X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=4d3074844e985b5f927a67addbd7dcc34068d9c3;hb=00cb7fb9361c17af653e1e615620f7add2615ba6;hp=4469975cb745b13e302697a4f2c3b16245ef1e16;hpb=8ceb196758338574e45b021e0aa4f9a78a8c8bad;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 4469975..4d30748 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -24,9 +24,6 @@ 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
@@ -43,77 +40,81 @@ 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
- * USAGESTATS (true) 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
+ * service
+ * USAGESTATS (true) 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
+ * $SEQUENCE_ID$
+ * 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)
+ * 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
+ *
*
- *
+ *
*
*
*
@@ -162,7 +163,7 @@ public class Cache
"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");
@@ -340,7 +341,7 @@ public class Cache
* found
*
* @param key
- * Name of property
+ * Name of property
*
* @return Property value
*/
@@ -384,9 +385,9 @@ 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
*/
@@ -499,6 +500,7 @@ public class Cache
/**
* generate Das1Sources from the local das source list
+ *
* @return Vector of Das1Sources
*/
public static Vector getLocalDasSources()
@@ -518,10 +520,14 @@ 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));
@@ -531,41 +537,111 @@ public class Cache
}
return localSources;
}
+
/**
- * GA tracker object - null if tracking not enabled.
+ * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not enabled.
*/
- protected static JGoogleAnalyticsTracker tracker=null;
+ 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)
+ 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 (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.");
+ }
}
}
}