X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=b15c317657342c7f3514fd0c809399c56ccf59f0;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=b6ff253ac5cb2e3becf6d884198928574859ca2e;hpb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index b6ff253..b15c317 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,8 +20,9 @@
  */
 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;
@@ -32,6 +33,7 @@ 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;
@@ -207,8 +209,26 @@ import org.apache.log4j.SimpleLayout;
  * @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
+   */
+  private static Cache getInstance()
+  {
+    return (Cache) ApplicationSingletonProvider.getInstance(Cache.class);
+  }
+
   /**
    * property giving log4j level for CASTOR loggers
    */
@@ -265,7 +285,9 @@ public class Cache
   public static Logger log;
 
   /** Jalview Properties */
-  public static Properties applicationProperties = new Properties()
+  // BH 2019.05.08 was static
+  @SuppressWarnings("serial")
+  private Properties applicationProperties = new Properties()
   {
     // override results in properties output in alphabetical order
     @Override
@@ -276,9 +298,12 @@ public class Cache
   };
 
   /** Default file is ~/.jalview_properties */
-  static String propertiesFile;
+  private String propertiesFile;
 
-  private static boolean propsAreReadOnly = Platform.isJS();
+  /**
+   * 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_";
 
@@ -303,14 +328,14 @@ 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())));
@@ -332,20 +357,30 @@ public class Cache
    */
   public static void loadProperties(String propsFile)
   {
+    getInstance().loadPropertiesImpl(propsFile);
+  }
+
+  private void loadPropertiesImpl(String propsFile)
+  {
     propertiesFile = propsFile;
-    if (propsFile == null && !propsAreReadOnly)
-    {
-      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;
+      }
     }
 
     if (propertiesFile == null)
-    { // BH 2019
+    { // BH 2019 read properties from the Info object associated with this
+      // applet
       Platform.readInfoProperties(JS_PROPERTY_PREFIX,
               applicationProperties);
     }
@@ -417,9 +452,9 @@ public class Cache
     }
     if (authorDetails == null)
     {
-        applicationProperties.remove("AUTHORS");
-        applicationProperties.remove("AUTHORFNAMES");
-        applicationProperties.remove("YEAR");
+      applicationProperties.remove("AUTHORS");
+      applicationProperties.remove("AUTHORFNAMES");
+      applicationProperties.remove("YEAR");
     }
 
     // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
@@ -445,7 +480,7 @@ public class Cache
     }
     if (buildDetails == null)
     {
-        applicationProperties.remove("VERSION");
+      applicationProperties.remove("VERSION");
     }
     String jnlpVersion = System.getProperty("jalview.version");
     String codeVersion = getProperty("VERSION");
@@ -463,21 +498,20 @@ 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);
 
@@ -485,17 +519,16 @@ 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
@@ -566,14 +599,10 @@ 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");
@@ -595,13 +624,7 @@ 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);
-    }
-    return prop;
+    return getInstance().applicationProperties.getProperty(key);
   }
 
   /**
@@ -639,6 +662,40 @@ public class Cache
   }
 
   /**
+   * retrieve a dimension, such as for Jmol
+   * 
+   * @param property
+   * @param def
+   * @return
+   */
+  public static Dimension getDefaultDim(String property, Dimension def)
+  {
+    String s = getProperty(property);
+    if (s != null)
+    {
+      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;
+  }
+
+  /**
    * Answers the value of the given property, or the supplied default value if
    * the property is not set
    */
@@ -660,11 +717,21 @@ public class Cache
    */
   public static Object setProperty(String key, String obj)
   {
+    return getInstance().setPropertyImpl(key, obj, true);
+  }
+
+  public static void setPropertyNoSave(String key, String obj)
+  {
+    getInstance().setPropertyImpl(key, obj, false);
+  }
+
+  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---");
@@ -681,18 +748,36 @@ public class Cache
   /**
    * remove 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);
+  }
+
+  public static void removePropertyNoSave(String key)
+  {
+    getInstance().removePropertyImpl(key, false);
+  }
+
+  private void removePropertyImpl(String key, boolean andSave)
+  {
+    applicationProperties.remove(key);
+    if (andSave)
+    {
+      savePropertiesImpl();
+    }
+  }
+
+  public static void saveProperties()
+  {
+    getInstance().savePropertiesImpl();
   }
 
   /**
    * save the properties to the jalview properties path
    */
-  public static void saveProperties()
+  private void savePropertiesImpl()
   {
     if (!propsAreReadOnly)
     {
@@ -708,10 +793,17 @@ 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.
@@ -720,7 +812,7 @@ public class Cache
    */
   public static boolean vamsasJarsPresent()
   {
-    if (vamsasJarsArePresent == -1)
+    if (vamsasJarsArePresent == UNTESTED)
     {
       try
       {
@@ -729,7 +821,7 @@ 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())));
@@ -740,17 +832,18 @@ 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.
@@ -759,7 +852,7 @@ public class Cache
    */
   public static boolean groovyJarsPresent()
   {
-    if (groovyJarsArePresent == -1)
+    if (groovyJarsArePresent == UNTESTED)
     {
       try
       {
@@ -768,7 +861,7 @@ 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())));
@@ -779,15 +872,15 @@ 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);
   }
 
   /**
@@ -796,15 +889,18 @@ 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)
@@ -839,8 +935,7 @@ 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[]
@@ -1028,11 +1123,11 @@ 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);
     }
   }
 
@@ -1077,13 +1172,13 @@ 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);
       }
     }
   }