/*
* 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.
*
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
*
- 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 $SEQUENCE_ID$
*
- 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)
*
-
*
*
*
* @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";
/**
* 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())));
//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 && (
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;
}
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);
}
}