X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=eb503d5858440a6954f8a4db74b040549fceb438;hb=38299bef6dfd4b713f615781e631dcb66e1155f2;hp=d8a6d3d37b56b76a592236a65c5b524828ab2ca7;hpb=c3ded07cf4a7708564e9878bf1763fe837e03ddc;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index d8a6d3d..eb503d5 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,7 +22,10 @@ import java.io.*;
 
 import java.util.*;
 
-import java.net.*;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.apache.log4j.Level;
+import org.apache.log4j.ConsoleAppender;
 
 
 /**
@@ -30,7 +33,9 @@ import java.net.*;
  * <br><br>Current properties include:
  * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
  * <br>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
- * <br>jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.
+ * <br>logs.Jalview.Level - Cache.log stringified level.
+ * <br>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
+ * <br>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
  * <br>SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN
  * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
  * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
@@ -41,17 +46,52 @@ import java.net.*;
  */
 public class Cache
 {
+  /**
+   * Initialises the Apache Axis logger
+   */
+  public static Logger log;
 
     /** Jalview Properties */
-    public static Properties applicationProperties;
+    public static Properties applicationProperties = new Properties();
 
     /** Default file is  ~/.jalview_properties */
     static String propertiesFile;
 
+    public static void initLogger()
+    {
+      try
+      {
+        Logger laxis = Logger.getLogger("org.apache.axis");
+        Logger lcastor = Logger.getLogger("org.exolab.castor");
+        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())));
+        jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
+            "logs.Jalview.level",
+            Level.INFO.toString())));
+        ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+                                                 "System.err");
+        ap.setName("JalviewLogger");
+
+        laxis.addAppender(ap);
+        lcastor.addAppender(ap);
+        jalview.bin.Cache.log.addAppender(ap);
+        // Tell the user that debug is enabled
+        jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
+      }
+      catch (Exception ex)
+      {
+      System.err.println("Problems initializing the log4j system\n");
+      }
+    }
+
+
     /** Called when Jalview is started */
     public static void loadProperties(String propsFile)
     {
-        applicationProperties = new Properties();
         propertiesFile = propsFile;
         if (propsFile == null)
         {
@@ -71,6 +111,14 @@ public class Cache
           System.out.println("Error reading properties file: "+ex);
         }
 
+      if(getDefault("USE_PROXY", false))
+      {
+          System.out.println("Using proxyServer: "+getDefault("PROXY_SERVER", null)+
+                           " proxyPort: "+getDefault("PROXY_PORT", null));
+          System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
+          System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
+      }
+
         // 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
@@ -106,7 +154,8 @@ public class Cache
         }
 
 
-        System.out.println("Version: "+codeVersion);
+        System.out.println("Jalview Version: "+codeVersion);
+
 
         // jnlpVersion will be null if we're using InstallAnywhere
         // Dont do this check if running in headless mode
@@ -114,30 +163,61 @@ public class Cache
                 System.getProperty("java.awt.headless")==null
              || System.getProperty("java.awt.headless").equals("false")))
         {
-          try{
-            java.net.URL url = new java.net.URL("http://www.jalview.org/webstart/jalview.jnlp");
-            BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
-            String line = null;
-            while( (line = in.readLine()) !=null)
+
+          class VersionChecker
+              extends Thread
+          {
+            public void run()
             {
-              if(line.indexOf("jalview.version")==-1)
-                continue;
+              String jnlpVersion = null;
+              try
+              {
+                java.net.URL url = new java.net.URL(
+                    "http://www.jalview.org/webstart/jalview.jnlp");
+                BufferedReader in = new BufferedReader(new InputStreamReader(url.
+                    openStream()));
+                String line = null;
+                while ( (line = in.readLine()) != null)
+                {
+                  if (line.indexOf("jalview.version") == -1)
+                    continue;
+
+                  line = line.substring(line.indexOf("value=") + 7);
+                  line = line.substring(0, line.lastIndexOf("\""));
+                  jnlpVersion = line;
+                  break;
+                }
+              }
+              catch (Exception ex)
+              {
+                System.out.println(ex);
+                jnlpVersion = getProperty("VERSION");
+              }
 
-              line = line.substring(line.indexOf("value=")+7);
-              line = line.substring(0, line.lastIndexOf("\""));
-              jnlpVersion = line;
-              break;
+              setProperty("LATEST_VERSION", jnlpVersion);
             }
-          }catch(Exception ex)
-          {  jnlpVersion =  codeVersion; }
+          }
 
-          System.out.println("Latest : "+jnlpVersion);
+          VersionChecker vc = new VersionChecker();
+          vc.start();
+        }
+        else
+        {
+          if(jnlpVersion!=null)
+            setProperty("LATEST_VERSION", jnlpVersion);
+          else
+          applicationProperties.remove("LATEST_VERSION");
         }
 
-        setProperty("LATEST_VERSION", jnlpVersion);
         setProperty("VERSION", codeVersion);
+
+        //LOAD USERDEFINED COLOURS
+        jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
+        jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
     }
 
+
+
     /**
      * Gets Jalview application property of given key. Returns null
      * if key not found
@@ -151,6 +231,37 @@ public class Cache
         return applicationProperties.getProperty(key);
     }
 
+
+    /** These methods are used when checking if the saved preference
+     * is different to the default setting
+     */
+
+    public static boolean getDefault(String property, boolean def)
+    {
+      String string = getProperty(property);
+      if (string != null)
+      {
+        def = Boolean.valueOf(string).booleanValue();
+      }
+
+      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)
+    {
+      String string = getProperty(property);
+      if (string != null)
+      {
+        return string;
+      }
+
+      return def;
+    }
+
+
     /**
      * Stores property in the file "HOME_DIR/.jalview_properties"
      *
@@ -164,16 +275,24 @@ public class Cache
         try
         {
             FileOutputStream out = new FileOutputStream(propertiesFile);
-
             applicationProperties.setProperty(key, obj);
-
             applicationProperties.store(out, "---JalviewX Properties File---");
             out.close();
         }
         catch (Exception ex)
+        {   System.out.println("Error setting property: "+key+" "+obj+"\n"+ex);   }
+        return obj;
+    }
+
+    public static void saveProperties()
+    {
+        try
         {
+            FileOutputStream out = new FileOutputStream(propertiesFile);
+            applicationProperties.store(out, "---JalviewX Properties File---");
+            out.close();
         }
-
-        return obj;
+        catch (Exception ex)
+        {  System.out.println("Error saving properties: "+ex);  }
     }
 }