X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=cebb50414d00c84864a3e39439865d0010bc716e;hb=d423f22792e47dbc800ae220a58677f988971d06;hp=9c9b6b0bac92136109418009605d6682279a2199;hpb=797d4400e51c5786c080d7d746d5968589b5dc78;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 9c9b6b0..cebb504 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * Jalview 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 3 of the License, or (at your option) any later version.
  * 
- * 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
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.bin;
 
@@ -82,8 +81,8 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * service</li>
  * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
  * service</li>
- * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for collecting usage
- * statistics</li>
+ * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * collecting usage statistics</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>
@@ -98,14 +97,15 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * <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>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see jalview.utils.GroupURLLink for more info
- *  </li>
+ * <li>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see
+ * jalview.utils.GroupURLLink for more info</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>VERSION_CHECK (true) check for the latest release version from www.jalview.org</li>
+ * <li>VERSION_CHECK (true) check for the latest release version from
+ * www.jalview.org</li>
  * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
  * ID tooltip</li>
  * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
@@ -114,11 +114,16 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * displayed as '.'</li>
  * <li>SORT_BY_TREE (false) sort the current alignment view according to the
  * order of a newly displayed tree</li>
- * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from sequence ID strings before attempting retrieval from any datasource</li>
- * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the alignment.</li>
- * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups in the alignment.</li>
- * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's histogram.</li>
- * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence logo.</li>
+ * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
+ * sequence ID strings before attempting retrieval from any datasource</li>
+ * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
+ * alignment.</li>
+ * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
+ * in the alignment.</li>
+ * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
+ * histogram.</li>
+ * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo.</li>
  * 
  * <li></li>
  * 
@@ -167,8 +172,9 @@ public class Cache
   {
     try
     {
-      // TODO: redirect stdout and stderr here in order to grab the output of the log
-      
+      // TODO: redirect stdout and stderr here in order to grab the output of
+      // the log
+
       ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
               "System.err");
       ap.setName("JalviewLogger");
@@ -270,7 +276,7 @@ public class Cache
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null
-            && getDefault("VERSION_CHECK",true)
+            && getDefault("VERSION_CHECK", true)
             && (System.getProperty("java.awt.headless") == null || System
                     .getProperty("java.awt.headless").equals("false")))
     {
@@ -417,8 +423,10 @@ public class Cache
     }
     return obj;
   }
+
   /**
    * remove the specified property from the jalview properties file
+   * 
    * @param string
    */
   public static void removeProperty(String string)
@@ -426,6 +434,7 @@ public class Cache
     applicationProperties.remove(string);
     saveProperties();
   }
+
   /**
    * save the properties to the jalview properties path
    */
@@ -511,10 +520,11 @@ public class Cache
           // Tell the user that debug is enabled
           lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
         }
-      } catch (Error e) {
+      } catch (Error e)
+      {
         groovyJarsArePresent = 0;
-        jalview.bin.Cache.log.debug("Groovy Classes are not present",e);
-      }catch (Exception e)
+        jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+      } catch (Exception e)
       {
         groovyJarsArePresent = 0;
         jalview.bin.Cache.log.debug("Groovy Classes are not present");
@@ -522,6 +532,7 @@ public class Cache
     }
     return (groovyJarsArePresent > 0);
   }
+
   /**
    * generate Das1Sources from the local das source list
    * 
@@ -563,10 +574,13 @@ public class Cache
   }
 
   /**
-   * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not enabled.
+   * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
+   * enabled.
    */
   protected static Object tracker = null;
+
   protected static Class trackerfocus = null;
+
   protected static Class jgoogleanalyticstracker = null;
 
   /**
@@ -576,20 +590,24 @@ public class Cache
   {
     if (tracker == null)
     {
-      if (jgoogleanalyticstracker==null)
+      if (jgoogleanalyticstracker == null)
       {
         // try to get the tracker class
-        try {
-          jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
-          "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+        try
+        {
+          jgoogleanalyticstracker = Cache.class
+                  .getClassLoader()
+                  .loadClass(
+                          "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
           trackerfocus = Cache.class.getClassLoader().loadClass(
-          "com.boxysystems.jgoogleanalytics.FocusPoint");
+                  "com.boxysystems.jgoogleanalytics.FocusPoint");
         } catch (Exception e)
         {
-          log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+          log
+                  .debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
           tracker = null;
-          jgoogleanalyticstracker=null;
-          trackerfocus=null;
+          jgoogleanalyticstracker = null;
+          trackerfocus = null;
           return;
         }
       }
@@ -600,14 +618,21 @@ public class Cache
       try
       {
         // Google analytics tracking code for Library Finder
-        tracker = jgoogleanalyticstracker.getConstructor(new Class[] { String.class,String.class,String.class}).newInstance(new Object[] { "Jalview Desktop",
-                (vrs = jalview.bin.Cache.getProperty("VERSION")
-                        + "_"
-                        + jalview.bin.Cache.getDefault("BUILD_DATE",
-                                "unknown")), "UA-9060947-1"});
-        jgoogleanalyticstracker.getMethod("trackAsynchronously", new Class[] { trackerfocus })
-        .invoke(tracker, new Object[] { trackerfocus.getConstructor(
-                new Class[] { String.class}).newInstance(new Object[] { "Application Started." })});
+        tracker = jgoogleanalyticstracker.getConstructor(new Class[]
+        { String.class, String.class, String.class }).newInstance(
+                new Object[]
+                {
+                    "Jalview Desktop",
+                    (vrs = jalview.bin.Cache.getProperty("VERSION")
+                            + "_"
+                            + jalview.bin.Cache.getDefault("BUILD_DATE",
+                                    "unknown")), "UA-9060947-1" });
+        jgoogleanalyticstracker.getMethod("trackAsynchronously",
+                new Class[]
+                { trackerfocus }).invoke(tracker, new Object[]
+        { trackerfocus.getConstructor(new Class[]
+        { String.class }).newInstance(new Object[]
+        { "Application Started." }) });
       } catch (RuntimeException e)
       {
         re = e;