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JAL-3210 Barebones gradle/buildship/eclipse. See README
[jalview.git] / src / jalview / gui / Preferences.java
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index facc826..94f67f6 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -25,6 +25,7 @@ import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
 import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -37,7 +38,6 @@ import jalview.urls.UrlLinkTableModel;
 import jalview.urls.api.UrlProviderFactoryI;
 import jalview.urls.api.UrlProviderI;
 import jalview.urls.desktop.DesktopUrlProviderFactory;
-import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
@@ -81,7 +81,6 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  * @author $author$
  * @version $Revision$
  */
-@SuppressWarnings("serial")
 public class Preferences extends GPreferences
 {
   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
@@ -128,9 +127,9 @@ 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 UrlProviderI sequenceUrlLinks; // must be nonfinal for test
+  public static UrlProviderI sequenceUrlLinks;
 
-  public final static UrlLinkTableModel dataModel;
+  public static UrlLinkTableModel dataModel;
 
   /**
    * Holds name and link separated with | character. Sequence IDS and Sequences
@@ -140,8 +139,7 @@ public class Preferences extends GPreferences
    * (TODO: proper escape for using | to separate ids or sequences
    */
 
-  public static final List<String> groupURLLinks; // not implemented
-
+  public static List<String> groupURLLinks;
   static
   {
     // get links selected to be in the menu (SEQUENCE_LINKS)
@@ -167,7 +165,7 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new ArrayList<>(); // not implemented
+    groupURLLinks = new ArrayList<>();
   }
 
   JInternalFrame frame;
@@ -549,7 +547,10 @@ public class Preferences extends GPreferences
     /*
      * Set Backups tab defaults
      */
-    loadLastSavedBackupsOptions();
+    if (!Platform.isJS())
+    {
+      loadLastSavedBackupsOptions();
+    }
   }
 
   /**
@@ -602,65 +603,65 @@ public class Preferences extends GPreferences
     /*
      * Save Visual settings
      */
-    Cache.setPropertyNoSave("SHOW_JVSUFFIX",
+    Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
             Boolean.toString(seqLimit.isSelected()));
-    Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
+    Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
             Boolean.toString(rightAlign.isSelected()));
-    Cache.setPropertyNoSave("SHOW_FULLSCREEN",
+    Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
             Boolean.toString(fullScreen.isSelected()));
-    Cache.setPropertyNoSave("SHOW_OVERVIEW",
+    Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
             Boolean.toString(openoverv.isSelected()));
-    Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
             Boolean.toString(annotations.isSelected()));
-    Cache.setPropertyNoSave("SHOW_CONSERVATION",
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
             Boolean.toString(conservation.isSelected()));
-    Cache.setPropertyNoSave("SHOW_QUALITY",
+    Cache.applicationProperties.setProperty("SHOW_QUALITY",
             Boolean.toString(quality.isSelected()));
-    Cache.setPropertyNoSave("SHOW_IDENTITY",
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
             Boolean.toString(identity.isSelected()));
 
-    Cache.setPropertyNoSave("GAP_SYMBOL",
+    Cache.applicationProperties.setProperty("GAP_SYMBOL",
             gapSymbolCB.getSelectedItem().toString());
 
-    Cache.setPropertyNoSave("FONT_NAME",
+    Cache.applicationProperties.setProperty("FONT_NAME",
             fontNameCB.getSelectedItem().toString());
-    Cache.setPropertyNoSave("FONT_STYLE",
+    Cache.applicationProperties.setProperty("FONT_STYLE",
             fontStyleCB.getSelectedItem().toString());
-    Cache.setPropertyNoSave("FONT_SIZE",
+    Cache.applicationProperties.setProperty("FONT_SIZE",
             fontSizeCB.getSelectedItem().toString());
 
-    Cache.setPropertyNoSave("ID_ITALICS",
+    Cache.applicationProperties.setProperty("ID_ITALICS",
             Boolean.toString(idItalics.isSelected()));
-    Cache.setPropertyNoSave("SHOW_UNCONSERVED",
+    Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
             Boolean.toString(showUnconserved.isSelected()));
-    Cache.setPropertyNoSave(SHOW_OCCUPANCY,
+    Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
             Boolean.toString(showOccupancy.isSelected()));
-    Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
+    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
             Boolean.toString(showGroupConsensus.isSelected()));
-    Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
+    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
             Boolean.toString(showGroupConservation.isSelected()));
-    Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
+    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
             Boolean.toString(showConsensHistogram.isSelected()));
-    Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
+    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
             Boolean.toString(showConsensLogo.isSelected()));
-    Cache.setPropertyNoSave("ANTI_ALIAS",
+    Cache.applicationProperties.setProperty("ANTI_ALIAS",
             Boolean.toString(smoothFont.isSelected()));
-    Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
+    Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
             Boolean.toString(scaleProteinToCdna.isSelected()));
-    Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
+    Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
             Boolean.toString(showNpTooltip.isSelected()));
-    Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
+    Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
             Boolean.toString(showDbRefTooltip.isSelected()));
 
-    Cache.setPropertyNoSave("WRAP_ALIGNMENT",
+    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
             Boolean.toString(wrap.isSelected()));
 
-    Cache.setPropertyNoSave("STARTUP_FILE",
+    Cache.applicationProperties.setProperty("STARTUP_FILE",
             startupFileTextfield.getText());
-    Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
+    Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
             Boolean.toString(startupCheckbox.isSelected()));
 
-    Cache.setPropertyNoSave("SORT_ALIGNMENT",
+    Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
             sortby.getSelectedItem().toString());
 
     // convert description of sort order to enum name for save
@@ -668,20 +669,20 @@ public class Preferences extends GPreferences
             .forDescription(sortAnnBy.getSelectedItem().toString());
     if (annSortOrder != null)
     {
-      Cache.setPropertyNoSave(SORT_ANNOTATIONS,
+      Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
               annSortOrder.name());
     }
 
     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
-    Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
+    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
             Boolean.valueOf(showAutocalcFirst).toString());
 
     /*
      * Save Colours settings
      */
-    Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
             protColour.getSelectedItem().toString());
-    Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
             nucColour.getSelectedItem().toString());
     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
             minColour.getBackground());
@@ -693,77 +694,73 @@ public class Preferences extends GPreferences
      */
     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
-    Cache.setPropertyNoSave(USE_LEGACY_GAP,
+    Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
             Boolean.toString(useLegacyGap.isSelected()));
-    Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
+    Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
             Boolean.toString(showHiddenAtStart.isSelected()));
 
     /*
      * Save Structure settings
      */
-    Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
+    Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
             Boolean.toString(addTempFactor.isSelected()));
-    Cache.setPropertyNoSave(ADD_SS_ANN,
+    Cache.applicationProperties.setProperty(ADD_SS_ANN,
             Boolean.toString(addSecondaryStructure.isSelected()));
-    Cache.setPropertyNoSave(USE_RNAVIEW,
+    Cache.applicationProperties.setProperty(USE_RNAVIEW,
             Boolean.toString(useRnaView.isSelected()));
-    Cache.setPropertyNoSave(STRUCT_FROM_PDB,
+    Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
             Boolean.toString(structFromPdb.isSelected()));
-    Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
+    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
             structViewer.getSelectedItem().toString());
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
-    Cache.setPropertyNoSave("MAP_WITH_SIFTS",
+    Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
             Boolean.toString(siftsMapping.isSelected()));
     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 
     /*
      * Save Output settings
      */
-    Cache.setPropertyNoSave("EPS_RENDERING",
+    Cache.applicationProperties.setProperty("EPS_RENDERING",
             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
-    Cache.setPropertyNoSave("HTML_RENDERING",
+    Cache.applicationProperties.setProperty("HTML_RENDERING",
             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
-    Cache.setPropertyNoSave("SVG_RENDERING",
+    Cache.applicationProperties.setProperty("SVG_RENDERING",
             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 
-    if (!Platform.isJS())
-    /**
-     * @j2sNative
+    /*
+     * Save Connections settings
      */
-    {
-      // Java only
-      // Save Connections settings
-      Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
-      BrowserLauncher.resetBrowser();
-    }
+    Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+
+    jalview.util.BrowserLauncher.resetBrowser();
 
     // save user-defined and selected links
     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
     if (menuLinks.isEmpty())
     {
-      Cache.removePropertyNoSave("SEQUENCE_LINKS");
+      Cache.applicationProperties.remove("SEQUENCE_LINKS");
     }
     else
     {
-      Cache.setPropertyNoSave("SEQUENCE_LINKS",
+      Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
               menuLinks.toString());
     }
 
     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
     if (nonMenuLinks.isEmpty())
     {
-      Cache.removePropertyNoSave("STORED_LINKS");
+      Cache.applicationProperties.remove("STORED_LINKS");
     }
     else
     {
-      Cache.setPropertyNoSave("STORED_LINKS",
+      Cache.applicationProperties.setProperty("STORED_LINKS",
               nonMenuLinks.toString());
     }
 
-    Cache.setPropertyNoSave("DEFAULT_URL",
+    Cache.applicationProperties.setProperty("DEFAULT_URL",
             sequenceUrlLinks.getPrimaryUrlId());
 
-    Cache.setPropertyNoSave("USE_PROXY",
+    Cache.applicationProperties.setProperty("USE_PROXY",
             Boolean.toString(useProxy.isSelected()));
 
     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
@@ -802,38 +799,40 @@ public class Preferences extends GPreferences
     /*
      * Save Output settings
      */
-    Cache.setPropertyNoSave("BLC_JVSUFFIX",
+    Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
             Boolean.toString(blcjv.isSelected()));
-    Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
+    Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
             Boolean.toString(clustaljv.isSelected()));
-    Cache.setPropertyNoSave("FASTA_JVSUFFIX",
+    Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
             Boolean.toString(fastajv.isSelected()));
-    Cache.setPropertyNoSave("MSF_JVSUFFIX",
+    Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
             Boolean.toString(msfjv.isSelected()));
-    Cache.setPropertyNoSave("PFAM_JVSUFFIX",
+    Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
             Boolean.toString(pfamjv.isSelected()));
-    Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
+    Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
             Boolean.toString(pileupjv.isSelected()));
-    Cache.setPropertyNoSave("PIR_JVSUFFIX",
+    Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
             Boolean.toString(pirjv.isSelected()));
-    Cache.setPropertyNoSave("PIR_MODELLER",
+    Cache.applicationProperties.setProperty("PIR_MODELLER",
             Boolean.toString(modellerOutput.isSelected()));
-    Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
+    Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
             Boolean.toString(embbedBioJSON.isSelected()));
-    Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
+    jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
+    Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
             Boolean.toString(autoIdWidth.isSelected()));
     userIdWidth_actionPerformed();
-    Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
+    Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
             userIdWidth.getText());
 
     /*
      * Save Editing settings
      */
-    Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
+    Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
             Boolean.toString(autoCalculateConsCheck.isSelected()));
-    Cache.setPropertyNoSave("SORT_BY_TREE",
+    Cache.applicationProperties.setProperty("SORT_BY_TREE",
             Boolean.toString(sortByTree.isSelected()));
-    Cache.setPropertyNoSave("PAD_GAPS",
+    Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
     if (!Platform.isJS())
@@ -844,25 +843,32 @@ public class Preferences extends GPreferences
     /*
      * Save Backups settings
      */
-    Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
-            Boolean.toString(backupfilesConfirmDelete.isSelected()));
-    Cache.setPropertyNoSave(BackupFiles.ENABLED,
-            Boolean.toString(enableBackupFiles.isSelected()));
-    Cache.setPropertyNoSave(BackupFiles.NO_MAX,
-            Boolean.toString(backupfilesKeepAll.isSelected()));
-    Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
-            Boolean.toString(suffixReverse.isSelected()));
-    Cache.setPropertyNoSave(BackupFiles.SUFFIX,
-            suffixTemplate.getText());
-    Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
-            Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
-    Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
-            Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
-    Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET",
-            Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
+    Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+            Platform.isJS() ? Boolean.FALSE.toString()
+                    : Boolean.toString(enableBackupFiles.isSelected()));
+    if (!Platform.isJS())
+    {
+      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.getInstance().doConfigureStructurePrefs();
+    Desktop.instance.doConfigureStructurePrefs();
     try
     {
       frame.setClosed(true);
@@ -915,7 +921,7 @@ public class Preferences extends GPreferences
       FileFormatI format = chooser.getSelectedFormat();
       if (format != null)
       {
-        Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
+        Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
                 format.getName());
       }
       startupFileTextfield
@@ -973,7 +979,7 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.new_sequence_url_link"),
               JvOptionPane.OK_CANCEL_OPTION, -1,
               null) == JvOptionPane.OK_OPTION)
@@ -1025,7 +1031,7 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.edit_sequence_url_link"),
               JvOptionPane.OK_CANCEL_OPTION, -1,
               null) == JvOptionPane.OK_OPTION)
@@ -1112,11 +1118,6 @@ public class Preferences extends GPreferences
     super.showunconserved_actionPerformed(e);
   }
 
-  /**
-   * not implemented -- returns empty list
-   * 
-   * @return
-   */
   public static List<String> getGroupURLLinks()
   {
     return groupURLLinks;
@@ -1203,7 +1204,7 @@ public class Preferences extends GPreferences
     } catch (NumberFormatException x)
     {
       userIdWidth.setText("");
-      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager
                       .getString("warn.user_defined_width_requirements"),
               MessageManager.getString("label.invalid_id_column_width"),
@@ -1222,14 +1223,14 @@ public class Preferences extends GPreferences
    * Returns true if chimera path is to a valid executable, else show an error
    * dialog.
    */
-  protected boolean validateChimeraPath()
+  private boolean validateChimeraPath()
   {
     if (chimeraPath.getText().trim().length() > 0)
     {
       File f = new File(chimeraPath.getText());
       if (!f.canExecute())
       {
-        JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.invalid_chimera_path"),
                 MessageManager.getString("label.invalid_name"),
                 JvOptionPane.ERROR_MESSAGE);
@@ -1268,7 +1269,7 @@ public class Preferences extends GPreferences
     if (!found)
     {
       String[] options = { "OK", "Help" };
-      int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
+      int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
@@ -1341,7 +1342,7 @@ public class Preferences extends GPreferences
     }
   }
 
-  protected class UrlListSelectionHandler implements ListSelectionListener
+  private class UrlListSelectionHandler implements ListSelectionListener
   {
 
     @Override