-/*
- * 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
- *
- * 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
- */
package jalview.bin;
-import java.io.*;
-import java.util.*;
-
-import org.apache.log4j.*;
-import org.biojava.dasobert.dasregistry.Das1Source;
-
-/**
- * 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. <br>
- * <br>
- * Current properties include:
- * <ul>
- * <br>
- * logs.Axis.Level - one of the stringified Levels for log4j controlling the
- * logging level for axis (used for web services) <br>
- * </li>
- * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
- * the logging level for castor (used for serialization) <br>
- * </li>
- * <li>logs.Jalview.Level - Cache.log stringified level. <br>
- * </li>
- * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
- * startup</li>
- * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.</li>
- * <li>SCREEN_WIDTH</li>
- * <li>SCREEN_HEIGHT</li>
- * <li>SCREEN_Y=285</li>
- * <li>SCREEN_X=371</li>
- * <li>SHOW_FULLSCREEN boolean</li>
- * <li>FONT_NAME java font name for alignment text display</li>
- * <li>FONT_SIZE size of displayed alignment text</li>
- * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
- * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
- * <li>LAST_DIRECTORY last directory for browsing alignment</li>
- * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
- * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
- * <li>SHOW_IDENTITY show percentage identity annotation</li>
- * <li>SHOW_QUALITY show alignment quality annotation</li>
- * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
- * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
- * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
- * annotation row</li>
- * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
- * <li>DEFAULT_FILE_FORMAT file format used to save</li>
- * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
- * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
- * <li>VERSION the version of the jalview build</li>
- * <li>BUILD_DATE date of this build</li>
- * <li>LATEST_VERSION the latest jalview version advertised on the
- * www.jalview.org</li>
- * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
- * descriptions</li>
- * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
- * suffix to file</li>
- * <li>RECENT_URL list of recently retrieved URLs</li>
- * <li>RECENT_FILE list of recently opened files</li>
- * <li>USE_PROXY flag for whether a http proxy is to be used</li>
- * <li>PROXY_SERVER the proxy</li>
- * <li>PROXY_PORT</li>
- * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
- * service</li>
- * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
- * service</li>
- * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for collecting usage
- * statistics</li>
- * <li>DAS_LOCAL_SOURCE list of local das sources</li>
- * <li>SHOW_OVERVIEW boolean for overview window display</li>
- * <li>ANTI_ALIAS boolean for smooth fonts</li>
- * <li>RIGHT_ALIGN_IDS boolean</li>
- * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
- * <li>PAD_GAPS boolean</li>
- * <li>ID_ITALICS boolean</li>
- * <li>SHOW_JV_SUFFIX</li>
- * <li>WRAP_ALIGNMENT</li>
- * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
- * style check</li>
- * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
- * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
- * $SEQUENCE_ID$</li>
- * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see jalview.utils.GroupURLLink for more info
- * </li>
- * <li>DAS_REGISTRY_URL the registry to query</li>
- * <li>DEFAULT_BROWSER for unix</li>
- * <li>DAS_ACTIVE_SOURCE list of active sources</li>
- * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
- * (false)</li>
- * <li>VERSION_CHECK (true) check for the latest release version from www.jalview.org</li>
- * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
- * ID tooltip</li>
- * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
- * ID tooltip</li>
- * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
- * displayed as '.'</li>
- * <li>SORT_BY_TREE (false) sort the current alignment view according to the
- * order of a newly displayed tree</li>
- * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from sequence ID strings before attempting retrieval from any datasource</li>
- * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the alignment.</li>
- * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups in the alignment.</li>
- * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's histogram.</li>
- * <li>SHOW_CONSENSUS_PROFILE (false) Show consensus annotation row's sequence logo.</li>
- *
- * <li></li>
- *
- * <li></li>
- *
- * </ul>
- *
- * @author $author$
- * @version $Revision$
- */
-public class Cache
-{
- /**
- * 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();
-
- /** Default file is ~/.jalview_properties */
- static String propertiesFile;
-
- public static void initLogger()
- {
- 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)
- {
- System.err.println("Problems initializing the log4j system\n");
- ex.printStackTrace(System.err);
- }
- }
-
- /** Called when Jalview is started */
- public static void loadProperties(String propsFile)
- {
- propertiesFile = propsFile;
- if (propsFile == null)
- {
- 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);
- }
-
- 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");
- }
-
- 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);
-
- // 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")))
- {
-
- class VersionChecker extends Thread
- {
- public void run()
- {
- String orgtimeout = System
- .getProperty("sun.net.client.defaultConnectTimeout");
- if (orgtimeout == null)
- {
- 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)
- {
- 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);
-
- setProperty("LATEST_VERSION", jnlpVersion);
- }
- }
-
- VersionChecker vc = new VersionChecker();
- vc.start();
- }
- else
- {
- if (jnlpVersion != null)
- {
- setProperty("LATEST_VERSION", jnlpVersion);
- }
- else
- {
- applicationProperties.remove("LATEST_VERSION");
- }
- }
-
- 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;
- }
-
- /**
- * 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)
- {
- 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);
- }
- }
-
- /**
- * 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(
- "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 (vamsasJarsArePresent > 0);
- }
-
- /**
- * 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)
- {
- 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)
- {
- groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present");
- }
- }
- return (groovyJarsArePresent > 0);
- }
- /**
- * 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)
- {
- 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
- {
- // default is that all user added sources serve features
- source.setCapabilities(new String[]
- { "features" });
- }
-
- 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;
-
- /**
- * 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 {
- 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;
- }
- }
- // 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.");
- }
- }
- }
-
+public class Cache {
+ public static final String CASTORLOGLEVEL = null;
+ public static Log log;
+
+ public class Log {
+
+ public void error(String string) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public boolean isDebugEnabled() {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ }
+
+ public static String getDefault(String string, String string2) {
+ // TODO Auto-generated method stub
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff