-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.bin;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-import java.util.jar.*;\r
-\r
-\r
-public class Cache {\r
- public static String VERSION = "Release 2.0";\r
- public static String BUILD_DATE = "";\r
- public static Properties applicationProperties;\r
-\r
- // Current properties include:\r
- //\r
- // LAST_DIRECTORY , use this to cache record of where the user looked to find a file\r
- // UNIPROT_CACHE\r
- // USER_DEFINED_COLOUR - file describing last user set colours\r
- // FONT_NAME\r
- // FONT_STYLE\r
- // FONT_SIZE\r
- // logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)\r
- // logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)\r
- // jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.\r
- public static void loadProperties() {\r
- // get last build time.\r
- long date = 0;\r
-\r
- try {\r
- String localFile = Cache.class.getProtectionDomain().getCodeSource()\r
- .getLocation().toString();\r
- localFile = localFile.concat("!/");\r
-\r
- String tmpString = "jar:";\r
- String localJarFileString = tmpString.concat(localFile);\r
- java.net.URL localJarFileURL = new java.net.URL(localJarFileString);\r
- java.net.JarURLConnection localJarFile = (java.net.JarURLConnection) localJarFileURL.openConnection();\r
- date = localJarFile.getLastModified();\r
- } catch (Exception ex) {\r
- ex.printStackTrace();\r
- }\r
-\r
- if (date == 0) {\r
- // this is called for unpackaged class files, ie not in a Jar file\r
- // InstallAnywhere version will find build date this way\r
- // not entirely accurate as it only tells you when Cache.class was last compiled\r
- java.io.File f = new java.io.File(System.getProperty("user.dir") +\r
- "/jalview/bin/Cache.class");\r
- date = f.lastModified();\r
- }\r
-\r
- if (date != 0) {\r
- BUILD_DATE = new Date(date).toString();\r
- }\r
-\r
- applicationProperties = new Properties();\r
-\r
- try {\r
- FileInputStream in = new FileInputStream(System.getProperty(\r
- "user.home") + "/.jalview_properties");\r
- applicationProperties = new Properties();\r
- applicationProperties.load(in);\r
- in.close();\r
- } catch (Exception ex) {\r
- }\r
- }\r
-\r
- public static String getProperty(String key) {\r
- return applicationProperties.getProperty(key);\r
- }\r
-\r
- public static String setProperty(String key, String obj) {\r
- try {\r
- FileOutputStream out = new FileOutputStream(System.getProperty(\r
- "user.home") + "/.jalview_properties");\r
-\r
- applicationProperties.setProperty(key, obj);\r
-\r
- applicationProperties.store(out, "---JalviewX Properties File---");\r
- out.close();\r
- } catch (Exception ex) {\r
- }\r
-\r
- return obj;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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.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
+{
+ /**
+ * 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()
+ {
+ 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)
+ {
+ 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("org.vamsas.client.VorbaId")!=null) {
+ jalview.bin.Cache.log.debug("Found Vamsas Classes (org.vamsas.client.VorbaId can be loaded)");
+ vamsasJarsArePresent=1;
+ Logger lvclient = Logger.getLogger("org.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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff