Logger moved to prefs so that class not found error can be handled in main

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 480bf5d..0013c63 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -23,6 +23,10 @@ import java.io.*;
 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
@@ -30,7 +34,7 @@ import java.net.*;
  * <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>logs.Jalview.Level - Jalview.log stringified level.\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
@@ -43,6 +47,10 @@ import java.net.*;
  */\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 = new Properties();\r
@@ -50,6 +58,37 @@ public class Cache
     /** 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
+\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
+      }\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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e780f78..9a85471 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -37,28 +37,6 @@ import java.util.Vector;
  */\r
 public class Jalview\r
 {\r
-    /**\r
-     * Initialises the Apache Axis logger\r
-     */\r
-    public static Logger log;\r
-    private static void initLogger()\r
-    {\r
-        Logger laxis = Logger.getLogger("org.apache.axis");\r
-        Logger lcastor = Logger.getLogger("org.exolab.castor");\r
-        log = Logger.getLogger("jalview.bin.Jalview");\r
-\r
-        laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));\r
-        lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", Level.INFO.toString())));\r
-        log.setLevel(Level.toLevel(Cache.getDefault("logs.Jalview.level", Level.INFO.toString())));\r
-\r
-        ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),\r
-                "System.err");\r
-        ap.setName("JalviewLogger");\r
-\r
-        laxis.addAppender(ap);\r
-        lcastor.addAppender(ap);\r
-        log.addAppender(ap);\r
-    }\r
 \r
     /**\r
      * main class for Jalview application\r
@@ -110,17 +88,20 @@ public class Jalview
             headless = true;\r
           }\r
 \r
-        Cache.loadProperties(aparser.getValue("props"));\r
-\r
-        try\r
-        {\r
-          initLogger();\r
-        }\r
-        catch (Exception e)\r
-        {\r
-          System.err.println("Problems initializing the log4j system\n");\r
-        }\r
+          try\r
+          {\r
+            Cache.initLogger();\r
+          }\r
+          catch (java.lang.NoClassDefFoundError error)\r
+          {\r
+            error.printStackTrace();\r
+            System.out.println(\r
+                "\nEssential logging libraries not found."\r
+                +"\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");\r
+            System.exit(0);\r
+          }\r
 \r
+        Cache.loadProperties(aparser.getValue("props"));\r
 \r
         Desktop desktop = null;\r
         if( !headless )\r

diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java
index a7f139f..b30a05f 100755 (executable)
--- a/src/jalview/ws/Discoverer.java
+++ b/src/jalview/ws/Discoverer.java
@@ -93,7 +93,7 @@ public class Discoverer
     }
     catch (Exception ex)
     {
-      jalview.bin.Jalview.log.error(
+      jalview.bin.Cache.log.error(
           "Serious!  Service location failed\nfor URL :" + WsURL +
           "\n", ex);
 
@@ -127,20 +127,20 @@ public class Discoverer
           if (!urls.contains(u))
             urls.add(u);
           else
-            jalview.bin.Jalview.log.info("Ignoring duplicate url in DISCOVERY_URLS list");
+            jalview.bin.Cache.log.info("Ignoring duplicate url in DISCOVERY_URLS list");
         }
         catch (Exception ex)
         {
-          jalview.bin.Jalview.log.warn(
+          jalview.bin.Cache.log.warn(
               "Problem whilst trying to make a URL from '" +
               ( (url != null) ? url : "<null>")+"'");
-          jalview.bin.Jalview.log.warn("This was probably due to a malformed comma separated list"
+          jalview.bin.Cache.log.warn("This was probably due to a malformed comma separated list"
                                        +" in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
-          jalview.bin.Jalview.log.debug("Exception was ",ex);
+          jalview.bin.Cache.log.debug("Exception was ",ex);
         }
       }
     }catch(Exception ex)
-    {jalview.bin.Jalview.log.warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",ex);}
+    {jalview.bin.Cache.log.warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",ex);}
     if (urls.size()>0)
       return urls;
     return null;
@@ -157,7 +157,7 @@ public class Discoverer
       }
       else
       {
-        jalview.bin.Jalview.log.debug("Setting default services");
+        jalview.bin.Cache.log.debug("Setting default services");
         services = new Hashtable();
         // Muscle, Clustal and JPred.
         ServiceHandle[] defServices = {
@@ -204,14 +204,14 @@ public class Discoverer
     ServiceHandles shs = null;
     try
     {
-      jalview.bin.Jalview.log.debug("Discovering services using " + location);
+      jalview.bin.Cache.log.debug("Discovering services using " + location);
       shs = locateWebService(location).getServices();
     }
     catch (Exception e)
     {
-      jalview.bin.Jalview.log.debug("No Discovery service at " +
+      jalview.bin.Cache.log.debug("No Discovery service at " +
                          location);
-      jalview.bin.Jalview.log.debug(e);
+      jalview.bin.Cache.log.debug(e);
 
     }
     if ( (shs != null) && shs.getServices().length > 0)
@@ -237,7 +237,7 @@ public class Discoverer
     {
       if (!cat.contains(sh[i]))
       {
-        jalview.bin.Jalview.log.debug("A " + sh[i].getAbstractName() +
+        jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() +
                                       " service called " +
                                       sh[i].getName() + " exists at " +
                                       sh[i].getEndpointURL() + "\n");
@@ -260,7 +260,7 @@ public class Discoverer
               disc_serv = new java.net.URL(sh[i].getEndpointURL());
               if (!ServiceURLList.contains(disc_serv))
               {
-                jalview.bin.Jalview.log.debug(
+                jalview.bin.Cache.log.debug(
                     "Adding new discovery service at " + disc_serv);
                 ServiceURLList.add(disc_serv);
                 seenNewDiscovery = true;
@@ -268,7 +268,7 @@ public class Discoverer
             }
             catch (Exception e)
             {
-              jalview.bin.Jalview.log.debug(
+              jalview.bin.Cache.log.debug(
                   "Ignoring bad discovery service URL " + sh[i].getEndpointURL(),
                   e);
             }
@@ -287,7 +287,7 @@ public class Discoverer
     int s_url = 0;
     if (ServiceURLList==null)
     {
-      jalview.bin.Jalview.log.debug("No service endpoints to use for service discovery.");
+      jalview.bin.Cache.log.debug("No service endpoints to use for service discovery.");
       return;
     }
     while (s_url < ServiceURLList.size())
@@ -297,7 +297,7 @@ public class Discoverer
 
         buildServiceLists(sh, cat, sscat);
       } else {
-        jalview.bin.Jalview.log.warn(
+        jalview.bin.Cache.log.warn(
             "No services at "
             +((java.net.URL) ServiceURLList.get(s_url))
             +" - check DISCOVERY_URLS property in .jalview_properties");

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 45d4bd1..9fe7e27 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -190,7 +190,7 @@ public class JPredClient
                 "Timed out when communicating with server\nTry again later.\n"));\r
           }\r
           if (result.getState()==0)\r
-            jalview.bin.Jalview.log.debug("Finished "+jobId);\r
+            jalview.bin.Cache.log.debug("Finished "+jobId);\r
           if (result.isRunning())\r
           {\r
             wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
@@ -317,7 +317,7 @@ public class JPredClient
             "JPredWS Client: Failed to submit the prediction (Possibly a server error - see below)\n" +\r
             e.getMessage() + "\n");\r
 \r
-        jalview.bin.Jalview.log.debug("Failed Submission",e);\r
+        jalview.bin.Cache.log.debug("Failed Submission",e);\r
       }\r
     }\r
 \r
@@ -370,20 +370,20 @@ public class JPredClient
 \r
       try\r
       {\r
-        jalview.bin.Jalview.log.debug("Parsing output from JNet job.");\r
+        jalview.bin.Cache.log.debug("Parsing output from JNet job.");\r
         // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
         jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
             getPredfile(),\r
             "Paste");\r
         SequenceI[] preds = prediction.getSeqsAsArray();\r
-        jalview.bin.Jalview.log.debug("Got prediction profile.");\r
+        jalview.bin.Cache.log.debug("Got prediction profile.");\r
         Alignment al;\r
         int FirstSeq; // the position of the query sequence in Alignment al\r
         boolean noMsa = true; // set if no MSA has been returned by JPred\r
 \r
         if ( (this.msa != null) && (result.getAligfile() != null))\r
         {\r
-          jalview.bin.Jalview.log.debug("Getting associated alignment.");\r
+          jalview.bin.Cache.log.debug("Getting associated alignment.");\r
           // we ignore the returned alignment if we only predicted on a single sequence\r
           String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
               "Paste");\r
@@ -520,7 +520,7 @@ public class JPredClient
          */\r
 \r
         wsInfo.setProgressText(OutputHeader);\r
-        jalview.bin.Jalview.log.debug("Finished parsing output.");\r
+        jalview.bin.Cache.log.debug("Finished parsing output.");\r
         AlignFrame af = new AlignFrame(al);\r
 \r
         Desktop.addInternalFrame(af, altitle,\r
@@ -529,8 +529,8 @@ public class JPredClient
       }\r
       catch (Exception ex)\r
       {\r
-        jalview.bin.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction.");\r
-        jalview.bin.Jalview.log.debug("Exception: ",ex);\r
+        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.");\r
+        jalview.bin.Cache.log.debug("Exception: ",ex);\r
       }\r
     }\r
   }\r

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 214d120..253dfba 100755 (executable)
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -257,7 +257,7 @@ public class MsaWSClient
             throw (new Exception(\r
                 "Timed out when communicating with server\nTry again later.\n"));\r
           }\r
-          jalview.bin.Jalview.log.debug("Result state " + result.getState() +\r
+          jalview.bin.Cache.log.debug("Result state " + result.getState() +\r
                                         "(ServerError=" + result.isServerError() +\r
                                         ")");\r
           if (result.isRunning())\r