JAL-3626 from JAL-3253-applet Cache applicationProperties made private

-- adds remove/setPropertyNoSave

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index c532b7a..2c8986c 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -266,7 +266,7 @@ public class Cache
   public static Logger log;
 
   /** Jalview Properties */
-  public static Properties applicationProperties = new Properties()
+  private static Properties applicationProperties = new Properties()
   {
     // override results in properties output in alphabetical order
     @Override
@@ -333,6 +333,20 @@ public class Cache
    */
   public static void loadProperties(String propsFile)
   {
+    /* for JalviewJS should be 
+    
+    getInstance().
+    
+   */
+    loadPropertiesImpl(propsFile);
+    
+  }
+
+  private /* JalviewJS should not be static */
+  static //
+  void loadPropertiesImpl(String propsFile)
+  {
+    
     propertiesFile = propsFile;
     if (propsFile == null && !propsAreReadOnly)
     {
@@ -620,12 +634,17 @@ public class Cache
    */
   public static String getProperty(String key)
   {
-    String prop = applicationProperties.getProperty(key);
-    if (prop == null && Platform.isJS())
-    {
-      prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
-              + "_" + JS_PROPERTY_PREFIX + key);
-    }
+    String prop =     /* for JalviewJS should be 
+    
+    getInstance().
+    
+   */
+            applicationProperties.getProperty(key);
+//    if (prop == null && Platform.isJS())
+//    {
+//      prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+//              + "_" + JS_PROPERTY_PREFIX + key);
+//    }
     return prop;
   }
 
@@ -704,14 +723,53 @@ public class Cache
   }
 
   /**
-   * remove the specified property from the jalview properties file
+   * Removes the specified property from the jalview properties file
    * 
-   * @param string
+   * @param key
+   */
+  public static void removeProperty(String key)
+  {
+    /* for JalviewJS should be 
+    
+    getInstance().
+    
+   */
+    removePropertyImpl(key, true);
+  }
+
+  /**
+   * Removes the named property for the running application, without saving the
+   * properties file
+   * 
+   * BH noting that ColourMenuHelper calls this. If the intent is to save, 
+   * then simply chanet that call to removeProperty(key).
+   * 
+   * @param key
+   */
+  public static void removePropertyNoSave(String key)
+  {
+    /* for JalviewJS should be 
+    
+    getInstance().
+    
+   */
+    removePropertyImpl(key, false);
+  }
+
+  /**
+   * Removes the named property, and optionally saves the current properties to
+   * file
+   * 
+   * @param key
+   * @param andSave
    */
-  public static void removeProperty(String string)
+  private /* JalviewJS should not be static */
+  static //
+  void removePropertyImpl(String key, boolean andSave)
   {
-    applicationProperties.remove(string);
-    saveProperties();
+    applicationProperties.remove(key);
+    if (andSave)
+      saveProperties();
   }
 
   /**
@@ -1102,6 +1160,11 @@ public class Cache
     {
       if (coloursFound.toString().length() > 1)
       {
+        /* for JalviewJS should be 
+        
+        getInstance().
+        
+       */
         setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
                 coloursFound.toString());
       }
@@ -1177,7 +1240,7 @@ public class Cache
   
   /**
    * 
-   * For AppletParams
+   * For AppletParams and Preferences ok_actionPerformed and startupFileTextfield_mouseClicked
    * 
    * Sets a property value for the running application, without saving it to the
    * properties file

diff --git a/src/jalview/gui/ColourMenuHelper.java b/src/jalview/gui/ColourMenuHelper.java
index 6eab07d..43d7015 100644 (file)
--- a/src/jalview/gui/ColourMenuHelper.java
+++ b/src/jalview/gui/ColourMenuHelper.java
@@ -314,7 +314,7 @@ public class ColourMenuHelper
     }
     else
     {
-      Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+      Cache.removePropertyNoSave("USER_DEFINED_COLOURS");
     }
   }
 }

diff --git a/src/jalview/gui/LineartOptions.java b/src/jalview/gui/LineartOptions.java
index d55733c..9704b39 100644 (file)
--- a/src/jalview/gui/LineartOptions.java
+++ b/src/jalview/gui/LineartOptions.java
@@ -188,7 +188,7 @@ public class LineartOptions extends JPanel
     }
     else
     {
-      Cache.applicationProperties.remove(preferencesKey);
+      Cache.removePropertyNoSave(preferencesKey);
     }
   }
 

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index bd795af..646bf61 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -698,65 +698,65 @@ public class Preferences extends GPreferences
     /*
      * Save Visual settings
      */
-    Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
+    Cache.setPropertyNoSave("SHOW_JVSUFFIX",
             Boolean.toString(seqLimit.isSelected()));
-    Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
+    Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
             Boolean.toString(rightAlign.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
+    Cache.setPropertyNoSave("SHOW_FULLSCREEN",
             Boolean.toString(fullScreen.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
+    Cache.setPropertyNoSave("SHOW_OVERVIEW",
             Boolean.toString(openoverv.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+    Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
             Boolean.toString(annotations.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+    Cache.setPropertyNoSave("SHOW_CONSERVATION",
             Boolean.toString(conservation.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_QUALITY",
+    Cache.setPropertyNoSave("SHOW_QUALITY",
             Boolean.toString(quality.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+    Cache.setPropertyNoSave("SHOW_IDENTITY",
             Boolean.toString(identity.isSelected()));
 
-    Cache.applicationProperties.setProperty("GAP_SYMBOL",
+    Cache.setPropertyNoSave("GAP_SYMBOL",
             gapSymbolCB.getSelectedItem().toString());
 
-    Cache.applicationProperties.setProperty("FONT_NAME",
+    Cache.setPropertyNoSave("FONT_NAME",
             fontNameCB.getSelectedItem().toString());
-    Cache.applicationProperties.setProperty("FONT_STYLE",
+    Cache.setPropertyNoSave("FONT_STYLE",
             fontStyleCB.getSelectedItem().toString());
-    Cache.applicationProperties.setProperty("FONT_SIZE",
+    Cache.setPropertyNoSave("FONT_SIZE",
             fontSizeCB.getSelectedItem().toString());
 
-    Cache.applicationProperties.setProperty("ID_ITALICS",
+    Cache.setPropertyNoSave("ID_ITALICS",
             Boolean.toString(idItalics.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+    Cache.setPropertyNoSave("SHOW_UNCONSERVED",
             Boolean.toString(showUnconserved.isSelected()));
-    Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
+    Cache.setPropertyNoSave(SHOW_OCCUPANCY,
             Boolean.toString(showOccupancy.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+    Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
             Boolean.toString(showGroupConsensus.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
+    Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
             Boolean.toString(showGroupConservation.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
+    Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
             Boolean.toString(showConsensHistogram.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+    Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
             Boolean.toString(showConsensLogo.isSelected()));
-    Cache.applicationProperties.setProperty("ANTI_ALIAS",
+    Cache.setPropertyNoSave("ANTI_ALIAS",
             Boolean.toString(smoothFont.isSelected()));
-    Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+    Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
             Boolean.toString(scaleProteinToCdna.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+    Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
             Boolean.toString(showNpTooltip.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+    Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
             Boolean.toString(showDbRefTooltip.isSelected()));
 
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
+    Cache.setPropertyNoSave("WRAP_ALIGNMENT",
             Boolean.toString(wrap.isSelected()));
 
-    Cache.applicationProperties.setProperty("STARTUP_FILE",
+    Cache.setPropertyNoSave("STARTUP_FILE",
             startupFileTextfield.getText());
-    Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
+    Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
             Boolean.toString(startupCheckbox.isSelected()));
 
-    Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+    Cache.setPropertyNoSave("SORT_ALIGNMENT",
             sortby.getSelectedItem().toString());
 
     // convert description of sort order to enum name for save
@@ -764,20 +764,20 @@ public class Preferences extends GPreferences
             .forDescription(sortAnnBy.getSelectedItem().toString());
     if (annSortOrder != null)
     {
-      Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
+      Cache.setPropertyNoSave(SORT_ANNOTATIONS,
               annSortOrder.name());
     }
 
     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
-    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+    Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
             Boolean.valueOf(showAutocalcFirst).toString());
 
     /*
      * Save Colours settings
      */
-    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+    Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
             protColour.getSelectedItem().toString());
-    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+    Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
             nucColour.getSelectedItem().toString());
     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
             minColour.getBackground());
@@ -789,37 +789,37 @@ public class Preferences extends GPreferences
      */
     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
-    Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+    Cache.setPropertyNoSave(USE_LEGACY_GAP,
             Boolean.toString(useLegacyGap.isSelected()));
-    Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+    Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
             Boolean.toString(showHiddenAtStart.isSelected()));
 
     /*
      * Save Structure settings
      */
-    Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+    Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
             Boolean.toString(addTempFactor.isSelected()));
-    Cache.applicationProperties.setProperty(ADD_SS_ANN,
+    Cache.setPropertyNoSave(ADD_SS_ANN,
             Boolean.toString(addSecondaryStructure.isSelected()));
-    Cache.applicationProperties.setProperty(USE_RNAVIEW,
+    Cache.setPropertyNoSave(USE_RNAVIEW,
             Boolean.toString(useRnaView.isSelected()));
-    Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+    Cache.setPropertyNoSave(STRUCT_FROM_PDB,
             Boolean.toString(structFromPdb.isSelected()));
-    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
+    Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
             structViewer.getSelectedItem().toString());
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
-    Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+    Cache.setPropertyNoSave("MAP_WITH_SIFTS",
             Boolean.toString(siftsMapping.isSelected()));
     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 
     /*
      * Save Output settings
      */
-    Cache.applicationProperties.setProperty("EPS_RENDERING",
+    Cache.setPropertyNoSave("EPS_RENDERING",
             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
-    Cache.applicationProperties.setProperty("HTML_RENDERING",
+    Cache.setPropertyNoSave("HTML_RENDERING",
             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
-    Cache.applicationProperties.setProperty("SVG_RENDERING",
+    Cache.setPropertyNoSave("SVG_RENDERING",
             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 
     /*
@@ -833,29 +833,29 @@ public class Preferences extends GPreferences
     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
     if (menuLinks.isEmpty())
     {
-      Cache.applicationProperties.remove("SEQUENCE_LINKS");
+      Cache.removeNoSave("SEQUENCE_LINKS");
     }
     else
     {
-      Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+      Cache.setPropertyNoSave("SEQUENCE_LINKS",
               menuLinks.toString());
     }
 
     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
     if (nonMenuLinks.isEmpty())
     {
-      Cache.applicationProperties.remove("STORED_LINKS");
+      Cache.removeNoSave("STORED_LINKS");
     }
     else
     {
-      Cache.applicationProperties.setProperty("STORED_LINKS",
+      Cache.setPropertyNoSave("STORED_LINKS",
               nonMenuLinks.toString());
     }
 
-    Cache.applicationProperties.setProperty("DEFAULT_URL",
+    Cache.setPropertyNoSave("DEFAULT_URL",
             sequenceUrlLinks.getPrimaryUrlId());
 
-    Cache.applicationProperties.setProperty("USE_PROXY",
+    Cache.setPropertyNoSave("USE_PROXY",
             Boolean.toString(useProxy.isSelected()));
 
     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
@@ -894,40 +894,40 @@ public class Preferences extends GPreferences
     /*
      * Save Output settings
      */
-    Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
+    Cache.setPropertyNoSave("BLC_JVSUFFIX",
             Boolean.toString(blcjv.isSelected()));
-    Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
+    Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
             Boolean.toString(clustaljv.isSelected()));
-    Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
+    Cache.setPropertyNoSave("FASTA_JVSUFFIX",
             Boolean.toString(fastajv.isSelected()));
-    Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
+    Cache.setPropertyNoSave("MSF_JVSUFFIX",
             Boolean.toString(msfjv.isSelected()));
-    Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
+    Cache.setPropertyNoSave("PFAM_JVSUFFIX",
             Boolean.toString(pfamjv.isSelected()));
-    Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
+    Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
             Boolean.toString(pileupjv.isSelected()));
-    Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
+    Cache.setPropertyNoSave("PIR_JVSUFFIX",
             Boolean.toString(pirjv.isSelected()));
-    Cache.applicationProperties.setProperty("PIR_MODELLER",
+    Cache.setPropertyNoSave("PIR_MODELLER",
             Boolean.toString(modellerOutput.isSelected()));
-    Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+    Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
             Boolean.toString(embbedBioJSON.isSelected()));
     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 
-    Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+    Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
             Boolean.toString(autoIdWidth.isSelected()));
     userIdWidth_actionPerformed();
-    Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
+    Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
             userIdWidth.getText());
 
     /*
      * Save Editing settings
      */
-    Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+    Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
             Boolean.toString(autoCalculateConsCheck.isSelected()));
-    Cache.applicationProperties.setProperty("SORT_BY_TREE",
+    Cache.setPropertyNoSave("SORT_BY_TREE",
             Boolean.toString(sortByTree.isSelected()));
-    Cache.applicationProperties.setProperty("PAD_GAPS",
+    Cache.setPropertyNoSave("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
     if (!Platform.isJS())
@@ -938,10 +938,10 @@ public class Preferences extends GPreferences
     /*
      * Save Backups settings
      */
-    Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+    Cache.setPropertyNoSave(BackupFiles.ENABLED,
             Boolean.toString(enableBackupFiles.isSelected()));
     int preset = getComboIntStringKey(backupfilesPresetsCombo);
-    Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+    Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 
     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
     {
@@ -955,7 +955,7 @@ public class Preferences extends GPreferences
 
     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
             .get(preset);
-    Cache.applicationProperties.setProperty(
+    Cache.setPropertyNoSave(
             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 
     Cache.saveProperties();
@@ -1012,7 +1012,7 @@ public class Preferences extends GPreferences
       FileFormatI format = chooser.getSelectedFormat();
       if (format != null)
       {
-        Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+        Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
                 format.getName());
       }
       startupFileTextfield