X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=1481666637ec4f457f61ca750d283cbce5ecc26c;hb=c68ebaddf1925d9458aab5f2fea6e6f3240b3b99;hp=dad7326bdea2a31af710ae0cc9d5ff918b8113e6;hpb=67d61f58fbff9bdb395ebb12ed389a58e6e75a03;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index dad7326..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 (Version 2.4)
- * Copyright (C) 2008 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;
@@ -24,9 +23,6 @@ import java.util.*;
import org.apache.log4j.*;
import org.biojava.dasobert.dasregistry.Das1Source;
-import com.boxysystems.jgoogleanalytics.FocusPoint;
-import com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker;
-
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* list entries are separated by '|' symbols unless otherwise stated (|) clauses
@@ -43,76 +39,97 @@ import com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker;
*
* logs.Jalview.Level - Cache.log stringified level.
*
- * DISCOVERY_START - Boolean - controls if discovery services are queried
- * on startup
- * DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
- *
- * SCREEN_WIDTH
- * SCREEN_HEIGHT
- * SCREEN_Y=285
- * SCREEN_X=371
- * SHOW_FULLSCREEN boolean
- * FONT_NAME java font name for alignment text display
- * FONT_SIZE size of displayed alignment text
- * FONT_STYLE style of font displayed (sequence labels are always italic)
- *
- * GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
- * LAST_DIRECTORY last directory for browsing alignment
- * USER_DEFINED_COLOURS list of user defined colour scheme files
- * SHOW_FULL_ID show id with '/start-end' numbers appended
- * SHOW_IDENTITY show percentage identity annotation
- * SHOW_QUALITY show alignment quality annotation
- * SHOW_ANNOTATIONS show alignment annotation rows
- * SHOW_CONSERVATION show alignment conservation annotation
+ * DISCOVERY_START - Boolean - controls if discovery services are queried on
+ * startup
+ * DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
+ * SCREEN_WIDTH
+ * SCREEN_HEIGHT
+ * SCREEN_Y=285
+ * SCREEN_X=371
+ * SHOW_FULLSCREEN boolean
+ * FONT_NAME java font name for alignment text display
+ * FONT_SIZE size of displayed alignment text
+ * FONT_STYLE style of font displayed (sequence labels are always italic)
+ * GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
+ * LAST_DIRECTORY last directory for browsing alignment
+ * USER_DEFINED_COLOURS list of user defined colour scheme files
+ * SHOW_FULL_ID show id with '/start-end' numbers appended
+ * SHOW_IDENTITY show percentage identity annotation
+ * SHOW_QUALITY show alignment quality annotation
+ * SHOW_ANNOTATIONS show alignment annotation rows
+ * SHOW_CONSERVATION show alignment conservation annotation
* CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
- * annotation row
- * DEFAULT_COLOUR default colour scheme to apply for a new alignment
- * DEFAULT_FILE_FORMAT file format used to save
- * STARTUP_FILE file loaded on startup (may be a fully qualified url)
- * SHOW_STARTUP_FILE flag to control loading of startup file
- * VERSION the version of the jalview build
- * BUILD_DATE date of this build
+ * annotation row
+ * DEFAULT_COLOUR default colour scheme to apply for a new alignment
+ * DEFAULT_FILE_FORMAT file format used to save
+ * STARTUP_FILE file loaded on startup (may be a fully qualified url)
+ * SHOW_STARTUP_FILE flag to control loading of startup file
+ * VERSION the version of the jalview build
+ * BUILD_DATE date of this build
* LATEST_VERSION the latest jalview version advertised on the
- * www.jalview.org
+ * www.jalview.org
* PIR_MODELLER boolean indicating if PIR files are written with MODELLER
- * descriptions
+ * descriptions
* (FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
- * suffix to file
- * RECENT_URL list of recently retrieved URLs
- * RECENT_FILE list of recently opened files
- * USE_PROXY flag for whether a http proxy is to be used
- * PROXY_SERVER the proxy
- * PROXY_PORT
+ * suffix to file
+ * RECENT_URL list of recently retrieved URLs
+ * RECENT_FILE list of recently opened files
+ * USE_PROXY flag for whether a http proxy is to be used
+ * PROXY_SERVER the proxy
+ * PROXY_PORT
* NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
- * service
+ * service
* QUESTIONNAIRE last questionnaire:responder id string from questionnaire
- * service
- * DAS_LOCAL_SOURCE list of local das sources
- * SHOW_OVERVIEW boolean for overview window display
- * ANTI_ALIAS boolean for smooth fonts
- * RIGHT_ALIGN_IDS boolean
- * AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
- *
- * PAD_GAPS boolean
- * ID_ITALICS boolean
- * SHOW_JV_SUFFIX
- * WRAP_ALIGNMENT
+ * service
+ * 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
+ * RIGHT_ALIGN_IDS boolean
+ * AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
+ * PAD_GAPS boolean
+ * ID_ITALICS boolean
+ * SHOW_JV_SUFFIX
+ * WRAP_ALIGNMENT
* EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
- * style check
- * SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
+ * style check
+ * SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
* SEQUENCE_LINKS list of name|URL pairs for opening a url with
- * $SEQUENCE_ID$
- * DAS_REGISTRY_URL the registry to query
- * DEFAULT_BROWSER for unix
- * DAS_ACTIVE_SOURCE list of active sources
+ * $SEQUENCE_ID$
+ * 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)
- * SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence ID tooltip
- * SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence ID tooltip
- * SHOW_UNCONSERVED (false) only render unconserved residues - conserved displayed as '.'
- * SORT_BY_TREE (false) sort the current alignment view according to the order of a newly displayed tree
+ * (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
+ * ID tooltip
+ * SHOW_UNCONSERVED (false) only render unconserved residues - conserved
+ * 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.
+ *
+ *
*
- *
+ *
*
*
*
@@ -155,13 +172,20 @@ 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");
org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
- // log output
+ // log output
Logger laxis = Logger.getLogger("org.apache.axis");
Logger lcastor = Logger.getLogger("org.exolab.castor");
jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
@@ -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")))
{
@@ -339,7 +364,7 @@ public class Cache
* found
*
* @param key
- * Name of property
+ * Name of property
*
* @return Property value
*/
@@ -383,9 +408,9 @@ public class Cache
* Stores property in the file "HOME_DIR/.jalview_properties"
*
* @param key
- * Name of object
+ * Name of object
* @param obj
- * String value of property
+ * String value of property
*
* @return String value of property
*/
@@ -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;
@@ -498,6 +541,7 @@ public class Cache
/**
* generate Das1Sources from the local das source list
+ *
* @return Vector of Das1Sources
*/
public static Vector getLocalDasSources()
@@ -517,10 +561,14 @@ public class Cache
{
source.setUrl(source.getUrl().substring(9));
// this source also serves sequences as well as features
- source.setCapabilities(new String[] { "sequence", "features"});
- } else {
+ source.setCapabilities(new String[]
+ { "sequence", "features" });
+ }
+ else
+ {
// default is that all user added sources serve features
- source.setCapabilities(new String[] { "features"});
+ source.setCapabilities(new String[]
+ { "features" });
}
source.setNickname(token.substring(0, bar));
@@ -530,37 +578,126 @@ public class Cache
}
return localSources;
}
-
- public static JGoogleAnalyticsTracker tracker=null;
-
+
+ /**
+ * 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;
+
+ /**
+ * Initialise the google tracker if it is not done already.
+ */
public static void initGoogleTracker()
{
- if (tracker==null)
- {
- String vrs="No Version Accessible";
- try {
- //Google analytics tracking code for Library Finder
- tracker = new JGoogleAnalyticsTracker("Jalview Desktop",
- (vrs=jalview.bin.Cache.getProperty("VERSION")+"_"+jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")),
- "UA-9060947-1");
- tracker.trackAsynchronously(new FocusPoint("Application Started."));
- } catch (RuntimeException e)
+ if (tracker == null)
{
- if (log!=null) {
- log.debug("Caught runtime exception in googletracker init:",e);
- }
- // quietly return.
- }
- catch (Exception e)
- {
- // unexpected error
- if (log!=null)
+ if (jgoogleanalyticstracker == null)
+ {
+ // try to get the tracker class
+ try
+ {
+ jgoogleanalyticstracker = Cache.class
+ .getClassLoader()
+ .loadClass(
+ "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+ trackerfocus = Cache.class.getClassLoader().loadClass(
+ "com.boxysystems.jgoogleanalytics.FocusPoint");
+ } catch (Exception e)
{
- log.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "+vrs,e);
- } else {
- log.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "+vrs,e);
+ log
+ .debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ tracker = null;
+ jgoogleanalyticstracker = null;
+ trackerfocus = null;
+ return;
}
- }
+ }
+ // now initialise tracker
+ Exception re = null, ex = null;
+ Error err = null;
+ String vrs = "No Version Accessible";
+ 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." }) });
+ } catch (RuntimeException e)
+ {
+ re = e;
+ } catch (Exception e)
+ {
+ ex = e;
+ } catch (Error e)
+ {
+ err = e;
+ }
+ if (re != null || ex != null || err != null)
+ {
+ if (log != null)
+ {
+ if (re != null)
+ log
+ .debug(
+ "Caught runtime exception in googletracker init:",
+ re);
+ if (ex != null)
+ log.warn(
+ "Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs, ex);
+ if (err != null)
+ log.error(
+ "Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs, err);
+ }
+ else
+ {
+ if (re != null)
+ {
+ System.err
+ .println("Debug: Caught runtime exception in googletracker init:"
+ + vrs);
+ re.printStackTrace();
+ }
+ if (ex != null)
+ {
+ System.err
+ .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs);
+ ex.printStackTrace();
+ }
+
+ if (err != null)
+ {
+ System.err
+ .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs);
+ err.printStackTrace();
+ }
+ }
+ }
+ else
+ {
+ log.debug("Successfully initialised tracker.");
+ }
}
}
+
}