-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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.*;
-
-/**
- * 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>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>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>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>
- * </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.Castor.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";
-
- /**
- * 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
- {
- 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())));
- 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 && (
- System.getProperty("java.awt.headless") == null
- || System.getProperty("java.awt.headless").equals("false")))
- {
-
- class VersionChecker
- extends Thread
- {
- public void run()
- {
- String jnlpVersion = null;
- try
- {
- 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(ex);
- jnlpVersion = getProperty("VERSION");
- }
-
- 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;
- }
-
- 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 (Exception e)
- {
- groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present");
- }
- }
- return (groovyJarsArePresent > 0);
- }
-
+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