/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
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.*;
/**
* 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>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
- * <br>logs.Jalview.Level - Cache.log stringified level.
- * <br>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
- * <br>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
- * <br>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
+ * <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
{
/**
- * 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.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();
+ /** 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()
+ {
+ 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)
{
- 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") +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));
- }
+ propertiesFile = System.getProperty("user.home") + File.separatorChar +
+ ".jalview_properties";
+ }
- // 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");
- }
+ 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);
+ }
- String jnlpVersion = System.getProperty("jalview.version");
- String codeVersion = getProperty("VERSION");
+ 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");
+ }
- 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 && (
+ 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 jnlpVersion = null;
+ try
{
- public void run()
+ 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)
{
- String jnlpVersion = null;
- try
+ if (line.indexOf("jalview.version") == -1)
{
- 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");
+ 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(ex);
+ jnlpVersion = getProperty("VERSION");
+ }
- 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);
-
- //LOAD USERDEFINED COLOURS
- jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
- jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+ 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
+ */
- /**
- * 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)
+ public static boolean getDefault(String property, boolean def)
+ {
+ String string = getProperty(property);
+ if (string != null)
{
- return applicationProperties.getProperty(key);
+ 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 boolean getDefault(String property, boolean 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)
{
- String string = getProperty(property);
- if (string != null)
- {
- def = Boolean.valueOf(string).booleanValue();
- }
-
- return def;
+ return string;
}
- /** 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;
+ }
- 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;
+ }
-
- /**
- * 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)
+ public static void saveProperties()
+ {
+ try
{
- 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;
+ FileOutputStream out = new FileOutputStream(propertiesFile);
+ applicationProperties.store(out, "---JalviewX Properties File---");
+ out.close();
}
+ catch (Exception ex)
+ {
+ System.out.println("Error saving properties: " + ex);
+ }
+ }
- public static void saveProperties()
+ /**
+ * 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
+ try
+ {
+ if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
+ "uk.ac.vamsas.client.VorbaId") != null)
{
- FileOutputStream out = new FileOutputStream(propertiesFile);
- applicationProperties.store(out, "---JalviewX Properties File---");
- out.close();
+ 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 ex)
- { System.out.println("Error saving properties: "+ex); }
+ }
+ catch (Exception e)
+ {
+ vamsasJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+ }
}
- /**
- * 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.");
- }
- } 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.");
}
}
- return (vamsasJarsArePresent>0);
+ catch (Exception e)
+ {
+ groovyJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Groovy Classes are not present");
+ }
}
+ return (groovyJarsArePresent > 0);
+ }
}
git://source.jalview.org / jalview.git / blobdiff