X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=c88c92a519d600470e8867e77d90b2b61159432d;hb=f24dacb1da56fccf05d684e2f4899facec2aecf7;hp=66518fad2b98ed56ba362d041ebf2190c89dcc79;hpb=338584e2151df68daca4085183a757610aa55909;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 66518fa..c88c92a 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,100 +1,296 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.bin;
 
+import java.io.*;
 
-package jalview.bin;
 import java.util.*;
-import java.io.*;
 
-import java.util.jar.*;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.apache.log4j.Level;
+import org.apache.log4j.ConsoleAppender;
+
+
+/**
+ * Stores and retrieves Jalview Application Properties
+ * <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>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,
+ * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE
+
+ * @author $author$
+ * @version $Revision$
+ */
 public class Cache
 {
-  public static String  VERSION = "Release 2.0";
-  public static String  BUILD_DATE = "";
-
-  public static Properties applicationProperties;
-  // Current properties include:
-  //
-  // LAST_DIRECTORY   , use this to cache record of where the user looked to find a file
-  // UNIPROT_CACHE
-  // USER_DEFINED_COLOUR - file describing last user set colours
-  // FONT_NAME
-  // FONT_STYLE
-  // FONT_SIZE
-  // logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
-
-  public static void loadProperties()
-  {
-    // get last build time.
-    long date = 0;
-    try{
-          String localFile = Cache.class.getProtectionDomain().getCodeSource().getLocation().toString();
-          localFile = localFile.concat("!/");
-          String tmpString = "jar:";
-          String localJarFileString = tmpString.concat(localFile);
-          java.net.URL localJarFileURL = new java.net.URL(localJarFileString);
-          java.net.JarURLConnection localJarFile = (java.net.JarURLConnection)localJarFileURL.openConnection();
-          date = localJarFile.getLastModified();
-    }catch(Exception ex){ex.printStackTrace();}
-    if(date==0)
+  /**
+   * Initialises the Apache Axis logger
+   */
+  public static Logger log;
+
+    /** Jalview Properties */
+    public static Properties applicationProperties = new Properties();
+
+    /** Default file is  ~/.jalview_properties */
+    static String propertiesFile;
+
+    public static void initLogger()
     {
-      // this is called for unpackaged class files, ie not in a Jar file
-      // InstallAnywhere version will find build date this way
-      // not entirely accurate as it only tells you when Cache.class was last compiled
+      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())));
 
-     java.io.File f = new java.io.File(System.getProperty("user.dir") + "/jalview/bin/Cache.class" );
-     date = f.lastModified();
-    }
+        ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+                                                 "System.err");
+        ap.setName("JalviewLogger");
 
-    if(date!=0)
-      BUILD_DATE = new Date( date ).toString();
+        laxis.addAppender(ap);
+        lcastor.addAppender(ap);
+        jalview.bin.Cache.log.addAppender(ap);
+      }
+      catch (Exception ex)
+      {
+      System.err.println("Problems initializing the log4j system\n");
+      }
+    }
 
-    applicationProperties = new Properties();
 
-    try
+    /** Called when Jalview is started */
+    public static void loadProperties(String propsFile)
     {
-      FileInputStream in = new FileInputStream(System.getProperty("user.home") +
-                                               "/.jalview_properties");
-      applicationProperties = new Properties();
-      applicationProperties.load(in);
-      in.close();
+        propertiesFile = propsFile;
+        if (propsFile == null)
+        {
+          propertiesFile = System.getProperty("user.home") + "/.jalview_properties";
+        }
+
+        try
+        {
+            FileInputStream fis = new FileInputStream(propertiesFile);
+            applicationProperties.load(fis);
+            applicationProperties.remove("LATEST_VERSION");
+            applicationProperties.remove("VERSION");
+            fis.close();
+        }
+        catch (Exception ex)
+        {
+          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
+         try
+         {
+             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)
+         {
+           System.out.println("Error reading build details: "+ex);
+           applicationProperties.remove("VERSION");
+        }
+
+        String jnlpVersion = System.getProperty("jalview.version");
+        String codeVersion = getProperty("VERSION");
+
+
+        if(codeVersion==null)
+        {
+          // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+          codeVersion = "Test";
+          jnlpVersion = "Test";
+        }
+
+
+        System.out.println("Jalview Version: "+codeVersion);
+
+
+        // jnlpVersion will be null if we're using InstallAnywhere
+        // Dont do this check if running in headless mode
+        if(jnlpVersion==null && (
+                System.getProperty("java.awt.headless")==null
+             || System.getProperty("java.awt.headless").equals("false")))
+        {
+
+          class VersionChecker
+              extends Thread
+          {
+            public void run()
+            {
+              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");
+              }
+
+              setProperty("LATEST_VERSION", jnlpVersion);
+            }
+          }
+
+          VersionChecker vc = new VersionChecker();
+          vc.start();
+        }
+        else
+        {
+          if(jnlpVersion!=null)
+            setProperty("LATEST_VERSION", jnlpVersion);
+          else
+          applicationProperties.remove("LATEST_VERSION");
+        }
+
+        setProperty("VERSION", codeVersion);
+
+        //LOAD USERDEFINED COLOURS
+        jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
     }
-    catch (Exception ex)
-    { }
-  }
-
-  public static String getProperty(String key)
-  {
-    return  applicationProperties.getProperty(key);
-  }
-
-  public static String setProperty(String key, String obj)
-  {
-    try
-    {
-      FileOutputStream out = new FileOutputStream(System.getProperty(
-          "user.home") + "/.jalview_properties");
 
-      applicationProperties.setProperty(key, obj);
 
-      applicationProperties.store(out, "---JalviewX Properties File---");
-      out.close();
+
+    /**
+     * Gets Jalview application property of given key. Returns null
+     * if key not found
+     *
+     * @param key Name of property
+     *
+     * @return Property value
+     */
+    public static String getProperty(String key)
+    {
+        return applicationProperties.getProperty(key);
     }
-    catch (Exception ex)
-    {}
 
-    return obj;
 
-  }
+    /** 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"
+     *
+     * @param key Name of object
+     * @param obj String value of property
+     *
+     * @return String value of property
+     */
+    public static String setProperty(String key, String obj)
+    {
+        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();
+        }
+        catch (Exception ex)
+        {  System.out.println("Error saving properties: "+ex);  }
+    }
 }