings
+     */
+    Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+            Boolean.toString(enableBackupFiles.isSelected()));
+    int preset = getComboIntStringKey(backupfilesPresetsCombo);
+    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());
+    }
+
+    BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+            .get(preset);
+    Cache.applicationProperties.setProperty(
+            BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
+
     Cache.saveProperties();
     Desktop.instance.doConfigureStructurePrefs();
     try
@@ -1237,7 +1270,7 @@ public class Preferences extends GPreferences
   {
     useLegacyGap.setSelected(false);
     useLegacyGaps_actionPerformed(null);
-    showHiddenAtStart.setSelected(true);
+    showHiddenAtStart.setSelected(false);
     hiddenColour.setBackground(
             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
   }