default value boolean parameter getter

[jalview.git] / src / jalview / bin / Cache.java

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index a73481e..9c9b6b0 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -82,7 +82,7 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * service</li>
  * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
  * service</li>
- * <li>USAGESTATS (true) Enable google analytics tracker for collecting usage
+ * <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>
@@ -98,11 +98,14 @@ 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>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>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
@@ -111,6 +114,13 @@ 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></li>
  * 
  * <li></li>
  * 
@@ -157,6 +167,8 @@ public class Cache
   {
     try
     {
+      // 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");
@@ -258,6 +270,7 @@ 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)
             && (System.getProperty("java.awt.headless") == null || System
                     .getProperty("java.awt.headless").equals("false")))
     {
@@ -404,7 +417,18 @@ public class Cache
     }
     return obj;
   }
-
+  /**
+   * remove the specified property from the jalview properties file
+   * @param string
+   */
+  public static void removeProperty(String string)
+  {
+    applicationProperties.remove(string);
+    saveProperties();
+  }
+  /**
+   * save the properties to the jalview properties path
+   */
   public static void saveProperties()
   {
     try
@@ -487,7 +511,10 @@ public class Cache
           // Tell the user that debug is enabled
           lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
         }
-      } catch (Exception e)
+      } catch (Error e) {
+        groovyJarsArePresent = 0;
+        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");
@@ -495,7 +522,6 @@ public class Cache
     }
     return (groovyJarsArePresent > 0);
   }
-
   /**
    * generate Das1Sources from the local das source list
    * 
@@ -642,4 +668,5 @@ public class Cache
       }
     }
   }
+
 }