/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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 3
* of the License, or (at your option) any later version.
*
* Jalview 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 Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.net.Authenticator;
import java.net.PasswordAuthentication;
import java.net.URL;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Properties;
import java.util.StringTokenizer;
import java.util.TreeSet;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
import jalview.analytics.Plausible;
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
import jalview.gui.UserDefinedColours;
import jalview.log.JLoggerLog4j;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.UserColourScheme;
import jalview.structure.StructureImportSettings;
import jalview.urls.IdOrgSettings;
import jalview.util.ChannelProperties;
import jalview.util.ColorUtils;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
/**
* 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.
*
* 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
* SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
* LABEL_AND_SEQUENCE
* SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
* sequence annotations
* 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
* USAGESTATS (false - user prompted) Enable analytics tracker for
* collecting usage statistics
* 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
* BITMAP_SCALE - scale factor for PNG export - default 0.0 - native
* resolution
* BITMAP_HEIGHT - height bound for PNG export or 0 for unbound
* BITMAP_WIDTH - width bound for PNG export or 0 for unbound
* SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
* SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$
* STORED_LINKS list of name|url pairs which user has entered but are not
* currently used
* DEFAULT_LINK name of single url to be used when user double clicks a
* sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
* GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info
* DEFAULT_BROWSER for unix
* SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)
* VERSION_CHECK (true) check for the latest release version from
* www.jalview.org (or the alias given by the www.jalview.org property)
* SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
* ID tooltip
* SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
* ID tooltip
* SHOW_UNCONSERVED (false) only render unconserved residues - conserved
* displayed as '.'
* SORT_BY_TREE (false) sort the current alignment view according to the
* order of a newly displayed tree
* DBFETCH_USEPICR (false) use PICR to recover valid DB references from
* sequence ID strings before attempting retrieval from any datasource
* SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
* alignment.
* SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
* in the alignment.
* SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
* histogram.
* SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
* logo.
* NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
* logo normalised to row height rather than histogram height.
* FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
*
* SHOW_JWS2_SERVICES (true) when set to false, jalview will not
* auto-discover JABAWS services
* JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services
* SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
* warning dialog box is displayed.
* ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
* when shading by annotation
* ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
* when shading by annotation
* www.jalview.org (https://www.jalview.org) a property enabling all HTTP
* requests to be redirected to a mirror of https://www.jalview.org
* FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
* alignment figure to accommodate even the longest sequence ID or annotation
* label.
* FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
* when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
* will override this).
* STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
* record
* USE_RNAVIEW (false) use RNAViewer to derive secondary structure
* ADD_SS_ANN (false) add secondary structure annotation to alignment
* display
* ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
* display
* STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
* display
* CHIMERA_PATH specify full path to Chimera program (if non-standard)
* ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
*
* NONEWS - when set disables Jalview News from automatically appearing
* NOHTMLTEMPLATES - when set, the
* https://github.com/jalview/exporter-templates/tree/master/biojs repository is
* not downloaded automatically
* NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
* available URL linkouts via www.jalview.org/services/identifiers
*
*
* Deprecated settings:
*
* *
* DISCOVERY_START - Boolean - controls if discovery services are queried on
* startup (JWS1 services only)
* DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
* (JWS1 services only)
* SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
* services in the desktop GUI
* ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
* panel in web service preferences
*
*
* @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";
// for tests
public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
/**
* Sifts settings
*/
public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
.getProperty("user.home") + File.separatorChar
+ ".sifts_downloads" + File.separatorChar;
private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
/**
* Identifiers.org download settings
*/
private static final String ID_ORG_FILE = System.getProperty("user.home")
+ File.separatorChar + ".identifiers.org.ids.json";
/**
* Allowed values are PDB or mmCIF
*/
private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
.toString();
private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
.toString();
/*
* a date formatter using a fixed (rather than the user's) locale;
* this ensures that date properties can be written and re-read successfully
* even if the user changes their locale setting
*/
private static final DateFormat date_format = SimpleDateFormat
.getDateTimeInstance(SimpleDateFormat.MEDIUM,
SimpleDateFormat.MEDIUM, Locale.UK);
/**
* Initialises the Jalview Application Log
*/
public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
// save the proxy properties set at startup
public final static String[] startupProxyProperties = {
System.getProperty("http.proxyHost"),
System.getProperty("http.proxyPort"),
System.getProperty("https.proxyHost"),
System.getProperty("https.proxyPort"),
System.getProperty("http.proxyUser"),
System.getProperty("http.proxyPassword"),
System.getProperty("https.proxyUser"),
System.getProperty("https.proxyPassword"),
System.getProperty("http.nonProxyHosts") };
public final static String PROXYTYPE_NONE = "none";
// "false" and "true" for backward compatibility
public final static String PROXYTYPE_SYSTEM = "false";
public final static String PROXYTYPE_CUSTOM = "true";
// in-memory only storage of proxy password, safer to use char array
public static char[] proxyAuthPassword = null;
/**
* Session properties, set by command line, try not to affect stored
* properties!
*/
private static Map sessionProperties = new HashMap<>();
private static boolean bypassSessionProperties = false;
public static void enableSessionProperties()
{
bypassSessionProperties = false;
}
public static void disableSessionProperties()
{
bypassSessionProperties = true;
}
/** Jalview Properties */
public static Properties applicationProperties = new Properties()
{
// override results in properties output in alphabetical order
@Override
public synchronized Enumeration keys()
{
return Collections.enumeration(new TreeSet<>(super.keySet()));
}
};
/* build Properties (not all saved to .jalview_properties) */
public static Properties buildProperties = new Properties();
/** Default file is ~/.jalview_properties */
static String propertiesFile;
private static final String fallbackPropertiesFile = ".jalview_properties";
private static boolean propsAreReadOnly = Platform.isJS();
public static boolean isPropsAreReadOnly()
{
return propsAreReadOnly;
}
public static void setPropsAreReadOnly(boolean propsAreReadOnly)
{
Cache.propsAreReadOnly = propsAreReadOnly;
}
private final static String JS_PROPERTY_PREFIX = "jalview_";
/**
* Loads properties from the given properties file. Any existing properties
* are first cleared.
*/
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
String releasePropertiesFile = null;
boolean defaultProperties = false;
if (propsFile == null && !propsAreReadOnly)
{
String channelPrefsFilename = ChannelProperties
.getProperty("preferences.filename");
String releasePrefsFilename = fallbackPropertiesFile;
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ channelPrefsFilename;
releasePropertiesFile = System.getProperty("user.home")
+ File.separatorChar + releasePrefsFilename;
defaultProperties = true;
}
else
{
// don't corrupt the file we've been given.
propsAreReadOnly = true;
}
if (propertiesFile == null)
{ // BH 2019
Platform.readInfoProperties(JS_PROPERTY_PREFIX,
applicationProperties);
}
else
{
try
{
InputStream fis;
try
{
// props file provided as URL
fis = HttpUtils.openStream(new URL(propertiesFile));
if (!Jalview.quiet())
{
jalview.bin.Console.outPrintln(
"Loading jalview properties from : " + propertiesFile);
jalview.bin.Console.outPrintln(
"Disabling Jalview writing to user's local properties file.");
}
propsAreReadOnly = true;
} catch (Exception ex)
{
fis = null;
}
if (fis == null)
{
String readPropertiesFile = propertiesFile;
// if we're using the usual properties file and the channel properties
// file doesn't exist, read .jalview_properties
// (but we'll still save to the channel properties file).
if (defaultProperties && (!new File(propertiesFile).exists())
&& (new File(releasePropertiesFile).exists()))
{
readPropertiesFile = releasePropertiesFile;
}
fis = new FileInputStream(readPropertiesFile);
}
applicationProperties.clear();
applicationProperties.load(fis);
// remove any old build properties
deleteBuildProperties();
fis.close();
} catch (Exception ex)
{
if (!Jalview.quiet())
jalview.bin.Console
.outPrintln("Error reading properties file: " + ex);
}
}
/* TO BE REPLACED WITH PROXY_TYPE SETTINGS
if (getDefault("USE_PROXY", false))
{
String proxyServer = getDefault("PROXY_SERVER", ""),
proxyPort = getDefault("PROXY_PORT", "8080");
}
*/
// PROXY TYPE settings (now three options "none", "false", "true", but using
// backward compatible strings)
String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM);
// default to upgrading old settings
switch (proxyType)
{
case PROXYTYPE_NONE:
clearProxyProperties();
break;
case PROXYTYPE_SYSTEM: // use system settings
resetProxyProperties();
break;
case PROXYTYPE_CUSTOM: // use specified proxy settings
String httpHost = getDefault("PROXY_SERVER", "");
String httpPort = getDefault("PROXY_PORT", "8080");
String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
String httpUser = getDefault("PROXY_AUTH_USER", null);
// https.proxyUser and https.proxyPassword are not able to be
// independently set in Preferences yet (or http.nonProxyHosts)
String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
break;
default:
String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ proxyType;
Console.warn(message);
}
// LOAD THE AUTHORS FROM THE authors.props file
String authorDetails = resolveResourceURLFor("/authors.props");
try
{
if (authorDetails != null)
{
URL localJarFileURL = new URL(authorDetails);
InputStream in = localJarFileURL.openStream();
applicationProperties.load(in);
in.close();
}
} catch (Exception ex)
{
if (!Jalview.quiet())
jalview.bin.Console
.outPrintln("Error reading author details: " + ex);
authorDetails = null;
}
if (authorDetails == null)
{
applicationProperties.remove("AUTHORS");
applicationProperties.remove("AUTHORFNAMES");
applicationProperties.remove("YEAR");
}
loadBuildProperties(false);
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
SiftsSettings.setSiftDownloadDirectory(Cache
.getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setFailSafePIDThreshold(
Cache.getDefault("sifts_fail_safe_pid_threshold",
DEFAULT_FAIL_SAFE_PID_THRESHOLD));
SiftsSettings.setCacheThresholdInDays(
Cache.getDefault("sifts_cache_threshold_in_days",
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
"https://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
StructureImportSettings.setDefaultStructureFileFormat(
Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
// .setDefaultPDBFileParser(Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
String jnlpVersion = System.getProperty("jalview.version");
// jnlpVersion will be null if a latest version check for the channel needs
// to be done
// 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
{
@Override
public void run()
{
String remoteBuildPropertiesUrl = Cache
.getAppbaseBuildProperties();
String orgtimeout = System
.getProperty("sun.net.client.defaultConnectTimeout");
if (orgtimeout == null)
{
orgtimeout = "30";
Console.debug("Setting default net timeout to " + orgtimeout
+ " seconds.");
}
String remoteVersion = null;
if (remoteBuildPropertiesUrl.startsWith("http"))
{
try
{
System.setProperty("sun.net.client.defaultConnectTimeout",
"5000");
URL url = new URL(remoteBuildPropertiesUrl);
BufferedReader in = new BufferedReader(
new InputStreamReader(HttpUtils.openStream(url)));
Properties remoteBuildProperties = new Properties();
remoteBuildProperties.load(in);
remoteVersion = remoteBuildProperties.getProperty("VERSION");
} catch (Exception ex)
{
if (!Jalview.quiet())
{
jalview.bin.Console.errPrintln(
"Non-fatal exception when checking version at "
+ remoteBuildPropertiesUrl + ":");
jalview.bin.Console.printStackTrace(ex);
}
remoteVersion = getProperty("VERSION");
}
}
System.setProperty("sun.net.client.defaultConnectTimeout",
orgtimeout);
setProperty("LATEST_VERSION", remoteVersion);
}
}
VersionChecker vc = new VersionChecker();
vc.start();
}
else
{
if (jnlpVersion != null)
{
setProperty("LATEST_VERSION", jnlpVersion);
}
else
{
applicationProperties.remove("LATEST_VERSION");
}
}
// LOAD USERDEFINED COLOURS
Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
false);
}
/**
* construct a resource URL for the given absolute resource pathname
*
* @param resourcePath
* @return
*/
private static String resolveResourceURLFor(String resourcePath)
{
String url = null;
if (Platform.isJS() || !Cache.class.getProtectionDomain()
.getCodeSource().getLocation().toString().endsWith(".jar"))
{
try
{
url = Cache.class.getResource(resourcePath).toString();
} catch (Exception ex)
{
jalview.bin.Console.errPrintln("Failed to resolve resource "
+ resourcePath + ": " + ex.getMessage());
}
}
else
{
url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
.getLocation().toString().concat("!" + resourcePath));
}
return url;
}
public static void loadBuildProperties(boolean reportVersion)
{
String codeInstallation = getProperty("INSTALLATION");
boolean printVersion = codeInstallation == null;
/*
* read build properties - from the Jalview jar for a Java distribution,
* or from codebase file in test or JalviewJS context
*/
try
{
String buildDetails = resolveResourceURLFor("/.build_properties");
URL localJarFileURL = new URL(buildDetails);
InputStream in = localJarFileURL.openStream();
buildProperties.load(in);
in.close();
if (buildProperties.getProperty("BUILD_DATE", null) != null)
{
applicationProperties.put("BUILD_DATE",
buildProperties.getProperty("BUILD_DATE"));
}
if (buildProperties.getProperty("INSTALLATION", null) != null)
{
applicationProperties.put("INSTALLATION",
buildProperties.getProperty("INSTALLATION"));
}
if (buildProperties.getProperty("VERSION", null) != null)
{
applicationProperties.put("VERSION",
buildProperties.getProperty("VERSION"));
}
if (buildProperties.getProperty("JAVA_COMPILE_VERSION", null) != null)
{
applicationProperties.put("JAVA_COMPILE_VERSION",
buildProperties.getProperty("JAVA_COMPILE_VERSION"));
}
} catch (Exception ex)
{
if (!Jalview.quiet())
jalview.bin.Console
.outPrintln("Error reading build details: " + ex);
applicationProperties.remove("VERSION");
}
String codeVersion = getProperty("VERSION");
codeInstallation = getProperty("INSTALLATION");
if (codeVersion == null)
{
// THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
codeVersion = "Test";
codeInstallation = "";
}
else
{
codeInstallation = " (" + codeInstallation + ")";
}
setProperty("VERSION", codeVersion);
new BuildDetails(codeVersion, null, codeInstallation);
if (printVersion && reportVersion)
{
jalview.bin.Console
.outPrintln(ChannelProperties.getProperty("app_name")
+ " version: " + codeVersion + codeInstallation);
}
}
private static void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
applicationProperties.remove("VERSION");
applicationProperties.remove("AUTHORS");
applicationProperties.remove("AUTHORFNAMES");
applicationProperties.remove("YEAR");
applicationProperties.remove("BUILD_DATE");
applicationProperties.remove("INSTALLATION");
}
/**
* 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 getProperty(key, false);
}
public static String getProperty(String key,
boolean skipSessionProperties)
{
String prop = null;
if (!(skipSessionProperties || bypassSessionProperties))
{
prop = getSessionProperty(key);
}
if (prop == null)
{
prop = applicationProperties.getProperty(key);
}
if (prop == null && Platform.isJS())
{
prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+ "_" + JS_PROPERTY_PREFIX + key);
}
return prop;
}
/**
* 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;
}
public static int getDefault(String property, int def)
{
String string = getProperty(property);
if (string != null)
{
try
{
def = Integer.parseInt(string);
} catch (NumberFormatException e)
{
if (!Jalview.quiet())
jalview.bin.Console.errPrintln("Error parsing int property '"
+ property + "' with value '" + string + "'");
}
}
return def;
}
public static float getDefault(String property, float def)
{
String string = getProperty(property);
if (string != null)
{
try
{
def = Float.parseFloat(string);
} catch (NumberFormatException e)
{
if (!Jalview.quiet())
jalview.bin.Console.errPrintln("Error parsing float property '"
+ property + "' with value '" + string + "'");
}
}
return def;
}
/**
* Answers the value of the given property, or the supplied default value if
* the property is not set
*/
public static String getDefault(String property, String def)
{
String value = getProperty(property);
return value == null ? def : value;
}
/**
* Stores property in the file "HOME_DIR/.jalview_properties"
*
* @param key
* Name of object
* @param obj
* String value of property
*
* @return previous value of property (or null)
*/
public static Object setProperty(String key, String obj)
{
Object oldValue = null;
try
{
oldValue = applicationProperties.setProperty(key, obj);
if (propertiesFile != null && !propsAreReadOnly
// don't rewrite if new value is same as old value
&& !((obj == null && oldValue == null)
|| (obj != null && obj.equals(oldValue))))
{
// reset the session property too
if (sessionProperties.containsKey(key))
{
sessionProperties.remove(key);
}
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
out.close();
}
} catch (Exception ex)
{
if (!Jalview.quiet())
jalview.bin.Console.errPrintln(
"Error setting property: " + key + " " + obj + "\n" + ex);
}
return oldValue;
}
/**
* 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()
{
if (!propsAreReadOnly)
{
try
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
out.close();
} catch (Exception ex)
{
if (!Jalview.quiet())
jalview.bin.Console.errPrintln("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)
{
Console.debug(
"Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
Console.getCachedLogLevel("logs.Vamsas.Level"));
JLoggerLog4j.addAppender(lvclient, Console.log,
JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lvclient.debug(ChannelProperties.getProperty("app_name")
+ " Vamsas Client Debugging Output Follows.");
}
} catch (Exception e)
{
vamsasJarsArePresent = 0;
Console.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)
{
Console.debug(
"Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
Console.getCachedLogLevel("logs.Groovy.Level"));
JLoggerLog4j.addAppender(lgclient, Console.log,
JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lgclient.debug(ChannelProperties.getProperty("app_name")
+ " Groovy Client Debugging Output Follows.");
}
} catch (Error e)
{
groovyJarsArePresent = 0;
Console.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
Console.debug("Groovy Classes are not present");
}
}
return (groovyJarsArePresent > 0);
}
/**
* Initialise the tracker if it is not done already.
*/
public static void initAnalytics()
{
Plausible.setEnabled(true);
String appName = ChannelProperties.getProperty("app_name") + " Desktop";
String version = Cache.getProperty("VERSION") + "_"
+ Cache.getDefault("BUILD_DATE", "unknown");
String path;
/* we don't want to encode ':' as "%3A" for backward compatibility with the UA setup
try
{
path = "/" + String.join("/", URLEncoder.encode(appName, "UTF-8"),
URLEncoder.encode(version, "UTF-8"),
URLEncoder.encode(APPLICATION_STARTED, "UTF-8"));
} catch (UnsupportedEncodingException e)
{
*/
List pathParts = new ArrayList<>();
pathParts.add(appName);
pathParts.add(version);
pathParts.add(APPLICATION_STARTED);
path = ("/" + String.join("/", pathParts)).replace(' ', '+');
/*
}
*/
Plausible plausible = Plausible.getInstance();
// This will send a new "application_launch" event with parameters
// including the old-style "path", the channel name and version
plausible.sendEvent("application_launch", path, true);
}
private static final String APPLICATION_STARTED = "Application Started";
/**
* get the user's default colour if available
*
* @param property
* @param defcolour
* @return
*/
public static Color getDefaultColour(String property, Color defcolour)
{
String colprop = getProperty(property);
if (colprop == null)
{
return defcolour;
}
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
Console.warn("Couldn't parse '" + colprop + "' as a colour for "
+ property);
}
return (col == null) ? defcolour : col;
}
/**
* store a colour as a Jalview user default property
*
* @param property
* @param colour
*/
public static void setColourProperty(String property, Color colour)
{
setProperty(property, jalview.util.Format.getHexString(colour));
}
/**
* Stores a formatted date in a jalview property, using a fixed locale.
*
* @param propertyName
* @param date
* @return the formatted date string
*/
public static String setDateProperty(String propertyName, Date date)
{
String formatted = date_format.format(date);
setProperty(propertyName, formatted);
return formatted;
}
/**
* Reads a date stored in a Jalview property, parses it (using a fixed locale
* format) and returns as a Date, or null if parsing fails
*
* @param propertyName
* @return
*
*/
public static Date getDateProperty(String propertyName)
{
String val = getProperty(propertyName);
if (val != null)
{
try
{
return date_format.parse(val);
} catch (Exception ex)
{
jalview.bin.Console
.errPrintln("Invalid or corrupt date in property '"
+ propertyName + "' : value was '" + val + "'");
}
}
return null;
}
/**
* get and parse a property as an integer. send any parsing problems to
* System.err
*
* @param property
* @return null or Integer
*/
public static Integer getIntegerProperty(String property)
{
String val = getProperty(property);
if (val != null && (val = val.trim()).length() > 0)
{
try
{
return Integer.valueOf(val);
} catch (NumberFormatException x)
{
jalview.bin.Console.errPrintln("Invalid integer in property '"
+ property + "' (value was '" + val + "')");
}
}
return null;
}
/**
* Set the specified value, or remove it if null or empty. Does not save the
* properties file.
*
* @param propName
* @param value
*/
public static void setOrRemove(String propName, String value)
{
if (propName == null)
{
return;
}
if (value == null || value.trim().length() < 1)
{
Cache.applicationProperties.remove(propName);
}
else
{
Cache.applicationProperties.setProperty(propName, value);
}
}
/**
* Loads in user colour schemes from files.
*
* @param files
* a '|'-delimited list of file paths
*/
public static void initUserColourSchemes(String files)
{
if (files == null || files.length() == 0)
{
return;
}
// In case colours can't be loaded, we'll remove them
// from the default list here.
StringBuffer coloursFound = new StringBuffer();
StringTokenizer st = new StringTokenizer(files, "|");
while (st.hasMoreElements())
{
String file = st.nextToken();
try
{
UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
if (ucs != null)
{
if (coloursFound.length() > 0)
{
coloursFound.append("|");
}
coloursFound.append(file);
ColourSchemes.getInstance().registerColourScheme(ucs);
}
} catch (Exception ex)
{
if (!Jalview.quiet())
jalview.bin.Console
.outPrintln("Error loading User ColourFile\n" + ex);
}
}
if (!files.equals(coloursFound.toString()))
{
if (coloursFound.toString().length() > 1)
{
setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
coloursFound.toString());
}
else
{
applicationProperties
.remove(UserDefinedColours.USER_DEFINED_COLOURS);
}
}
}
/**
* Initial logging information helper for various versions output
*
* @param prefix
* @param value
* @param defaultValue
*/
private static void appendIfNotNull(StringBuilder sb, String prefix,
String value, String suffix, String defaultValue)
{
if (value == null && defaultValue == null)
{
return;
}
if (prefix != null)
sb.append(prefix);
sb.append(value == null ? defaultValue : value);
if (suffix != null)
sb.append(suffix);
}
/**
*
* @return Jalview version, build details and JVM platform version for console
*/
public static String getVersionDetailsForConsole()
{
StringBuilder sb = new StringBuilder();
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Version: ");
sb.append(Cache.getDefault("VERSION", "TEST"));
sb.append("\n");
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Installation: ");
sb.append(Cache.getDefault("INSTALLATION", "unknown"));
sb.append("\n");
sb.append("Build Date: ");
sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
sb.append("\n");
sb.append("Java version: ");
sb.append(System.getProperty("java.version"));
sb.append("\n");
sb.append("Java platform: ");
sb.append(System.getProperty("os.arch"));
sb.append(" ");
sb.append(System.getProperty("os.name"));
sb.append(" ");
sb.append(System.getProperty("os.version"));
sb.append("\n");
appendIfNotNull(sb, "Install4j version: ",
System.getProperty("sys.install4jVersion"), "\n", null);
appendIfNotNull(sb, "Install4j template version: ",
System.getProperty("installer_template_version"), "\n", null);
appendIfNotNull(sb, "Launcher version: ",
System.getProperty("launcher_version"), "\n", null);
LookAndFeel laf = UIManager.getLookAndFeel();
String lafName = laf == null ? "Not obtained" : laf.getName();
String lafClass = laf == null ? "unknown" : laf.getClass().getName();
sb.append("LookAndFeel: ");
sb.append(lafName);
sb.append(" (");
sb.append(lafClass);
sb.append(")\n");
appendIfNotNull(sb, "Channel: ",
ChannelProperties.getProperty("channel"), "\n", null);
if (Console.isDebugEnabled()
|| !"release".equals(ChannelProperties.getProperty("channel")))
{
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdowninstanceappdir"), "\n", null);
appendIfNotNull(sb, "Getdown appbase: ",
System.getProperty("getdowninstanceappbase"), "\n", null);
appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
"\n", "unknown");
appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n",
"unknown");
}
return sb.toString();
}
/**
*
* @return build details as reported in splashscreen
*/
public static String getBuildDetailsForSplash()
{
// consider returning more human friendly info
// eg 'built from Source' or update channel
return Cache.getDefault("INSTALLATION", "unknown");
}
public static String getStackTraceString(Throwable t)
{
StringWriter sw = new StringWriter();
PrintWriter pw = new PrintWriter(sw);
t.printStackTrace(pw);
return sw.toString();
}
// proxy properties methods
public static void clearProxyProperties()
{
setProxyProperties(null, null, null, null, null, null, null, null,
null);
}
public static void resetProxyProperties()
{
setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
startupProxyProperties[2], startupProxyProperties[3],
startupProxyProperties[4],
startupProxyProperties[5] == null ? null
: startupProxyProperties[5].toCharArray(),
startupProxyProperties[6],
startupProxyProperties[7] == null ? null
: startupProxyProperties[7].toCharArray(),
startupProxyProperties[8]);
StringBuilder sb = new StringBuilder();
sb.append("Setting proxy properties to: http.proxyHost=")
.append(startupProxyProperties[0]).append(", http.proxyPort=")
.append(startupProxyProperties[1])
.append(startupProxyProperties[4] != null
&& !startupProxyProperties[4].isEmpty()
? " [" + startupProxyProperties[4] + "]"
: "")
.append(", https.proxyHost=").append(startupProxyProperties[2])
.append(", https.proxyPort=").append(startupProxyProperties[3])
.append(startupProxyProperties[6] != null
&& !startupProxyProperties[6].isEmpty()
? " [" + startupProxyProperties[6] + "]"
: "");
Console.debug(sb.toString());
}
public static void setProxyPropertiesFromPreferences()
{
setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
}
public static void setProxyPropertiesFromPreferences(
String previousProxyType)
{
String proxyType = Cache.getDefault("USE_PROXY",
Cache.PROXYTYPE_SYSTEM);
if (previousProxyType != null
&& !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
// customProxy
&& proxyType.equals(previousProxyType))
{
// no change
return;
}
switch (proxyType)
{
case Cache.PROXYTYPE_NONE:
if (!previousProxyType.equals(proxyType))
{
Console.info("Setting no proxy settings");
Cache.setProxyProperties(null, null, null, null, null, null, null,
null, null);
}
break;
case Cache.PROXYTYPE_CUSTOM:
// always re-set a custom proxy -- it might have changed, particularly
// password
Console.info("Setting custom proxy settings");
boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
Cache.getDefault("PROXY_PORT", null),
Cache.getDefault("PROXY_SERVER_HTTPS", null),
Cache.getDefault("PROXY_PORT_HTTPS", null),
proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
: null,
proxyAuthSet ? Cache.proxyAuthPassword : null,
proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
: null,
proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
break;
default: // system proxy settings by default
Console.info("Setting system proxy settings");
Cache.resetProxyProperties();
}
}
public static void setProxyProperties(String httpHost, String httpPort,
String httpsHost, String httpsPort, String httpUser,
char[] httpPassword, String httpsUser, char[] httpsPassword,
String nonProxyHosts)
{
setOrClearSystemProperty("http.proxyHost", httpHost);
setOrClearSystemProperty("http.proxyPort", httpPort);
setOrClearSystemProperty("https.proxyHost", httpsHost);
setOrClearSystemProperty("https.proxyPort", httpsPort);
setOrClearSystemProperty("http.proxyUser", httpUser);
setOrClearSystemProperty("https.proxyUser", httpsUser);
// note: passwords for http.proxyPassword and https.proxyPassword are sent
// via the Authenticator, properties do not need to be set
// are we using a custom proxy (password prompt might be required)?
boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
.equals(PROXYTYPE_CUSTOM);
/*
* A bug in Java means the AuthCache does not get reset, so once it has working credentials,
* it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
* is not re-called).
* This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
* the AuthCache.
* see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
* ...
* Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
*/
/*
try
{
sun.net.www.protocol.http.AuthCacheValue
.setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
} catch (Throwable t)
{
Cache.error(t.getMessage());
Cache.debug(getStackTraceString(t));
}
*/
if (httpUser != null || httpsUser != null)
{
try
{
char[] displayHttpPw = new char[httpPassword == null ? 0
: httpPassword.length];
Arrays.fill(displayHttpPw, '*');
Console.debug(
"CACHE Proxy: setting new Authenticator with httpUser='"
+ httpUser + "' httpPassword='" + displayHttpPw
+ "'");
if (!Platform.isJS())
/* *
* java.net.Authenticator not implemented in SwingJS yet
*
* @j2sIgnore
*
*/
{
Authenticator.setDefault(new Authenticator()
{
@Override
protected PasswordAuthentication getPasswordAuthentication()
{
if (getRequestorType() == RequestorType.PROXY)
{
String protocol = getRequestingProtocol();
boolean needProxyPasswordSet = false;
if (customProxySet &&
// we have a username but no password for the scheme being
// requested
(protocol.equalsIgnoreCase("http")
&& (httpUser != null
&& httpUser.length() > 0
&& (httpPassword == null
|| httpPassword.length == 0)))
|| (protocol.equalsIgnoreCase("https")
&& (httpsUser != null
&& httpsUser.length() > 0
&& (httpsPassword == null
|| httpsPassword.length == 0))))
{
// open Preferences -> Connections
String message = MessageManager
.getString("label.proxy_password_required");
Preferences.openPreferences(
Preferences.TabRef.CONNECTIONS_TAB, message);
Preferences.getInstance()
.proxyAuthPasswordCheckHighlight(true, true);
}
else
{
try
{
if (protocol.equalsIgnoreCase("http")
&& getRequestingHost()
.equalsIgnoreCase(httpHost)
&& getRequestingPort() == Integer
.valueOf(httpPort))
{
Console.debug(
"AUTHENTICATOR returning PasswordAuthentication(\""
+ httpUser + "\", '"
+ new String(displayHttpPw) + "')");
return new PasswordAuthentication(httpUser,
httpPassword);
}
if (protocol.equalsIgnoreCase("https")
&& getRequestingHost()
.equalsIgnoreCase(httpsHost)
&& getRequestingPort() == Integer
.valueOf(httpsPort))
{
char[] displayHttpsPw = new char[httpPassword.length];
Arrays.fill(displayHttpsPw, '*');
Console.debug(
"AUTHENTICATOR returning PasswordAuthentication(\""
+ httpsUser + "\", '" + displayHttpsPw
+ "'");
return new PasswordAuthentication(httpsUser,
httpsPassword);
}
} catch (NumberFormatException e)
{
Console.error("Problem with proxy port values [http:"
+ httpPort + ", https:" + httpsPort + "]");
}
Console.debug(
"AUTHENTICATOR after trying to get PasswordAuthentication");
}
}
// non proxy request
Console.debug("AUTHENTICATOR returning null");
return null;
}
});
} // end of j2sIgnore for java.net.Authenticator
// required to re-enable basic authentication (should be okay for a
// local proxy)
Console.debug(
"AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
} catch (SecurityException e)
{
Console.error("Could not set default Authenticator");
Console.debug(getStackTraceString(e));
}
}
else
{
// reset the Authenticator to protect http.proxyUser and
// http.proxyPassword Just In Case
/* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
* has working credentials. No workaround for Java 11.
*/
if (!Platform.isJS())
/* *
* java.net.Authenticator not implemented in SwingJS yet
*
* @j2sIgnore
*
*/
{
Console.debug(
"AUTHENTICATOR setting default Authenticator to null");
Authenticator.setDefault(null);
}
}
// nonProxyHosts not currently configurable in Preferences
Console.debug(
"AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ nonProxyHosts + "\"");
setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
}
public static void setOrClearSystemProperty(String key, char[] value)
{
setOrClearSystemProperty(key,
(value == null) ? null : new String(value));
}
public static void setOrClearSystemProperty(String key, String value)
{
if (key == null)
{
return;
}
if (value == null)
{
System.clearProperty(key);
}
else
{
System.setProperty(key, value);
}
}
/**
* Getdown appbase methods
*/
private static final String releaseAppbase;
private static String getdownAppbase;
private static String getdownDistDir;
static
{
if (!Platform.isJS())
{
Float specversion = Float
.parseFloat(System.getProperty("java.specification.version"));
releaseAppbase = (specversion < 9)
? "https://www.jalview.org/getdown/release/1.8"
: "https://www.jalview.org/getdown/release/11";
}
else
{
// this value currenly made up, can be changed to URL that will be
// "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
releaseAppbase = "https://www.jalview.org/jalview-js";
getdownAppbase = releaseAppbase;
getdownDistDir = "/swingjs/j2s";
}
}
// look for properties (passed in by getdown) otherwise default to release
private static void setGetdownAppbase()
{
if (getdownAppbase != null)
{
return;
}
String appbase = System.getProperty("getdownappbase");
String distDir = System.getProperty("getdowndistdir");
if (appbase == null)
{
appbase = buildProperties.getProperty("GETDOWNAPPBASE");
distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
}
if (appbase == null)
{
appbase = releaseAppbase;
distDir = "release";
}
if (appbase.endsWith("/"))
{
appbase = appbase.substring(0, appbase.length() - 1);
}
if (distDir == null)
{
distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
}
getdownAppbase = appbase;
getdownDistDir = distDir;
}
public static String getGetdownAppbase()
{
setGetdownAppbase();
return getdownAppbase;
}
public static String getAppbaseBuildProperties()
{
String appbase = getGetdownAppbase();
return appbase + "/" + getdownDistDir + "/build_properties";
}
private static final Collection bootstrapProperties = new ArrayList<>(
Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST));
public static Properties bootstrapProperties(String filename)
{
Properties bootstrapProps = new Properties();
File file = null;
if (filename != null)
{
file = new File(filename);
}
if (file == null || !file.exists())
{
if (file != null)
{
jalview.bin.Console
.errPrintln("Could not load bootstrap preferences file '"
+ file.getPath() + "'");
}
String channelPrefsFilename = ChannelProperties
.getProperty("preferences.filename");
String propertiesFilename = System.getProperty("user.home")
+ File.separatorChar + channelPrefsFilename;
jalview.bin.Console.errPrintln(
"Using default properties file '" + propertiesFilename + "'");
file = new File(propertiesFilename);
}
if (file == null || !file.exists())
{
String releasePrefsFilename = fallbackPropertiesFile;
String releasePropertiesFilename = System.getProperty("user.home")
+ File.separatorChar + releasePrefsFilename;
jalview.bin.Console.errPrintln("Falling back to properties file '"
+ releasePropertiesFilename + "'");
file = new File(releasePropertiesFilename);
}
if (!file.exists())
{
jalview.bin.Console
.errPrintln("Could not load bootstrap preferences file '"
+ file.getPath() + "'");
return null;
}
try
{
FileInputStream in = new FileInputStream(file.getAbsoluteFile());
Properties props = new Properties();
props.load(in);
for (String prop : bootstrapProperties)
{
if (props.containsKey(prop))
bootstrapProps.put(prop, props.getProperty(prop));
}
} catch (FileNotFoundException e)
{
jalview.bin.Console
.errPrintln("Could not find bootstrap preferences file '"
+ file.getAbsolutePath() + "'");
} catch (IOException e)
{
jalview.bin.Console.errPrintln(
"IOException when loading bootstrap preferences file '"
+ file.getAbsolutePath() + "'");
}
return bootstrapProps;
}
public static void setSessionProperty(String key, String val)
{
if (key != null)
{
sessionProperties.put(key, val);
}
}
public static String getSessionProperty(String key)
{
return key == null ? null : sessionProperties.get(key);
}
public static boolean getArgCacheDefault(Arg a, String pref, boolean def)
{
ArgParser ap = Jalview.getInstance().getArgParser();
return ap.isSet(a) ? ap.getBoolean(a) : getDefault(pref, def);
}
}