/*
* 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 jalview.datamodel.PDBEntry;
import jalview.gui.UserDefinedColours;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.UserColourScheme;
import jalview.structure.StructureImportSettings;
import jalview.urls.IdOrgSettings;
import jalview.util.ColorUtils;
import jalview.ws.sifts.SiftsSettings;
import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Collections;
import java.util.Date;
import java.util.Enumeration;
import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.TreeMap;
import java.util.TreeSet;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
/**
* 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)
*
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 google 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
*
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.
*
*
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 (http://www.jalview.org) a property enabling all HTTP
* requests to be redirected to a mirror of http://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
*
*
*
* 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";
/**
* 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 static Logger log;
/** Jalview Properties */
public static Properties applicationProperties = new Properties();
/** Default file is ~/.jalview_properties */
static String propertiesFile;
private static boolean propsAreReadOnly = false;
public static void initLogger()
{
if (log != null)
{
return;
}
try
{
// TODO: redirect stdout and stderr here in order to grab the output of
// the log
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);
}
}
/**
* Loads properties from the given properties file. Any existing properties
* are first cleared.
*/
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
if (propsFile == null)
{
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ ".jalview_properties";
}
else
{
// don't corrupt the file we've been given.
propsAreReadOnly = true;
}
try
{
InputStream fis;
try
{
fis = new java.net.URL(propertiesFile).openStream();
System.out.println(
"Loading jalview properties from : " + propertiesFile);
System.out.println(
"Disabling Jalview writing to user's local properties file.");
propsAreReadOnly = true;
} catch (Exception ex)
{
fis = null;
}
if (fis == null)
{
fis = new FileInputStream(propertiesFile);
}
applicationProperties.clear();
applicationProperties.load(fis);
// remove any old build properties
deleteBuildProperties();
fis.close();
} catch (Exception ex)
{
System.out.println("Error reading properties file: " + ex);
}
if (getDefault("USE_PROXY", false))
{
String proxyServer = getDefault("PROXY_SERVER", ""),
proxyPort = getDefault("PROXY_PORT", "8080");
System.out.println("Using proxyServer: " + proxyServer
+ " proxyPort: " + proxyPort);
System.setProperty("http.proxyHost", proxyServer);
System.setProperty("http.proxyPort", proxyPort);
}
// LOAD THE AUTHORS FROM THE authors.props file
try
{
String authorDetails = "jar:"
.concat(Cache.class.getProtectionDomain().getCodeSource()
.getLocation().toString().concat("!/authors.props"));
java.net.URL localJarFileURL = new java.net.URL(authorDetails);
InputStream in = localJarFileURL.openStream();
applicationProperties.load(in);
in.close();
} catch (Exception ex)
{
System.out.println("Error reading author details: " + ex);
applicationProperties.remove("AUTHORS");
applicationProperties.remove("AUTHORFNAMES");
applicationProperties.remove("YEAR");
}
// 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");
String codeInstallation = getProperty("INSTALLATION");
if (codeVersion == null)
{
// THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
codeVersion = "Test";
jnlpVersion = "Test";
codeInstallation = "";
}
else
{
codeInstallation = " (" + codeInstallation + ")";
}
new BuildDetails(codeVersion, null, codeInstallation);
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
.getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setFailSafePIDThreshold(
jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
DEFAULT_FAIL_SAFE_PID_THRESHOLD));
SiftsSettings.setCacheThresholdInDays(
jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
"http://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
// .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
// jnlpVersion will be null if we're using InstallAnywhere
// 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 orgtimeout = System
.getProperty("sun.net.client.defaultConnectTimeout");
if (orgtimeout == null)
{
orgtimeout = "30";
System.out.println("# INFO: Setting default net timeout to "
+ orgtimeout + " seconds.");
}
String remoteVersion = null;
try
{
System.setProperty("sun.net.client.defaultConnectTimeout",
"5000");
java.net.URL url = new java.net.URL(Cache
.getDefault("www.jalview.org", "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("\""));
remoteVersion = line;
break;
}
} catch (Exception ex)
{
System.out.println(
"Non-fatal exception when checking version at www.jalview.org :");
System.out.println(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");
}
}
setProperty("VERSION", codeVersion);
// LOAD USERDEFINED COLOURS
jalview.bin.Cache
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
false);
}
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 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;
}
public static int getDefault(String property, int def)
{
String string = getProperty(property);
if (string != null)
{
try
{
def = Integer.parseInt(string);
} catch (NumberFormatException e)
{
System.out.println("Error parsing int property '" + property
+ "' with value '" + string + "'");
}
}
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 previous value of property (or null)
*/
public static Object setProperty(String key, String obj)
{
Object oldValue = null;
try
{
oldValue = applicationProperties.setProperty(key, obj);
if (!propsAreReadOnly)
{
saveProperties();
}
} catch (Exception ex)
{
System.out.println(
"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
{
Properties orderedProperties = new Properties()
{
// override so properties are output in alphabetical order (Java 8)
@Override
public synchronized Enumeration