X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=07e346f6a2c977f2b8323353f9f2bcbf0a29ff3f;hb=76f9992a5fd8e818f8051130e25c6aefb4ef51ad;hp=1f031b2abc390451b4cb9145f5d23c7972ea3ea1;hpb=66b1a1e003d38ea506f87c42173bb5de37b38edc;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 1f031b2..07e346f 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,17 +20,20 @@
  */
 package jalview.bin;
 
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.datamodel.PDBEntry;
-import jalview.gui.UserDefinedColours;
+import jalview.gui.Preferences;
 import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureImportSettings;
 import jalview.urls.IdOrgSettings;
 import jalview.util.ColorUtils;
+import jalview.util.Platform;
 import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Color;
+import java.awt.Dimension;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
@@ -114,7 +117,6 @@ import org.apache.log4j.SimpleLayout;
  * service</li>
  * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
  * collecting usage statistics</li>
- * <li>DAS_LOCAL_SOURCE list of local das sources</li>
  * <li>SHOW_OVERVIEW boolean for overview window display</li>
  * <li>ANTI_ALIAS boolean for smooth fonts</li>
  * <li>RIGHT_ALIGN_IDS boolean</li>
@@ -134,9 +136,7 @@ import org.apache.log4j.SimpleLayout;
  * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
  * <li>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see
  * jalview.utils.GroupURLLink for more info</li>
- * <li>DAS_REGISTRY_URL the registry to query</li>
  * <li>DEFAULT_BROWSER for unix</li>
- * <li>DAS_ACTIVE_SOURCE list of active sources</li>
  * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
  * (false)</li>
  * <li>VERSION_CHECK (true) check for the latest release version from
@@ -206,11 +206,27 @@ import org.apache.log4j.SimpleLayout;
  * panel in web service preferences</li>
  * </ul>
  * 
- * @author $author$
- * @version $Revision$
  */
-public class Cache
+public class Cache implements ApplicationSingletonI
 {
+
+  private Cache()
+  {
+    // private singleton
+  }
+
+  /**
+   * In Java, this will be a static field instance, which will be
+   * application-specific; in JavaScript it will be an applet-specific instance
+   * tied to the applet's ThreadGroup.
+   * 
+   * @return
+   */
+  public static Cache getInstance()
+  {
+    return (Cache) ApplicationSingletonProvider.getInstance(Cache.class);
+  }
+
   /**
    * property giving log4j level for CASTOR loggers
    */
@@ -226,12 +242,6 @@ public class Cache
    */
   public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
 
-  public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
-
-  public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
-
-  public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
-
   /**
    * Sifts settings
    */
@@ -273,7 +283,9 @@ public class Cache
   public static Logger log;
 
   /** Jalview Properties */
-  public static Properties applicationProperties = new Properties()
+  // BH 2019.05.08 was static
+  @SuppressWarnings("serial")
+  public Properties applicationProperties = new Properties()
   {
     // override results in properties output in alphabetical order
     @Override
@@ -284,10 +296,14 @@ public class Cache
   };
 
   /** Default file is ~/.jalview_properties */
-  static String propertiesFile;
+  private String propertiesFile;
 
-  private static boolean propsAreReadOnly = /** @j2sNative true || */
-          false;
+  /**
+   * flag to possibly allow properties to be written to a property file
+   */
+  private boolean propsAreReadOnly = Platform.isJS();
+
+  private final static String JS_PROPERTY_PREFIX = "jalview_";
 
   public static void initLogger()
   {
@@ -310,14 +326,14 @@ public class Cache
       jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
 
       laxis.setLevel(Level.toLevel(
-              Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
-      lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
-              Level.INFO.toString())));
+              getDefault("logs.Axis.Level", Level.INFO.toString())));
+      lcastor.setLevel(Level.toLevel(
+              getDefault("logs.Castor.Level", Level.INFO.toString())));
       lcastor = Logger.getLogger("org.exolab.castor.xml");
-      lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
-              Level.INFO.toString())));
+      lcastor.setLevel(Level.toLevel(
+              getDefault("logs.Castor.Level", Level.INFO.toString())));
       // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
-      // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+      // lcastor.setLevel(Level.toLevel(getDefault("logs.Castor.Level",
       // Level.INFO.toString())));
       jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
               .getDefault("logs.Jalview.level", Level.INFO.toString())));
@@ -339,50 +355,67 @@ public class Cache
    */
   public static void loadProperties(String propsFile)
   {
+    getInstance().loadPropertiesImpl(propsFile);
+  }
+
+  private void loadPropertiesImpl(String propsFile)
+  {
     propertiesFile = propsFile;
-    if (propsFile == null)
-    {
-      propertiesFile = System.getProperty("user.home") + File.separatorChar
-              + ".jalview_properties";
-    }
-    else
+    if (!propsAreReadOnly)
     {
-      // don't corrupt the file we've been given.
-      propsAreReadOnly = true;
+      // Java only
+      if (propsFile == null)
+      {
+        propertiesFile = System.getProperty("user.home")
+                + File.separatorChar + ".jalview_properties";
+      }
+      else
+      {
+        // don't corrupt the file we've been given.
+        propsAreReadOnly = true;
+      }
     }
 
-    try
+    if (propertiesFile == null)
+    { // BH 2019 read properties from the Info object associated with this
+      // applet
+      Platform.readInfoProperties(JS_PROPERTY_PREFIX,
+              applicationProperties);
+    }
+    else
     {
-      InputStream fis;
       try
       {
-        fis = new java.net.URL(propertiesFile).openStream();
-        System.out.println(
-                "Loading jalview properties from : " + propertiesFile);
-        System.out.println(
-                "Disabling Jalview writing to user's local properties file.");
-        propsAreReadOnly = true;
+        InputStream fis;
+        try
+        {
+          fis = new java.net.URL(propertiesFile).openStream();
+          System.out.println(
+                  "Loading jalview properties from : " + propertiesFile);
+          System.out.println(
+                  "Disabling Jalview writing to user's local properties file.");
+          propsAreReadOnly = true;
+
+        } catch (Exception ex)
+        {
+          fis = null;
+        }
+        if (fis == null)
+        {
+          fis = new FileInputStream(propertiesFile);
+        }
+        applicationProperties.clear();
+        applicationProperties.load(fis);
+
+        // remove any old build properties
 
+        deleteBuildProperties();
+        fis.close();
       } catch (Exception ex)
       {
-        fis = null;
-      }
-      if (fis == null)
-      {
-        fis = new FileInputStream(propertiesFile);
+        System.out.println("Error reading properties file: " + ex);
       }
-      applicationProperties.clear();
-      applicationProperties.load(fis);
-
-      // remove any old build properties
-
-      deleteBuildProperties();
-      fis.close();
-    } catch (Exception ex)
-    {
-      System.out.println("Error reading properties file: " + ex);
     }
-
     if (getDefault("USE_PROXY", false))
     {
       String proxyServer = getDefault("PROXY_SERVER", ""),
@@ -396,21 +429,27 @@ public class Cache
     }
 
     // LOAD THE AUTHORS FROM THE authors.props file
+    String authorDetails = (Platform.isJS() ? null
+            : "jar:".concat(Cache.class.getProtectionDomain()
+                    .getCodeSource().getLocation().toString()
+                    .concat("!/authors.props")));
+
     try
     {
-      String authorDetails = /** @j2sNative "xxx" || */
-              "jar:"
-              .concat(Cache.class.getProtectionDomain().getCodeSource()
-                      .getLocation().toString().concat("!/authors.props"));
-
-      java.net.URL localJarFileURL = new java.net.URL(authorDetails);
-
-      InputStream in = localJarFileURL.openStream();
-      applicationProperties.load(in);
-      in.close();
+      if (authorDetails != null)
+      {
+        java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+        InputStream in = localJarFileURL.openStream();
+        applicationProperties.load(in);
+        in.close();
+      }
     } catch (Exception ex)
     {
       System.out.println("Error reading author details: " + ex);
+      authorDetails = null;
+    }
+    if (authorDetails == null)
+    {
       applicationProperties.remove("AUTHORS");
       applicationProperties.remove("AUTHORFNAMES");
       applicationProperties.remove("YEAR");
@@ -419,24 +458,28 @@ public class Cache
     // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
     // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
     // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
-    try
+    String buildDetails = (Platform.isJS() ? null
+            : "jar:".concat(Cache.class.getProtectionDomain()
+                    .getCodeSource().getLocation().toString()
+                    .concat("!/.build_properties")));
+    if (buildDetails != null)
     {
-      String buildDetails = /** @j2sNative "xxx" || */
-              "jar:".concat(Cache.class.getProtectionDomain()
-              .getCodeSource().getLocation().toString()
-              .concat("!/.build_properties"));
-
-      java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
-      InputStream in = localJarFileURL.openStream();
-      applicationProperties.load(in);
-      in.close();
-    } catch (Exception ex)
+      try
+      {
+        java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+        InputStream in = localJarFileURL.openStream();
+        applicationProperties.load(in);
+        in.close();
+      } catch (Exception ex)
+      {
+        System.out.println("Error reading build details: " + ex);
+        buildDetails = null;
+      }
+    }
+    if (buildDetails == null)
     {
-      System.out.println("Error reading build details: " + ex);
       applicationProperties.remove("VERSION");
     }
-
     String jnlpVersion = System.getProperty("jalview.version");
     String codeVersion = getProperty("VERSION");
     String codeInstallation = getProperty("INSTALLATION");
@@ -453,21 +496,20 @@ public class Cache
     }
     new BuildDetails(codeVersion, null, codeInstallation);
 
-    SiftsSettings
-            .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+    SiftsSettings.setMapWithSifts(getDefault("MAP_WITH_SIFTS", false));
 
     SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
             .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
 
     SiftsSettings.setFailSafePIDThreshold(
-            jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+            getDefault("sifts_fail_safe_pid_threshold",
                     DEFAULT_FAIL_SAFE_PID_THRESHOLD));
 
     SiftsSettings.setCacheThresholdInDays(
-            jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+            getDefault("sifts_cache_threshold_in_days",
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
-    IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
+    IdOrgSettings.setUrl(getDefault(Preferences.ID_ORG_HOSTURL,
             "http://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
@@ -475,17 +517,16 @@ public class Cache
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
-            .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+            .getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT));
     StructureImportSettings
             .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
     // StructureImportSettings
-    // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+    // .setDefaultPDBFileParser(jalview.bin.getDefault(
     // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
-    if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
-            && (System.getProperty("java.awt.headless") == null || System
-                    .getProperty("java.awt.headless").equals("false")))
+    if (jnlpVersion == null && !Jalview.isHeadlessMode()
+            && getDefault("VERSION_CHECK", true))
     {
 
       class VersionChecker extends Thread
@@ -556,13 +597,10 @@ public class Cache
     setProperty("VERSION", codeVersion);
 
     // LOAD USERDEFINED COLOURS
-    jalview.bin.Cache
-            .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
-    jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
-            false);
+    initUserColourSchemes(getProperty(Preferences.USER_DEFINED_COLOURS));
   }
 
-  private static void deleteBuildProperties()
+  private void deleteBuildProperties()
   {
     applicationProperties.remove("LATEST_VERSION");
     applicationProperties.remove("VERSION");
@@ -584,41 +622,99 @@ public class Cache
    */
   public static String getProperty(String key)
   {
-    return applicationProperties.getProperty(key);
+    return getInstance().applicationProperties.getProperty(key);
   }
 
   /**
-   * These methods are used when checking if the saved preference is different
-   * to the default setting
+   * Returns the boolean property value for the given property name. If the
+   * value is absent then the default value is returned instead.
+   * 
+   * @param property
+   * @param def
+   * @return
    */
+  public static boolean getDefault(String property, final boolean def)
+  {
+    String string = getProperty(property);
+    return string == null ? def : Boolean.parseBoolean(string);
+  }
 
-  public static boolean getDefault(String property, boolean def)
+  /**
+   * Returns the integer property value for the given property name. If the
+   * value is absent, or malformed (not an integer), then the default value is
+   * returned instead.
+   * 
+   * @param property
+   * @param def
+   * @return
+   */
+  public static int getDefault(String property, final int def)
   {
     String string = getProperty(property);
     if (string != null)
     {
-      def = Boolean.valueOf(string).booleanValue();
+      try
+      {
+        return Integer.parseInt(string);
+      } catch (NumberFormatException e)
+      {
+        System.out.println("Error parsing int property '" + property
+                + "' with value '" + string + "'");
+      }
     }
 
     return def;
   }
 
   /**
-   * These methods are used when checking if the saved preference is different
-   * to the default setting
+   * retrieve a dimension, such as for Jmol
+   * 
+   * @param property
+   * @param def
+   * @return
    */
-  public static String getDefault(String property, String def)
+  public static Dimension getDefaultDim(String property, Dimension def)
   {
-    String string = getProperty(property);
-    if (string != null)
+    String s = getProperty(property);
+    if (s != null)
     {
-      return string;
+      if (s.indexOf(',') < 0)
+      {
+        s = s.trim().replace(' ', ',');
+        if (s.indexOf(',') < 0)
+        {
+          s += "," + s;
+        }
+      }
+      try
+      {
+        int pt = s.indexOf(",");
+        return new Dimension(Integer.parseInt(s.substring(0, pt)),
+                Integer.parseInt(s.substring(pt + 1)));
+      } catch (NumberFormatException e)
+      {
+        System.out.println("Error parsing Dimension property '" + property
+                + "' with value '" + s + "'");
+      }
     }
-
     return def;
   }
 
   /**
+   * Returns the value of the given property, or the supplied default value if
+   * the property is not set
+   * 
+   * @param property
+   * @param def
+   * @return
+   */
+  public static String getDefault(String property, final String def)
+  {
+    String value = getProperty(property);
+    return value == null ? def : value;
+  }
+
+  /**
    * Stores property in the file "HOME_DIR/.jalview_properties"
    * 
    * @param key
@@ -630,11 +726,37 @@ public class Cache
    */
   public static Object setProperty(String key, String obj)
   {
+    return getInstance().setPropertyImpl(key, obj, true);
+  }
+
+  /**
+   * Sets a property value for the running application, without saving it to the
+   * properties file
+   * 
+   * @param key
+   * @param obj
+   */
+  public static void setPropertyNoSave(String key, String obj)
+  {
+    getInstance().setPropertyImpl(key, obj, false);
+  }
+
+  /**
+   * Sets a property value, and optionally also saves the current properties to
+   * file
+   * 
+   * @param key
+   * @param obj
+   * @param andSave
+   * @return
+   */
+  private Object setPropertyImpl(String key, String obj, boolean andSave)
+  {
     Object oldValue = null;
     try
     {
       oldValue = applicationProperties.setProperty(key, obj);
-      if (!propsAreReadOnly)
+      if (andSave && !propsAreReadOnly && propertiesFile != null)
       {
         FileOutputStream out = new FileOutputStream(propertiesFile);
         applicationProperties.store(out, "---JalviewX Properties File---");
@@ -649,21 +771,55 @@ 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 string)
+  public static void removeProperty(String key)
   {
-    applicationProperties.remove(string);
-    saveProperties();
+    getInstance().removePropertyImpl(key, true);
   }
 
   /**
-   * save the properties to the jalview properties path
+   * Removes the named property for the running application, without saving the
+   * properties file
+   * 
+   * @param key
+   */
+  public static void removePropertyNoSave(String key)
+  {
+    getInstance().removePropertyImpl(key, false);
+  }
+
+  /**
+   * Removes the named property, and optionally saves the current properties to
+   * file
+   * 
+   * @param key
+   * @param andSave
+   */
+  private void removePropertyImpl(String key, boolean andSave)
+  {
+    applicationProperties.remove(key);
+    if (andSave)
+    {
+      savePropertiesImpl();
+    }
+  }
+
+  /**
+   * Saves the current properties to file
    */
   public static void saveProperties()
   {
+    getInstance().savePropertiesImpl();
+  }
+
+  /**
+   * save the properties to the jalview properties path
+   */
+  private void savePropertiesImpl()
+  {
     if (!propsAreReadOnly)
     {
       try
@@ -678,10 +834,17 @@ public class Cache
     }
   }
 
+  private final static int UNTESTED = -1;
+
+  private final static int TRUE = 1;
+
+  private final static int FALSE = 0;
+
   /**
    * internal vamsas class discovery state
    */
-  private static int vamsasJarsArePresent = -1;
+  private static int vamsasJarsArePresent = (Platform.isJS() ? FALSE
+          : UNTESTED);
 
   /**
    * Searches for vamsas client classes on class path.
@@ -690,7 +853,7 @@ public class Cache
    */
   public static boolean vamsasJarsPresent()
   {
-    if (vamsasJarsArePresent == -1)
+    if (vamsasJarsArePresent == UNTESTED)
     {
       try
       {
@@ -699,7 +862,7 @@ public class Cache
         {
           jalview.bin.Cache.log.debug(
                   "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
-          vamsasJarsArePresent = 1;
+          vamsasJarsArePresent = TRUE;
           Logger lvclient = Logger.getLogger("uk.ac.vamsas");
           lvclient.setLevel(Level.toLevel(Cache
                   .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
@@ -710,17 +873,18 @@ public class Cache
         }
       } catch (Exception e)
       {
-        vamsasJarsArePresent = 0;
+        vamsasJarsArePresent = FALSE;
         jalview.bin.Cache.log.debug("Vamsas Classes are not present");
       }
     }
-    return (vamsasJarsArePresent > 0);
+    return (vamsasJarsArePresent == TRUE);
   }
 
   /**
    * internal vamsas class discovery state
    */
-  private static int groovyJarsArePresent = -1;
+  private static int groovyJarsArePresent = (Platform.isJS() ? FALSE
+          : UNTESTED);
 
   /**
    * Searches for vamsas client classes on class path.
@@ -729,7 +893,7 @@ public class Cache
    */
   public static boolean groovyJarsPresent()
   {
-    if (groovyJarsArePresent == -1)
+    if (groovyJarsArePresent == UNTESTED)
     {
       try
       {
@@ -738,7 +902,7 @@ public class Cache
         {
           jalview.bin.Cache.log.debug(
                   "Found Groovy (groovy.lang.GroovyObject can be loaded)");
-          groovyJarsArePresent = 1;
+          groovyJarsArePresent = TRUE;
           Logger lgclient = Logger.getLogger("groovy");
           lgclient.setLevel(Level.toLevel(Cache
                   .getDefault("logs.Groovy.Level", Level.INFO.toString())));
@@ -749,15 +913,15 @@ public class Cache
         }
       } catch (Error e)
       {
-        groovyJarsArePresent = 0;
+        groovyJarsArePresent = FALSE;
         jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
       } catch (Exception e)
       {
-        groovyJarsArePresent = 0;
+        groovyJarsArePresent = FALSE;
         jalview.bin.Cache.log.debug("Groovy Classes are not present");
       }
     }
-    return (groovyJarsArePresent > 0);
+    return (groovyJarsArePresent == TRUE);
   }
 
   /**
@@ -766,15 +930,18 @@ public class Cache
    */
   protected static Object tracker = null;
 
-  protected static Class trackerfocus = null;
+  protected static Class<?> trackerfocus = null;
 
-  protected static Class jgoogleanalyticstracker = null;
+  protected static Class<?> jgoogleanalyticstracker = null;
 
   /**
    * Initialise the google tracker if it is not done already.
    */
   public static void initGoogleTracker()
   {
+
+    // TODO: SwingJS JavaScript tracker?
+
     if (tracker == null)
     {
       if (jgoogleanalyticstracker == null)
@@ -809,8 +976,7 @@ public class Cache
                 .newInstance(new Object[]
                 { "Jalview Desktop",
                     (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
-                            + jalview.bin.Cache.getDefault("BUILD_DATE",
-                                    "unknown")),
+                            + getDefault("BUILD_DATE", "unknown")),
                     "UA-9060947-1" });
         jgoogleanalyticstracker
                 .getMethod("trackAsynchronously", new Class[]
@@ -887,18 +1053,24 @@ public class Cache
   }
 
   /**
-   * get the user's default colour if available
+   * Returns the Color value of the given property's value, or the supplied
+   * default colour if no property is found, or it cannot be parsed to a colour.
+   * Colours are normally saved as hex rgb values, though other formats may be
+   * parseable.
    * 
    * @param property
-   * @param defcolour
+   * @param defaultColour
    * @return
+   * @see Cache#setColourPropertyNoSave(String, Color)
+   * @see ColorUtils#parseColourString(String)
    */
-  public static Color getDefaultColour(String property, Color defcolour)
+  public static Color getDefaultColour(String property,
+          final Color defaultColour)
   {
     String colprop = getProperty(property);
     if (colprop == null)
     {
-      return defcolour;
+      return defaultColour;
     }
     Color col = ColorUtils.parseColourString(colprop);
     if (col == null)
@@ -906,22 +1078,24 @@ public class Cache
       log.warn("Couldn't parse '" + colprop + "' as a colour for "
               + property);
     }
-    return (col == null) ? defcolour : col;
+    return (col == null) ? defaultColour : col;
   }
 
   /**
-   * store a colour as a Jalview user default property
+   * Stores a colour as a Jalview property, converted to hex values for rgb.
+   * Properties are not saved to file.
    * 
    * @param property
    * @param colour
    */
-  public static void setColourProperty(String property, Color colour)
+  public static void setColourPropertyNoSave(String property, Color colour)
   {
     setProperty(property, jalview.util.Format.getHexString(colour));
   }
 
   /**
    * Stores a formatted date in a jalview property, using a fixed locale.
+   * Updated properties are written out to the properties file.
    * 
    * @param propertyName
    * @param date
@@ -998,11 +1172,11 @@ public class Cache
     }
     if (value == null || value.trim().length() < 1)
     {
-      Cache.applicationProperties.remove(propName);
+      getInstance().applicationProperties.remove(propName);
     }
     else
     {
-      Cache.applicationProperties.setProperty(propName, value);
+      getInstance().applicationProperties.setProperty(propName, value);
     }
   }
 
@@ -1047,14 +1221,15 @@ public class Cache
     {
       if (coloursFound.toString().length() > 1)
       {
-        setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
+        setProperty(Preferences.USER_DEFINED_COLOURS,
                 coloursFound.toString());
       }
       else
       {
-        applicationProperties
-                .remove(UserDefinedColours.USER_DEFINED_COLOURS);
+        getInstance().applicationProperties
+                .remove(Preferences.USER_DEFINED_COLOURS);
       }
     }
   }
+
 }