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