X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=5688ae1eb06727bd13811434fa182c475068677a;hb=94e5a196ee42f9571348786abd0ee727014b65ae;hp=32a11e210bb21e19941f096e07cc78acc6c3214e;hpb=57677416c9d03530e3cbe373fc9bf40c1df2eb38;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 32a11e2..5688ae1 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,328 +1,701 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, 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 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.
- *
- * 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 - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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;
import java.io.*;
-
import java.util.*;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-import org.apache.log4j.Level;
-import org.apache.log4j.ConsoleAppender;
-
+import org.apache.log4j.*;
+import org.biojava.dasobert.dasregistry.Das1Source;
/**
- * Stores and retrieves Jalview Application Properties
- *
Current properties include:
- *
logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
- *
logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
- *
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
- * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
- * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
- * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE
-
+ * Stores and retrieves Jalview Application Properties Lists and fields within
+ * list entries are separated by '|' symbols unless otherwise stated (|) clauses
+ * are alternative values for a tag.
+ *
+ * Current properties include:
+ *
+ *
+ * logs.Axis.Level - one of the stringified Levels for log4j controlling the
+ * logging level for axis (used for web services)
+ *
+ * - logs.Castor.Level - one of the stringified Levels for log4j controlling
+ * the logging level for castor (used for serialization)
+ *
+ * - 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
+ * - 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
+ * - LATEST_VERSION the latest jalview version advertised on the
+ * www.jalview.org
+ * - PIR_MODELLER boolean indicating if PIR files are written with MODELLER
+ * 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
+ * - NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
+ * service
+ * - QUESTIONNAIRE last questionnaire:responder id string from questionnaire
+ * 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)
+ * - 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
+ * 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.
+ *
+ *
+ *
+ *
+ *
+ *
+ *
* @author $author$
* @version $Revision$
*/
public class Cache
{
/**
- * Initialises the Apache Axis logger
+ * property giving log4j level for CASTOR loggers
+ */
+ public static final String CASTORLOGLEVEL = "logs.Castor.level";
+
+ /**
+ * property giving log4j level for AXIS loggers
+ */
+ public static final String AXISLOGLEVEL = "logs.Axis.level";
+
+ /**
+ * property giving log4j level for Jalview Log
+ */
+ public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+
+ public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
+
+ public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
+
+ public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+
+ /**
+ * Initialises the Jalview Application Log
*/
public static Logger log;
- /** Jalview Properties */
- public static Properties applicationProperties = new Properties();
+ /** Jalview Properties */
+ public static Properties applicationProperties = new Properties();
- /** Default file is ~/.jalview_properties */
- static String propertiesFile;
+ /** Default file is ~/.jalview_properties */
+ static String propertiesFile;
- public static void initLogger()
+ 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
+ Logger laxis = Logger.getLogger("org.apache.axis");
+ Logger lcastor = Logger.getLogger("org.exolab.castor");
+ jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
+
+ laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
+ Level.INFO.toString())));
+ lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ Level.INFO.toString())));
+ lcastor = Logger.getLogger("org.exolab.castor.xml");
+ lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ Level.INFO.toString())));
+ // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
+ // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ // Level.INFO.toString())));
+ jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
+ "logs.Jalview.level", Level.INFO.toString())));
+ // laxis.addAppender(ap);
+ // lcastor.addAppender(ap);
+ // jalview.bin.Cache.log.addAppender(ap);
+ // Tell the user that debug is enabled
+ jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
+ } catch (Exception ex)
{
- try
- {
- Logger laxis = Logger.getLogger("org.apache.axis");
- Logger lcastor = Logger.getLogger("org.exolab.castor");
- jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
-
- laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
- Level.INFO.toString())));
- lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- Level.INFO.toString())));
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Jalview.level",
- Level.INFO.toString())));
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
- "System.err");
- ap.setName("JalviewLogger");
-
- laxis.addAppender(ap);
- lcastor.addAppender(ap);
- jalview.bin.Cache.log.addAppender(ap);
- // Tell the user that debug is enabled
- jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
- }
- catch (Exception ex)
- {
System.err.println("Problems initializing the log4j system\n");
- }
+ ex.printStackTrace(System.err);
}
+ }
-
- /** Called when Jalview is started */
- public static void loadProperties(String propsFile)
+ /** Called when Jalview is started */
+ public static void loadProperties(String propsFile)
+ {
+ propertiesFile = propsFile;
+ if (propsFile == null)
{
- propertiesFile = propsFile;
- if (propsFile == null)
- {
- propertiesFile = System.getProperty("user.home") + "/.jalview_properties";
- }
+ propertiesFile = System.getProperty("user.home") + File.separatorChar
+ + ".jalview_properties";
+ }
- try
- {
- FileInputStream fis = new FileInputStream(propertiesFile);
- applicationProperties.load(fis);
- applicationProperties.remove("LATEST_VERSION");
- applicationProperties.remove("VERSION");
- fis.close();
- }
- catch (Exception ex)
- {
- System.out.println("Error reading properties file: "+ex);
- }
+ try
+ {
+ FileInputStream fis = new FileInputStream(propertiesFile);
+ applicationProperties.load(fis);
+ applicationProperties.remove("LATEST_VERSION");
+ applicationProperties.remove("VERSION");
+ fis.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading properties file: " + ex);
+ }
- if(getDefault("USE_PROXY", false))
- {
- System.out.println("Using proxyServer: "+getDefault("PROXY_SERVER", null)+
- " proxyPort: "+getDefault("PROXY_PORT", null));
- System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
- System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
- }
+ if (getDefault("USE_PROXY", false))
+ {
+ System.out.println("Using proxyServer: "
+ + getDefault("PROXY_SERVER", null) + " proxyPort: "
+ + getDefault("PROXY_PORT", null));
+ System
+ .setProperty("http.proxyHost", getDefault("PROXY_SERVER",
+ null));
+ System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
+ }
- // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
- // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
- // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
- try
- {
- String buildDetails = "jar:"
- .concat(
- Cache.class.getProtectionDomain().getCodeSource().getLocation().toString()
- .concat("!/.build_properties")
- );
-
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- }
- catch (Exception ex)
- {
- System.out.println("Error reading build details: "+ex);
- applicationProperties.remove("VERSION");
- }
+ // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+ // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
+ // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
+ try
+ {
+ String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString().concat(
+ "!/.build_properties"));
- String jnlpVersion = System.getProperty("jalview.version");
- String codeVersion = getProperty("VERSION");
+ java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading build details: " + ex);
+ applicationProperties.remove("VERSION");
+ }
- if(codeVersion==null)
- {
- // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
- codeVersion = "Test";
- jnlpVersion = "Test";
- }
+ String jnlpVersion = System.getProperty("jalview.version");
+ String codeVersion = getProperty("VERSION");
+ if (codeVersion == null)
+ {
+ // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+ codeVersion = "Test";
+ jnlpVersion = "Test";
+ }
- System.out.println("Jalview Version: "+codeVersion);
+ System.out.println("Jalview Version: " + codeVersion);
+ // 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")))
+ {
- // jnlpVersion will be null if we're using InstallAnywhere
- // Dont do this check if running in headless mode
- if(jnlpVersion==null && (
- System.getProperty("java.awt.headless")==null
- || System.getProperty("java.awt.headless").equals("false")))
+ class VersionChecker extends Thread
+ {
+ public void run()
{
-
- class VersionChecker
- extends Thread
+ String orgtimeout = System
+ .getProperty("sun.net.client.defaultConnectTimeout");
+ if (orgtimeout == null)
{
- public void run()
- {
- String jnlpVersion = null;
- try
- {
- java.net.URL url = new java.net.URL(
+ orgtimeout = "30";
+ System.out.println("# INFO: Setting default net timeout to "
+ + orgtimeout + " seconds.");
+ }
+ String jnlpVersion = null;
+ try
+ {
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ "5000");
+ java.net.URL url = new java.net.URL(
"http://www.jalview.org/webstart/jalview.jnlp");
- BufferedReader in = new BufferedReader(new InputStreamReader(url.
- openStream()));
- String line = null;
- while ( (line = in.readLine()) != null)
- {
- if (line.indexOf("jalview.version") == -1)
- continue;
-
- line = line.substring(line.indexOf("value=") + 7);
- line = line.substring(0, line.lastIndexOf("\""));
- jnlpVersion = line;
- break;
- }
- }
- catch (Exception ex)
+ BufferedReader in = new BufferedReader(new InputStreamReader(
+ url.openStream()));
+ String line = null;
+ while ((line = in.readLine()) != null)
+ {
+ if (line.indexOf("jalview.version") == -1)
{
- System.out.println(ex);
- jnlpVersion = getProperty("VERSION");
+ continue;
}
- setProperty("LATEST_VERSION", jnlpVersion);
+ line = line.substring(line.indexOf("value=") + 7);
+ line = line.substring(0, line.lastIndexOf("\""));
+ jnlpVersion = line;
+ break;
}
+ } catch (Exception ex)
+ {
+ System.out
+ .println("Non-fatal exceptions when checking version at www.jalview.org :");
+ System.out.println(ex);
+ jnlpVersion = getProperty("VERSION");
}
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ orgtimeout);
- VersionChecker vc = new VersionChecker();
- vc.start();
- }
- else
- {
- if(jnlpVersion!=null)
- setProperty("LATEST_VERSION", jnlpVersion);
- else
- applicationProperties.remove("LATEST_VERSION");
+ setProperty("LATEST_VERSION", jnlpVersion);
}
+ }
- setProperty("VERSION", codeVersion);
+ VersionChecker vc = new VersionChecker();
+ vc.start();
+ }
+ else
+ {
+ if (jnlpVersion != null)
+ {
+ setProperty("LATEST_VERSION", jnlpVersion);
+ }
+ else
+ {
+ applicationProperties.remove("LATEST_VERSION");
+ }
+ }
- //LOAD USERDEFINED COLOURS
- jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
- jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+ setProperty("VERSION", codeVersion);
+
+ // LOAD USERDEFINED COLOURS
+ jalview.gui.UserDefinedColours
+ .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+ jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+ false);
+ }
+
+ /**
+ * Gets Jalview application property of given key. Returns null if key not
+ * found
+ *
+ * @param key
+ * Name of property
+ *
+ * @return Property value
+ */
+ public static String getProperty(String key)
+ {
+ return applicationProperties.getProperty(key);
+ }
+
+ /**
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
+ */
+
+ public static boolean getDefault(String property, boolean def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ def = Boolean.valueOf(string).booleanValue();
}
+ return def;
+ }
+ /**
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
+ */
+ public static String getDefault(String property, String def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ return string;
+ }
+
+ return def;
+ }
- /**
- * Gets Jalview application property of given key. Returns null
- * if key not found
- *
- * @param key Name of property
- *
- * @return Property value
- */
- public static String getProperty(String key)
+ /**
+ * Stores property in the file "HOME_DIR/.jalview_properties"
+ *
+ * @param key
+ * Name of object
+ * @param obj
+ * String value of property
+ *
+ * @return String value of property
+ */
+ public static String setProperty(String key, String obj)
+ {
+ try
+ {
+ FileOutputStream out = new FileOutputStream(propertiesFile);
+ applicationProperties.setProperty(key, obj);
+ applicationProperties.store(out, "---JalviewX Properties File---");
+ out.close();
+ } catch (Exception ex)
{
- return applicationProperties.getProperty(key);
+ System.out.println("Error setting property: " + key + " " + obj
+ + "\n" + ex);
}
+ 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
+ {
+ FileOutputStream out = new FileOutputStream(propertiesFile);
+ applicationProperties.store(out, "---JalviewX Properties File---");
+ out.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error saving properties: " + ex);
+ }
+ }
- /** These methods are used when checking if the saved preference
- * is different to the default setting
- */
+ /**
+ * internal vamsas class discovery state
+ */
+ private static int vamsasJarsArePresent = -1;
- public static boolean getDefault(String property, boolean def)
+ /**
+ * Searches for vamsas client classes on class path.
+ *
+ * @return true if vamsas client is present on classpath
+ */
+ public static boolean vamsasJarsPresent()
+ {
+ if (vamsasJarsArePresent == -1)
{
- String string = getProperty(property);
- if (string != null)
+ try
{
- def = Boolean.valueOf(string).booleanValue();
+ if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
+ "uk.ac.vamsas.client.VorbaId") != null)
+ {
+ jalview.bin.Cache.log
+ .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ vamsasJarsArePresent = 1;
+ Logger lvclient = Logger.getLogger("uk.ac.vamsas");
+ lvclient.setLevel(Level.toLevel(Cache.getDefault(
+ "logs.Vamsas.Level", Level.INFO.toString())));
+
+ lvclient.addAppender(log.getAppender("JalviewLogger"));
+ // Tell the user that debug is enabled
+ lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
+ }
+ } catch (Exception e)
+ {
+ vamsasJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Vamsas Classes are not present");
}
-
- return def;
}
+ return (vamsasJarsArePresent > 0);
+ }
- /** These methods are used when checking if the saved preference
- * is different to the default setting
- */
- public static String getDefault(String property, String def)
+ /**
+ * internal vamsas class discovery state
+ */
+ private static int groovyJarsArePresent = -1;
+
+ /**
+ * Searches for vamsas client classes on class path.
+ *
+ * @return true if vamsas client is present on classpath
+ */
+ public static boolean groovyJarsPresent()
+ {
+ if (groovyJarsArePresent == -1)
{
- String string = getProperty(property);
- if (string != null)
+ try
+ {
+ if (Cache.class.getClassLoader().loadClass(
+ "groovy.lang.GroovyObject") != null)
+ {
+ jalview.bin.Cache.log
+ .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ groovyJarsArePresent = 1;
+ Logger lgclient = Logger.getLogger("groovy");
+ lgclient.setLevel(Level.toLevel(Cache.getDefault(
+ "logs.Groovy.Level", Level.INFO.toString())));
+
+ lgclient.addAppender(log.getAppender("JalviewLogger"));
+ // 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)
{
- return string;
+ groovyJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Groovy Classes are not present");
}
-
- return def;
}
+ return (groovyJarsArePresent > 0);
+ }
-
- /**
- * Stores property in the file "HOME_DIR/.jalview_properties"
- *
- * @param key Name of object
- * @param obj String value of property
- *
- * @return String value of property
- */
- public static String setProperty(String key, String obj)
+ /**
+ * generate Das1Sources from the local das source list
+ *
+ * @return Vector of Das1Sources
+ */
+ public static Vector getLocalDasSources()
+ {
+ Vector localSources = new Vector();
+ String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
+ if (local != null)
{
- try
+ StringTokenizer st = new StringTokenizer(local, "\t");
+ while (st.hasMoreTokens())
+ {
+ String token = st.nextToken();
+ int bar = token.indexOf("|");
+ Das1Source source = new Das1Source();
+ source.setUrl(token.substring(bar + 1));
+ if (source.getUrl().startsWith("sequence:"))
+ {
+ source.setUrl(source.getUrl().substring(9));
+ // this source also serves sequences as well as features
+ source.setCapabilities(new String[]
+ { "sequence", "features" });
+ }
+ else
{
- FileOutputStream out = new FileOutputStream(propertiesFile);
- applicationProperties.setProperty(key, obj);
- applicationProperties.store(out, "---JalviewX Properties File---");
- out.close();
+ // default is that all user added sources serve features
+ source.setCapabilities(new String[]
+ { "features" });
}
- catch (Exception ex)
- { System.out.println("Error setting property: "+key+" "+obj+"\n"+ex); }
- return obj;
+
+ source.setNickname(token.substring(0, bar));
+
+ localSources.addElement(source);
+ }
}
+ return localSources;
+ }
+
+ /**
+ * 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;
- public static void saveProperties()
+ /**
+ * Initialise the google tracker if it is not done already.
+ */
+ public static void initGoogleTracker()
+ {
+ if (tracker == null)
{
+ if (jgoogleanalyticstracker == null)
+ {
+ // try to get the tracker class
try
{
- FileOutputStream out = new FileOutputStream(propertiesFile);
- applicationProperties.store(out, "---JalviewX Properties File---");
- out.close();
+ jgoogleanalyticstracker = Cache.class
+ .getClassLoader()
+ .loadClass(
+ "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+ trackerfocus = Cache.class.getClassLoader().loadClass(
+ "com.boxysystems.jgoogleanalytics.FocusPoint");
+ } catch (Exception e)
+ {
+ log
+ .debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ tracker = null;
+ jgoogleanalyticstracker = null;
+ trackerfocus = null;
+ return;
}
- catch (Exception ex)
- { System.out.println("Error saving properties: "+ex); }
- }
- /**
- * internal vamsas class discovery state
- */
- private static int vamsasJarsArePresent=-1;
- /**
- * Searches for vamsas client classes on class path.
- * @return true if vamsas client is present on classpath
- */
- public static boolean vamsasJarsPresent() {
- if (vamsasJarsArePresent==-1) {
- try {
- if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass("org.vamsas.client.VorbaId")!=null) {
- jalview.bin.Cache.log.debug("Found Vamsas Classes (org.vamsas.client.VorbaId can be loaded)");
- vamsasJarsArePresent=1;
- Logger lvclient = Logger.getLogger("org.vamsas");
- lvclient.setLevel(Level.toLevel(Cache.getDefault("logs.Vamsas.Level",
- Level.INFO.toString())));
-
- lvclient.addAppender(log.getAppender("JalviewLogger"));
- // Tell the user that debug is enabled
- lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
+ }
+ // 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();
}
- } catch (Exception e) {
- vamsasJarsArePresent=0;
- jalview.bin.Cache.log.debug("Vamsas Classes are not present");
}
}
- return (vamsasJarsArePresent>0);
+ else
+ {
+ log.debug("Successfully initialised tracker.");
+ }
}
+ }
}