/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
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)
+ * 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>
- * </li><li>logs.Jalview.Level - Cache.log stringified level.
+ * Current properties include:
+ * <ul>
* <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>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>
+ * 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>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 $Revision$
*/
* 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";
/**
/** Jalview Properties */
public static Properties applicationProperties = new Properties();
- /** Default file is ~/.jalview_properties */
+ /** Default file is ~/.jalview_properties */
static String propertiesFile;
public static void initLogger()
try
{
ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
- "System.err");
+ "System.err");
ap.setName("JalviewLogger");
- org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for log output
+ 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())));
+ Level.INFO.toString())));
lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- Level.INFO.toString())));
+ 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())));
+ // 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);
+ "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)
+ } catch (Exception ex)
{
System.err.println("Problems initializing the log4j system\n");
ex.printStackTrace(System.err);
propertiesFile = propsFile;
if (propsFile == null)
{
- propertiesFile = System.getProperty("user.home") + File.separatorChar +
- ".jalview_properties";
+ propertiesFile = System.getProperty("user.home") + File.separatorChar
+ + ".jalview_properties";
}
try
applicationProperties.remove("LATEST_VERSION");
applicationProperties.remove("VERSION");
fis.close();
- }
- catch (Exception ex)
+ } 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.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));
}
// VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
try
{
- String buildDetails = "jar:"
- .concat(
- Cache.class.getProtectionDomain().getCodeSource().getLocation().
- toString()
- .concat("!/.build_properties")
- );
+ 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)
+ } catch (Exception ex)
{
System.out.println("Error reading build details: " + ex);
applicationProperties.remove("VERSION");
// 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")))
+ if (jnlpVersion == null
+ && (System.getProperty("java.awt.headless") == null || System
+ .getProperty("java.awt.headless").equals("false")))
{
- class VersionChecker
- extends Thread
+ class VersionChecker extends Thread
{
public void run()
{
- String orgtimeout = System.getProperty("sun.net.client.defaultConnectTimeout");
- if (orgtimeout==null)
+ String orgtimeout = System
+ .getProperty("sun.net.client.defaultConnectTimeout");
+ if (orgtimeout == null)
{
- orgtimeout="30";
- System.out.println("# INFO: Setting default net timeout to "+orgtimeout+" seconds.");
+ orgtimeout = "30";
+ System.out.println("# INFO: Setting default net timeout to "
+ + orgtimeout + " seconds.");
}
String jnlpVersion = null;
try
{
- System.setProperty("sun.net.client.defaultConnectTimeout", "5000");
+ 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()));
+ "http://www.jalview.org/webstart/jalview.jnlp");
+ BufferedReader in = new BufferedReader(new InputStreamReader(
+ url.openStream()));
String line = null;
- while ( (line = in.readLine()) != null)
+ while ((line = in.readLine()) != null)
{
if (line.indexOf("jalview.version") == -1)
{
jnlpVersion = line;
break;
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- System.out.println("Non-fatal exceptions when checking version at www.jalview.org :");
+ 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);
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ orgtimeout);
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);
+ // 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
- *
+ * 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
+ /**
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
*/
public static boolean getDefault(String property, boolean def)
return def;
}
- /** These methods are used when checking if the saved preference
- * is different to the default setting
+ /**
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
*/
public static String getDefault(String property, String def)
{
/**
* Stores property in the file "HOME_DIR/.jalview_properties"
- *
- * @param key Name of object
- * @param obj String value of property
- *
+ *
+ * @param key
+ * Name of object
+ * @param obj
+ * String value of property
+ *
* @return String value of property
*/
public static String setProperty(String key, String obj)
applicationProperties.setProperty(key, obj);
applicationProperties.store(out, "---JalviewX Properties File---");
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- System.out.println("Error setting property: " + key + " " + obj + "\n" +
- 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)
+ } 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()
try
{
if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
- "uk.ac.vamsas.client.VorbaId") != null)
+ "uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.log.debug(
- "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ 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.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)
+ } 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()
try
{
if (Cache.class.getClassLoader().loadClass(
- "groovy.lang.GroovyObject") != null)
+ "groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log.debug(
- "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ 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.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)
+ } catch (Exception e)
{
groovyJarsArePresent = 0;
jalview.bin.Cache.log.debug("Groovy Classes are not present");
git://source.jalview.org / jalview.git / blobdiff