X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=1481666637ec4f457f61ca750d283cbce5ecc26c;hb=40460cd7a6f6d80c6a8c2f86c5bc55d941445975;hp=a73481e045d25f116d9e4b7311bce56b7f8183de;hpb=9a5abc55a76fa3d709146f82207f580990a8180a;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index a73481e..1481666 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 .
*/
package jalview.bin;
@@ -82,8 +81,8 @@ 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
- * statistics
+ * 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
* ANTI_ALIAS boolean for smooth fonts
@@ -98,11 +97,15 @@ 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 +114,20 @@ 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.
+ * FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
+ * respond to selections made in other alignments containing the same sequences.
+ *
+ *
*
*
*
@@ -155,8 +172,15 @@ public class Cache
public static void initLogger()
{
+ if (log!=null)
+ {
+ return;
+ }
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 +282,7 @@ 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")))
{
@@ -405,6 +430,20 @@ 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
@@ -487,6 +526,10 @@ public class Cache
// Tell the user that debug is enabled
lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
}
+ } catch (Error e)
+ {
+ groovyJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
@@ -537,10 +580,13 @@ 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;
/**
@@ -550,20 +596,24 @@ 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;
}
}
@@ -574,14 +624,21 @@ 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;
@@ -642,4 +699,5 @@ public class Cache
}
}
}
+
}