X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=28bab15feec6fa01417699105c77be1efd1c31db;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=50db03b7c228c9448627e8528e613f075577d034;hpb=2ea1b352349a737f513131873551bfb7899d812f;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 50db03b..28bab15 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -52,6 +52,7 @@ import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.SimpleLayout;
 
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.datamodel.PDBEntry;
 import jalview.gui.Preferences;
 import jalview.gui.UserDefinedColours;
@@ -182,8 +183,8 @@ import jalview.ws.sifts.SiftsSettings;
  * when shading by annotation</li>
  * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
  * when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
  * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
  * alignment figure to accommodate even the longest sequence ID or annotation
  * label.</li>
@@ -220,8 +221,26 @@ import jalview.ws.sifts.SiftsSettings;
  * @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
    */
@@ -240,10 +259,8 @@ public class Cache
   /**
    * Sifts settings
    */
-  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
-          .getProperty("user.home") + File.separatorChar
-          + ".sifts_downloads" + File.separatorChar;
-
+  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = Platform.getUserPath(".sifts_downloads/");
+  
   private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
 
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
@@ -251,8 +268,7 @@ public class Cache
   /**
    * Identifiers.org download settings
    */
-  private static final String ID_ORG_FILE = System.getProperty("user.home")
-          + File.separatorChar + ".identifiers.org.ids.json";
+  private static final String ID_ORG_FILE = Platform.getUserPath(".identifiers.org.ids.json");
 
   /**
    * Allowed values are PDB or mmCIF
@@ -300,7 +316,7 @@ public class Cache
   public static char[] proxyAuthPassword = null;
 
   /** Jalview Properties */
-  public static Properties applicationProperties = new Properties()
+  private Properties applicationProperties = new Properties()
   {
     // override results in properties output in alphabetical order
     @Override
@@ -370,16 +386,31 @@ public class Cache
   }
 
   /**
-   * Loads properties from the given properties file. Any existing properties
-   * are first cleared.
+   * Loads properties from the given properties file. Any existing properties are
+   * first cleared.
    */
   public static void loadProperties(String propsFile)
   {
+
+    getInstance().loadPropertiesImpl(propsFile);
+
+  }
+
+  private void loadPropertiesImpl(String propsFile)
+  {
+
     propertiesFile = propsFile;
+    String releasePropertiesFile = null;
+    boolean defaultProperties = false;
     if (propsFile == null && !propsAreReadOnly)
     {
-      propertiesFile = System.getProperty("user.home") + File.separatorChar
-              + ".jalview_properties";
+      // TODO: @bsoares - for 2.12 testing: check test,develop,release props are located correctly
+      String channelPrefsFilename = ChannelProperties
+              .getProperty("preferences.filename");
+      String releasePrefsFilename = ".jalview_properties";
+      propertiesFile = Platform.getUserPath(channelPrefsFilename);
+      releasePropertiesFile = Platform.getUserPath(releasePrefsFilename);
+      defaultProperties = true;
     }
     else
     {
@@ -399,20 +430,29 @@ public class Cache
         InputStream fis;
         try
         {
+          // props file provided as URL
           fis = new 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);
+          String readPropertiesFile = propertiesFile;
+          // if we're using the usual properties file and the channel properties
+          // file doesn't exist, read .jalview_properties
+          // (but we'll still save to the channel properties file).
+          if (defaultProperties && (!new File(propertiesFile).exists())
+                  && (new File(releasePropertiesFile).exists()))
+          {
+            readPropertiesFile = releasePropertiesFile;
+          }
+          fis = new FileInputStream(readPropertiesFile);
         }
         applicationProperties.clear();
         applicationProperties.load(fis);
@@ -506,7 +546,7 @@ public class Cache
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
     IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
-            "http://www.jalview.org/services/identifiers"));
+            "https://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
@@ -534,7 +574,8 @@ public class Cache
         @Override
         public void run()
         {
-          String buildPropertiesUrl = Cache.getAppbaseBuildProperties();
+          String remoteBuildPropertiesUrl = Cache
+                  .getAppbaseBuildProperties();
 
           String orgtimeout = System
                   .getProperty("sun.net.client.defaultConnectTimeout");
@@ -549,7 +590,7 @@ public class Cache
           {
             System.setProperty("sun.net.client.defaultConnectTimeout",
                     "5000");
-            java.net.URL url = new java.net.URL(buildPropertiesUrl);
+            java.net.URL url = new java.net.URL(remoteBuildPropertiesUrl);
 
             BufferedReader in = new BufferedReader(
                     new InputStreamReader(url.openStream()));
@@ -561,7 +602,7 @@ public class Cache
           {
             System.out
                     .println("Non-fatal exception when checking version at "
-                            + buildPropertiesUrl + ":");
+                            + remoteBuildPropertiesUrl + ":");
             System.out.println(ex);
             remoteVersion = getProperty("VERSION");
           }
@@ -622,7 +663,7 @@ public class Cache
     return url;
   }
 
-  public static void loadBuildProperties(boolean reportVersion)
+  public void loadBuildProperties(boolean reportVersion)
   {
     String codeInstallation = getProperty("INSTALLATION");
     boolean printVersion = codeInstallation == null;
@@ -638,11 +679,21 @@ public class Cache
       InputStream in = localJarFileURL.openStream();
       buildProperties.load(in);
       in.close();
-      applicationProperties.put("BUILD_DATE",
-              buildProperties.get("BUILD_DATE"));
-      applicationProperties.put("INSTALLATION",
-              buildProperties.get("INSTALLATION"));
-      applicationProperties.put("VERSION", buildProperties.get("VERSION"));
+      if (buildProperties.getProperty("BUILD_DATE", null) != null)
+      {
+        applicationProperties.put("BUILD_DATE",
+                buildProperties.getProperty("BUILD_DATE"));
+      }
+      if (buildProperties.getProperty("INSTALLATION", null) != null)
+      {
+        applicationProperties.put("INSTALLATION",
+                buildProperties.getProperty("INSTALLATION"));
+      }
+      if (buildProperties.getProperty("VERSION", null) != null)
+      {
+        applicationProperties.put("VERSION",
+                buildProperties.getProperty("VERSION"));
+      }
     } catch (Exception ex)
     {
       System.out.println("Error reading build details: " + ex);
@@ -670,7 +721,7 @@ public class Cache
     }
   }
 
-  private static void deleteBuildProperties()
+  private void deleteBuildProperties()
   {
     applicationProperties.remove("LATEST_VERSION");
     applicationProperties.remove("VERSION");
@@ -682,28 +733,27 @@ public class Cache
   }
 
   /**
-   * Gets Jalview application property of given key. Returns null if key not
-   * found
+   * Gets Jalview application property of given key. Returns null if key not found
    * 
    * @param key
-   *          Name of property
+   *              Name of property
    * 
    * @return Property value
    */
   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 = getInstance().applicationProperties.getProperty(key);
+    // if (prop == null && Platform.isJS())
+    // {
+    // prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+    // + "_" + JS_PROPERTY_PREFIX + key);
+    // }
     return prop;
   }
 
   /**
-   * These methods are used when checking if the saved preference is different
-   * to the default setting
+   * These methods are used when checking if the saved preference is different to
+   * the default setting
    */
 
   public static boolean getDefault(String property, boolean def)
@@ -736,8 +786,8 @@ public class Cache
   }
 
   /**
-   * Answers the value of the given property, or the supplied default value if
-   * the property is not set
+   * Answers the value of the given property, or the supplied default value if the
+   * property is not set
    */
   public static String getDefault(String property, String def)
   {
@@ -749,41 +799,56 @@ public class Cache
    * Stores property in the file "HOME_DIR/.jalview_properties"
    * 
    * @param key
-   *          Name of object
+   *              Name of object
    * @param obj
-   *          String value of property
+   *              String value of property
    * 
    * @return previous value of property (or null)
    */
   public static Object setProperty(String key, String obj)
   {
-    Object oldValue = null;
-    try
-    {
-      oldValue = applicationProperties.setProperty(key, obj);
-      if (propertiesFile != null && !propsAreReadOnly)
-      {
-        FileOutputStream out = new FileOutputStream(propertiesFile);
-        applicationProperties.store(out, "---JalviewX Properties File---");
-        out.close();
-      }
-    } catch (Exception ex)
-    {
-      System.out.println(
-              "Error setting property: " + key + " " + obj + "\n" + ex);
-    }
-    return oldValue;
+    return getInstance().setPropertyImpl(key, obj, true);
   }
 
   /**
-   * 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);
+  }
+
+  /**
+   * 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)
+  {
+
+    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)
+      saveProperties();
   }
 
   /**
@@ -791,6 +856,15 @@ public class Cache
    */
   public static void saveProperties()
   {
+    getInstance().savePropertiesImpl();
+  }
+
+  /**
+   * save the properties to the jalview properties path
+   */
+  private void savePropertiesImpl()
+
+  {
     if (!propsAreReadOnly)
     {
       try
@@ -1044,9 +1118,9 @@ public class Cache
    * @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));
+    setPropertyNoSave(property, jalview.util.Format.getHexString(colour));
   }
 
   /**
@@ -1074,11 +1148,16 @@ public class Cache
   public static Date getDateProperty(String propertyName)
   {
     String val = getProperty(propertyName);
+    
     if (val != null)
     {
       try
       {
-        return date_format.parse(val);
+        if ((val = val.trim()).indexOf(",") < 0 && val.indexOf("-") >= 0 && val.indexOf(" ") == val.lastIndexOf(" ")) {
+          val = val.replace(" ",", ").replace('-',' ');
+        }
+        Date date =  date_format.parse(val);
+        return date;
       } catch (Exception ex)
       {
         System.err.println("Invalid or corrupt date in property '"
@@ -1127,11 +1206,11 @@ 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);
     }
   }
 
@@ -1139,7 +1218,7 @@ public class Cache
    * Loads in user colour schemes from files.
    * 
    * @param files
-   *          a '|'-delimited list of file paths
+   *                a '|'-delimited list of file paths
    */
   public static void initUserColourSchemes(String files)
   {
@@ -1181,7 +1260,7 @@ public class Cache
       }
       else
       {
-        applicationProperties
+        getInstance().applicationProperties
                 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
       }
     }
@@ -1220,8 +1299,8 @@ public class Cache
             .append(" Installation: ");
     sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
     sb.append("\n");
-    sb.append("Build Date: ");
-    sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+    sb.append("Build Date: "
+            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
     sb.append("\n");
     sb.append("Java version: ");
     sb.append(System.getProperty("java.version"));
@@ -1272,6 +1351,52 @@ public class Cache
     return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
   }
 
+  /**
+   * 
+   * For AppletParams and Preferences ok_actionPerformed and
+   * startupFileTextfield_mouseClicked
+   * 
+   * 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 (andSave && !propsAreReadOnly && propertiesFile != null)
+      {
+        FileOutputStream out = new FileOutputStream(propertiesFile);
+        applicationProperties.store(out, "---JalviewX Properties File---");
+        out.close();
+      }
+    } catch (Exception ex)
+    {
+      System.out.println(
+              "Error setting property: " + key + " " + obj + "\n" + ex);
+    }
+    return oldValue;
+  }
+
   public static String getStackTraceString(Throwable t)
   {
     StringWriter sw = new StringWriter();
@@ -1448,8 +1573,8 @@ public class Cache
                   // open Preferences -> Connections
                   String message = MessageManager
                           .getString("label.proxy_password_required");
-                  Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
-                          message);
+                  Preferences.openPreferences(
+                          Preferences.TabRef.CONNECTIONS_TAB, message);
                   Preferences.getInstance()
                           .proxyAuthPasswordCheckHighlight(true, true);
                 }
@@ -1641,11 +1766,22 @@ public class Cache
 
   static
   {
-    Float specversion = Float
-            .parseFloat(System.getProperty("java.specification.version"));
-    releaseAppbase = (specversion < 9)
-            ? "https://www.jalview.org/getdown/release/1.8"
-            : "https://www.jalview.org/getdown/release/11";
+    if (!Platform.isJS())
+    {
+      Float specversion = Float
+              .parseFloat(System.getProperty("java.specification.version"));
+      releaseAppbase = (specversion < 9)
+              ? "https://www.jalview.org/getdown/release/1.8"
+              : "https://www.jalview.org/getdown/release/11";
+    }
+    else
+    {
+      // this value currenly made up, can be changed to URL that will be
+      // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
+      releaseAppbase = "https://www.jalview.org/jalview-js";
+      getdownAppbase = releaseAppbase;
+      getdownDistDir = "/swingjs/j2s";
+    }
   }
 
   // look for properties (passed in by getdown) otherwise default to release