X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=9dcc949ee84d8b111e81d0964b0496d31d9f4aca;hb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;hp=dc5084347e9bc01cab00b33cf6a8a44479085053;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index dc50843..9dcc949 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -28,8 +28,7 @@ import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureImportSettings;
 import jalview.urls.IdOrgSettings;
 import jalview.util.ColorUtils;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+import jalview.util.Platform;
 import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Color;
@@ -116,7 +115,6 @@ 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>
@@ -136,9 +134,7 @@ 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
@@ -228,12 +224,6 @@ 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
    */
@@ -281,14 +271,16 @@ public class Cache
     @Override
     public synchronized Enumeration<Object> keys()
     {
-      return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+      return Collections.enumeration(new TreeSet<>(super.keySet()));
     }
   };
 
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
-  private static boolean propsAreReadOnly = false;
+  private static boolean propsAreReadOnly = Platform.isJS();
+
+  private final static String JS_PROPERTY_PREFIX = "jalview_";
 
   public static void initLogger()
   {
@@ -334,11 +326,14 @@ public class Cache
     }
   }
 
-  /** Called when Jalview is started */
+  /**
+   * Loads properties from the given properties file. Any existing properties
+   * are first cleared.
+   */
   public static void loadProperties(String propsFile)
   {
     propertiesFile = propsFile;
-    if (propsFile == null)
+    if (propsFile == null && !propsAreReadOnly)
     {
       propertiesFile = System.getProperty("user.home") + File.separatorChar
               + ".jalview_properties";
@@ -349,37 +344,45 @@ public class Cache
       propsAreReadOnly = true;
     }
 
-    try
+    if (propertiesFile == null)
+    { // BH 2019
+      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.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", ""),
@@ -393,45 +396,57 @@ 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 = "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);
-      applicationProperties.remove("AUTHORS");
-      applicationProperties.remove("AUTHORFNAMES");
-      applicationProperties.remove("YEAR");
+      authorDetails = null;
+    }
+    if (authorDetails == null)
+    {
+        applicationProperties.remove("AUTHORS");
+        applicationProperties.remove("AUTHORFNAMES");
+        applicationProperties.remove("YEAR");
     }
 
     // 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 = "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");
+        applicationProperties.remove("VERSION");
     }
-
     String jnlpVersion = System.getProperty("jalview.version");
     String codeVersion = getProperty("VERSION");
     String codeInstallation = getProperty("INSTALLATION");
@@ -557,6 +572,7 @@ public class Cache
             false);
   }
 
+
   private static void deleteBuildProperties()
   {
     applicationProperties.remove("LATEST_VERSION");
@@ -579,7 +595,13 @@ public class Cache
    */
   public static String getProperty(String key)
   {
-    return applicationProperties.getProperty(key);
+    String prop = applicationProperties.getProperty(key);
+    if (prop == null && Platform.isJS())
+    {
+      prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+              + "_" + JS_PROPERTY_PREFIX + key);
+    }
+    return prop;
   }
 
   /**
@@ -598,22 +620,35 @@ public class Cache
     return def;
   }
 
-  /**
-   * These methods are used when checking if the saved preference is different
-   * to the default setting
-   */
-  public static String getDefault(String property, String def)
+  public static int getDefault(String property, int def)
   {
     String string = getProperty(property);
     if (string != null)
     {
-      return string;
+      try
+      {
+        def = Integer.parseInt(string);
+      } catch (NumberFormatException e)
+      {
+        System.out.println("Error parsing int property '" + property
+                + "' with value '" + string + "'");
+      }
     }
 
     return def;
   }
 
   /**
+   * 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)
+  {
+    String value = getProperty(property);
+    return value == null ? def : value;
+  }
+
+  /**
    * Stores property in the file "HOME_DIR/.jalview_properties"
    * 
    * @param key
@@ -621,14 +656,14 @@ public class Cache
    * @param obj
    *          String value of property
    * 
-   * @return String value of property
+   * @return previous value of property (or null)
    */
-  public static String setProperty(String key, String obj)
+  public static Object setProperty(String key, String obj)
   {
-
+    Object oldValue = null;
     try
     {
-      applicationProperties.setProperty(key, obj);
+      oldValue = applicationProperties.setProperty(key, obj);
       if (!propsAreReadOnly)
       {
         FileOutputStream out = new FileOutputStream(propertiesFile);
@@ -640,7 +675,7 @@ public class Cache
       System.out.println(
               "Error setting property: " + key + " " + obj + "\n" + ex);
     }
-    return obj;
+    return oldValue;
   }
 
   /**
@@ -978,22 +1013,6 @@ public class Cache
     return null;
   }
 
-  private static DasSourceRegistryI sourceRegistry = null;
-
-  /**
-   * initialise and ..
-   * 
-   * @return instance of the das source registry
-   */
-  public static DasSourceRegistryI getDasSourceRegistry()
-  {
-    if (sourceRegistry == null)
-    {
-      sourceRegistry = new DasSourceRegistry();
-    }
-    return sourceRegistry;
-  }
-
   /**
    * Set the specified value, or remove it if null or empty. Does not save the
    * properties file.
@@ -1068,4 +1087,19 @@ public class Cache
       }
     }
   }
+
+	/**
+	 * Add a known domain that implements access-control-allow-origin:* bh 2018
+	 * 
+	 * @param defaultUniprotDomain
+	 */
+	public static void addJ2SDirectDatabaseCall(String domain) 
+	{
+
+		/**
+		 * @j2sNative
+		 * 
+		 * 			J2S.addDirectDatabaseCall(domain);
+		 */
+	}
 }