X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=9c9b6b0bac92136109418009605d6682279a2199;hb=0b1ca393b3e936f798048c8c92d52a31b3498fb0;hp=a73481e045d25f116d9e4b7311bce56b7f8183de;hpb=9a5abc55a76fa3d709146f82207f580990a8180a;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index a73481e..9c9b6b0 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -82,7 +82,7 @@ import org.biojava.dasobert.dasregistry.Das1Source;
* service
*
QUESTIONNAIRE last questionnaire:responder id string from questionnaire
* service
- * USAGESTATS (true) Enable google analytics tracker for collecting usage
+ * USAGESTATS (false - user prompted) Enable google analytics tracker for collecting usage
* statistics
* DAS_LOCAL_SOURCE list of local das sources
* SHOW_OVERVIEW boolean for overview window display
@@ -98,11 +98,14 @@ import org.biojava.dasobert.dasregistry.Das1Source;
* SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
* SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$
+ * GROUP_LINKS list of name|URL[|<separator>] tuples - see jalview.utils.GroupURLLink for more info
+ *
* DAS_REGISTRY_URL the registry to query
* DEFAULT_BROWSER for unix
* DAS_ACTIVE_SOURCE list of active sources
* SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)
+ * VERSION_CHECK (true) check for the latest release version from www.jalview.org
* SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
* ID tooltip
* SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
@@ -111,6 +114,13 @@ import org.biojava.dasobert.dasregistry.Das1Source;
* displayed as '.'
* SORT_BY_TREE (false) sort the current alignment view according to the
* order of a newly displayed tree
+ * DBFETCH_USEPICR (false) use PICR to recover valid DB references from sequence ID strings before attempting retrieval from any datasource
+ * SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the alignment.
+ * SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups in the alignment.
+ * SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's histogram.
+ * SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence logo.
+ *
+ *
*
*
*
@@ -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
}
}
}
+
}