X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FCache.java;h=9702a9231b54e9976e54ef77130d8ef0fa8007c5;hb=4944c2f33bb34b4f262fd2f3ae40dcdc2a825557;hp=8e5e240ac112920acdfa2887180ac591054ba04a;hpb=62737d15c0edb48128eb9ac6fe7fa419ab984125;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 8e5e240..9702a92 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.*;
*
Current properties include:
*
logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
*
logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
- *
jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.
+ *
logs.Jalview.Level - Cache.log stringified level.
+ *
DISCOVERY_START - Boolean - controls if discovery services are queried on startup
+ *
DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
*
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,
@@ -41,18 +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)
{
@@ -63,6 +102,8 @@ public class Cache
{
FileInputStream fis = new FileInputStream(propertiesFile);
applicationProperties.load(fis);
+ applicationProperties.remove("LATEST_VERSION");
+ applicationProperties.remove("VERSION");
fis.close();
}
catch (Exception ex)
@@ -70,6 +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
@@ -96,37 +145,78 @@ public class Cache
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";
- setProperty("jalview.version", jnlpVersion);
- setProperty("VERSION", codeVersion);
}
+ System.out.println("Jalview Version: "+codeVersion);
+
+
// jnlpVersion will be null if we're using InstallAnywhere
- if(jnlpVersion==null)
+ // 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")))
{
- 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("\""));
- setProperty("jalview.version", line);
+ 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);
}
- }catch(Exception ex)
- { setProperty("jalview.version", codeVersion); }
+ }
+
+ 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"));
}
+
+
/**
* Gets Jalview application property of given key. Returns null
* if key not found
@@ -140,6 +230,37 @@ 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"
*
@@ -153,16 +274,24 @@ 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); }
}
}