X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=8d003efc685847f30d8b4c4bb0bb548fa1614bb8;hb=fd29e047719a470cf304c5a41abfff5c1eac3ee8;hp=7dbdc94035b972ee4bba737e5af037c8522675df;hpb=602170f45acfb7a45d92d7ced1f2f1206d6fc4dd;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 7dbdc94..8d003ef 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,99 +1,451 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
-
-package jalview.bin;
-import java.util.*;
-import java.io.*;
-
-import java.util.jar.*;
-public class Cache
-{
-  public static String  VERSION = "ß test";
-  public static String  BUILD_DATE = "1-1-2005";
-
-  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)
-    {
-      // this is called for unpackaged class files.
-      // not entirely accurate as it only tells you when Cache.class was last compiled
-      java.net.URL url = Cache.class.getResource("/jalview/bin/Cache.class");
-      java.io.File f = new java.io.File(url.getFile());
-      date = f.lastModified();
-    }
-
-    BUILD_DATE = new Date( date ).toString();
-
-
-
-    applicationProperties = new Properties();
-
-    try
-    {
-      FileInputStream in = new FileInputStream(System.getProperty("user.home") +
-                                               "/.jalview_properties");
-      applicationProperties = new Properties();
-      applicationProperties.load(in);
-      in.close();
-    }
-    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();
-    }
-    catch (Exception ex)
-    {}
-
-    return obj;
-
-  }
-
-
-
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * 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.*;
+import java.util.*;
+
+import org.apache.log4j.*;
+
+/**
+ * Stores and retrieves Jalview Application Properties
+ * Lists and fields within list entries are separated by '|' symbols unless otherwise stated
+ * (|) clauses are alternative values for a tag.
+ * <br><br>Current properties include:
+ * <ul>
+ * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
+ * <br>
+ * </li><li>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
+ * <br>
+ * </li><li>logs.Jalview.Level - Cache.log stringified level.
+ * <br>
+ * </li><li>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
+ * </li><li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
+ * </li><li>SCREEN_WIDTH
+ * </li><li>SCREEN_HEIGHT
+ * </li><li>SCREEN_Y=285
+ * </li><li>SCREEN_X=371
+ * </li><li>SHOW_FULLSCREEN boolean
+ * </li><li>FONT_NAME java font name for alignment text display
+ * </li><li>FONT_SIZE size of displayed alignment text
+ * </li><li>FONT_STYLE style of font displayed (sequence labels are always italic)
+ * </li><li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
+ * </li><li>LAST_DIRECTORY last directory for browsing alignment
+ * </li><li>USER_DEFINED_COLOURS list of user defined colour scheme files
+ * </li><li>SHOW_FULL_ID show id with '/start-end' numbers appended
+ * </li><li>SHOW_IDENTITY show percentage identity annotation
+ * </li><li>SHOW_QUALITY show alignment quality annotation
+ * </li><li>SHOW_ANNOTATIONS show alignment annotation rows
+ * </li><li>SHOW_CONSERVATION show alignment conservation annotation
+ * </li><li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed annotation row 
+ * </li><li>DEFAULT_COLOUR default colour scheme to apply for a new alignment
+ * </li><li>DEFAULT_FILE_FORMAT file format used to save 
+ * </li><li>STARTUP_FILE file loaded on startup (may be a fully qualified url)
+ * </li><li>SHOW_STARTUP_FILE flag to control loading of startup file
+ * </li><li>VERSION the version of the jalview build
+ * </li><li>BUILD_DATE date of this build
+ * </li><li>LATEST_VERSION the latest jalview version advertised on the www.jalview.org
+ * </li><li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER descriptions
+ * </li><li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv suffix to file
+ * </li><li>RECENT_URL list of recently retrieved URLs
+ * </li><li>RECENT_FILE list of recently opened files
+ * </li><li>USE_PROXY flag for whether a http proxy is to be used
+ * </li><li>PROXY_SERVER the proxy
+ * </li><li>PROXY_PORT
+ * </li><li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire service
+ * </li><li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire service
+ * </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><li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
+ * </li><li>PAD_GAPS boolean
+ * </li><li>ID_ITALICS boolean 
+ * </li><li>SHOW_JV_SUFFIX
+ * </li><li>WRAP_ALIGNMENT
+ * </li><li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering style check
+ * </li><li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
+ * </li><li>SEQUENCE_LINKS list of name|URL pairs for opening a url with $SEQUENCE_ID$
+ * </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> 
+ * </li>
+ * 
+ * </ul>
+
+ * @author $author$
+ * @version $Revision$
+ */
+public class Cache
+{
+  /**
+   * property giving log4j level for CASTOR loggers
+   */
+  public static final String CASTORLOGLEVEL = "logs.Castor.level";
+  /**
+   * property giving log4j level for AXIS loggers
+   */
+  public static final String AXISLOGLEVEL = "logs.Axis.level";
+  /**
+   * property giving log4j level for Jalview Log
+   */
+  public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+  public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
+
+  /**
+   * Initialises the Jalview Application Log
+   */
+  public static Logger log;
+
+  /** Jalview Properties */
+  public static Properties applicationProperties = new Properties();
+
+  /** Default file is  ~/.jalview_properties */
+  static String propertiesFile;
+
+  public static void initLogger()
+  {
+    try
+    {
+      ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+      "System.err");
+      ap.setName("JalviewLogger");
+      org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for log output
+      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())));
+      lcastor = Logger.getLogger("org.exolab.castor.xml");
+      lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+              Level.INFO.toString())));
+      //lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
+      //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())));
+      //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");
+      ex.printStackTrace(System.err);
+    }
+  }
+
+  /** Called when Jalview is started */
+  public static void loadProperties(String propsFile)
+  {
+    propertiesFile = propsFile;
+    if (propsFile == null)
+    {
+      propertiesFile = System.getProperty("user.home") + File.separatorChar +
+          ".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"));
+    jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+  }
+
+  /**
+   * 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);
+  }
+
+  /** 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);
+    }
+  }
+
+  /**
+   * internal vamsas class discovery state
+   */
+  private static int vamsasJarsArePresent = -1;
+  /**
+   * Searches for vamsas client classes on class path.
+   * @return true if vamsas client is present on classpath
+   */
+  public static boolean vamsasJarsPresent()
+  {
+    if (vamsasJarsArePresent == -1)
+    {
+      try
+      {
+        if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
+            "uk.ac.vamsas.client.VorbaId") != null)
+        {
+          jalview.bin.Cache.log.debug(
+              "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+          vamsasJarsArePresent = 1;
+          Logger lvclient = Logger.getLogger("uk.ac.vamsas");
+          lvclient.setLevel(Level.toLevel(Cache.getDefault("logs.Vamsas.Level",
+              Level.INFO.toString())));
+
+          lvclient.addAppender(log.getAppender("JalviewLogger"));
+          // Tell the user that debug is enabled
+          lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
+        }
+      }
+      catch (Exception e)
+      {
+        vamsasJarsArePresent = 0;
+        jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+      }
+    }
+    return (vamsasJarsArePresent > 0);
+  }
+  /**
+   * internal vamsas class discovery state
+   */
+  private static int groovyJarsArePresent = -1;
+  /**
+   * Searches for vamsas client classes on class path.
+   * @return true if vamsas client is present on classpath
+   */
+  public static boolean groovyJarsPresent()
+  {
+    if (groovyJarsArePresent == -1)
+    {
+      try
+      {
+        if (Cache.class.getClassLoader().loadClass(
+            "groovy.lang.GroovyObject") != null)
+        {
+          jalview.bin.Cache.log.debug(
+              "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+          groovyJarsArePresent = 1;
+          Logger lgclient = Logger.getLogger("groovy");
+          lgclient.setLevel(Level.toLevel(Cache.getDefault("logs.Groovy.Level",
+              Level.INFO.toString())));
+
+          lgclient.addAppender(log.getAppender("JalviewLogger"));
+          // Tell the user that debug is enabled
+          lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
+        }
+      }
+      catch (Exception e)
+      {
+        groovyJarsArePresent = 0;
+        jalview.bin.Cache.log.debug("Groovy Classes are not present");
+      }
+    }
+    return (groovyJarsArePresent > 0);
+  }
+
+}