X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=85d23dffdeb016685027c6fed7d2c47c2dc0a8f9;hb=1d293bcfa2988c7fe62a48efd663074b9adb4eb3;hp=a48b750f08e23f7bb2814ad2ddd4b0f341fc39a3;hpb=6a1564abce042be6eb37fd3ae883921e00a2bd0c;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index a48b750..85d23df 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
@@ -20,8 +20,16 @@
*/
package jalview.bin;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+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.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
import java.awt.Color;
import java.io.BufferedReader;
@@ -30,12 +38,15 @@ import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.net.URL;
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.Properties;
+import java.util.StringTokenizer;
import java.util.TreeSet;
import org.apache.log4j.ConsoleAppender;
@@ -66,7 +77,8 @@ import org.apache.log4j.SimpleLayout;
*
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)
+ * 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
@@ -104,7 +116,6 @@ import org.apache.log4j.SimpleLayout;
* service
* USAGESTATS (false - user prompted) Enable google analytics tracker for
* collecting usage statistics
- * 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
@@ -118,11 +129,13 @@ import org.apache.log4j.SimpleLayout;
* 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
- * 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)
* VERSION_CHECK (true) check for the latest release version from
@@ -150,6 +163,7 @@ import org.apache.log4j.SimpleLayout;
* 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
@@ -173,6 +187,9 @@ import org.apache.log4j.SimpleLayout;
* 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:
@@ -208,11 +225,40 @@ public class Cache
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
- public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
+ /**
+ * Sifts settings
+ */
+ public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
+ .getProperty("user.home") + File.separatorChar
+ + ".sifts_downloads" + File.separatorChar;
- public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
+ private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
- public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+ 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
@@ -220,18 +266,22 @@ public class Cache
public static Logger log;
/** Jalview Properties */
- public static Properties applicationProperties = new 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()));
+ public synchronized Enumeration keys()
+ {
+ return Collections.enumeration(new TreeSet<>(super.keySet()));
}
};
/** Default file is ~/.jalview_properties */
static String propertiesFile;
- private static boolean propsAreReadOnly = false;
+ private static boolean propsAreReadOnly = Platform.isJS();
+
+ private final static String JS_PROPERTY_PREFIX = "jalview_";
public static void initLogger()
{
@@ -253,8 +303,8 @@ public class Cache
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())));
+ 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");
@@ -263,8 +313,11 @@ public class Cache
// 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())));
+ // we shouldn't need to do this
+ org.apache.log4j.Logger.getRootLogger().setLevel(org.apache.log4j.Level.INFO);
+
+ 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);
@@ -277,11 +330,14 @@ public class Cache
}
}
- /** Called when Jalview is started */
+ /**
+ * Loads properties from the given properties file. Any existing properties
+ * are first cleared.
+ */
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
- if (propsFile == null)
+ if (propsFile == null && !propsAreReadOnly)
{
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ ".jalview_properties";
@@ -292,41 +348,49 @@ public class Cache
propsAreReadOnly = true;
}
- try
+ if (propertiesFile == null)
+ { // BH 2019
+ Platform.readInfoProperties(JS_PROPERTY_PREFIX,
+ applicationProperties);
+ }
+ else
{
- 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;
+ 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)
{
- fis = null;
+ System.out.println("Error reading properties file: " + ex);
}
- if (fis == null)
- {
- fis = new FileInputStream(propertiesFile);
- }
- 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");
+ String proxyServer = getDefault("PROXY_SERVER", ""),
+ proxyPort = getDefault("PROXY_PORT", "8080");
System.out.println("Using proxyServer: " + proxyServer
+ " proxyPort: " + proxyPort);
@@ -336,67 +400,70 @@ public class Cache
}
// LOAD THE AUTHORS FROM THE authors.props file
+ String authorDetails = resolveResourceURLFor("/authors.props");
+
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();
+ if (authorDetails != null)
+ {
+ URL localJarFileURL = new 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");
+ authorDetails = 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
+ if (authorDetails == null)
{
- String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/.build_properties"));
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
+ }
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+ loadBuildProperties(false);
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading build details: " + ex);
- applicationProperties.remove("VERSION");
- }
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
- String jnlpVersion = System.getProperty("jalview.version");
- String codeVersion = getProperty("VERSION");
+ SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
- if (codeVersion == null)
- {
- // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
- codeVersion = "Test";
- jnlpVersion = "Test";
- }
+ SiftsSettings.setFailSafePIDThreshold(
+ jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+ DEFAULT_FAIL_SAFE_PID_THRESHOLD));
- System.out.println("Jalview Version: " + codeVersion);
+ SiftsSettings.setCacheThresholdInDays(
+ jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+ DEFAULT_CACHE_THRESHOLD_IN_DAYS));
- // jnlpVersion will be null if we're using InstallAnywhere
+ IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
+ "http://www.jalview.org/services/identifiers"));
+ IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
+
+ 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));
+
+ 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)
+
+ if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
{
-
- class VersionChecker extends Thread
+ new Thread()
{
+ @Override
public void run()
{
String orgtimeout = System
@@ -407,16 +474,16 @@ public class Cache
System.out.println("# INFO: Setting default net timeout to "
+ orgtimeout + " seconds.");
}
- String jnlpVersion = null;
+ 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")
+ 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()));
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(url.openStream()));
String line = null;
while ((line = in.readLine()) != null)
{
@@ -427,25 +494,22 @@ public class Cache
line = line.substring(line.indexOf("value=") + 7);
line = line.substring(0, line.lastIndexOf("\""));
- jnlpVersion = line;
+ remoteVersion = line;
break;
}
} catch (Exception ex)
{
- System.out
- .println("Non-fatal exceptions when checking version at www.jalview.org :");
+ System.out.println(
+ "Non-fatal exception when checking version at www.jalview.org :");
System.out.println(ex);
- jnlpVersion = getProperty("VERSION");
+ remoteVersion = getProperty("VERSION");
}
System.setProperty("sun.net.client.defaultConnectTimeout",
orgtimeout);
- setProperty("LATEST_VERSION", jnlpVersion);
+ setProperty("LATEST_VERSION", remoteVersion);
}
- }
-
- VersionChecker vc = new VersionChecker();
- vc.start();
+ }.start();
}
else
{
@@ -459,15 +523,84 @@ public class Cache
}
}
- setProperty("VERSION", codeVersion);
-
// LOAD USERDEFINED COLOURS
- jalview.gui.UserDefinedColours
- .initUserColourSchemes(getProperty("USER_DEFINED_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)
+ {
+ System.err.println("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();
+ applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("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)
+ {
+ System.out
+ .println("Jalview Version: " + codeVersion + codeInstallation);
+ }
+ }
+
private static void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
@@ -475,6 +608,8 @@ public class Cache
applicationProperties.remove("AUTHORS");
applicationProperties.remove("AUTHORFNAMES");
applicationProperties.remove("YEAR");
+ applicationProperties.remove("BUILD_DATE");
+ applicationProperties.remove("INSTALLATION");
}
/**
@@ -488,7 +623,13 @@ public class Cache
*/
public static String getProperty(String key)
{
- return applicationProperties.getProperty(key);
+ String prop = applicationProperties.getProperty(key);
+ if (prop == null && Platform.isJS())
+ {
+ prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+ + "_" + JS_PROPERTY_PREFIX + key);
+ }
+ return prop;
}
/**
@@ -507,22 +648,35 @@ public class Cache
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)
+ public static int getDefault(String property, int def)
{
String string = getProperty(property);
if (string != null)
{
- return string;
+ try
+ {
+ def = Integer.parseInt(string);
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Error parsing int 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
@@ -530,15 +684,15 @@ public class Cache
* @param obj
* String value of property
*
- * @return String value of property
+ * @return previous value of property (or null)
*/
- public static String setProperty(String key, String obj)
+ public static Object setProperty(String key, String obj)
{
-
+ Object oldValue = null;
try
{
- applicationProperties.setProperty(key, obj);
- if (!propsAreReadOnly)
+ oldValue = applicationProperties.setProperty(key, obj);
+ if (propertiesFile != null && !propsAreReadOnly)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
@@ -546,10 +700,10 @@ public class Cache
}
} 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;
+ return oldValue;
}
/**
@@ -598,15 +752,15 @@ public class Cache
{
try
{
- if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
- "uk.ac.vamsas.client.VorbaId") != null)
+ 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)");
+ 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
@@ -637,15 +791,15 @@ public class Cache
{
try
{
- if (Cache.class.getClassLoader().loadClass(
- "groovy.lang.GroovyObject") != null)
+ if (Cache.class.getClassLoader()
+ .loadClass("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
@@ -686,15 +840,14 @@ public class Cache
// try to get the tracker class
try
{
- jgoogleanalyticstracker = Cache.class
- .getClassLoader()
- .loadClass(
- "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
- trackerfocus = Cache.class.getClassLoader().loadClass(
- "com.boxysystems.jgoogleanalytics.FocusPoint");
+ jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
+ "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+ trackerfocus = Cache.class.getClassLoader()
+ .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
} catch (Exception e)
{
- log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ log.debug(
+ "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
tracker = null;
jgoogleanalyticstracker = null;
trackerfocus = null;
@@ -708,21 +861,22 @@ public class Cache
try
{
// Google analytics tracking code for Library Finder
- tracker = jgoogleanalyticstracker.getConstructor(new Class[]
- { String.class, String.class, String.class }).newInstance(
- new Object[]
- {
- "Jalview Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION")
- + "_"
+ tracker = jgoogleanalyticstracker
+ .getConstructor(new Class[]
+ { String.class, String.class, String.class })
+ .newInstance(new Object[]
+ { "Jalview Desktop",
+ (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
+ jalview.bin.Cache.getDefault("BUILD_DATE",
- "unknown")), "UA-9060947-1" });
- jgoogleanalyticstracker.getMethod("trackAsynchronously",
- new Class[]
- { trackerfocus }).invoke(tracker, new Object[]
- { trackerfocus.getConstructor(new Class[]
- { String.class }).newInstance(new Object[]
- { "Application Started." }) });
+ "unknown")),
+ "UA-9060947-1" });
+ jgoogleanalyticstracker
+ .getMethod("trackAsynchronously", new Class[]
+ { trackerfocus })
+ .invoke(tracker, new Object[]
+ { trackerfocus.getConstructor(new Class[] { String.class })
+ .newInstance(new Object[]
+ { "Application Started." }) });
} catch (RuntimeException e)
{
re = e;
@@ -739,42 +893,45 @@ public class Cache
{
if (re != null)
{
- log.debug("Caught runtime exception in googletracker init:", re);
+ log.debug("Caught runtime exception in googletracker init:",
+ re);
}
if (ex != null)
{
log.warn(
"Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs, ex);
+ + vrs,
+ ex);
}
if (err != null)
{
log.error(
"Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs, err);
+ + vrs,
+ err);
}
}
else
{
if (re != null)
{
- System.err
- .println("Debug: Caught runtime exception in googletracker init:"
+ System.err.println(
+ "Debug: Caught runtime exception in googletracker init:"
+ vrs);
re.printStackTrace();
}
if (ex != null)
{
- System.err
- .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
+ System.err.println(
+ "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
+ vrs);
ex.printStackTrace();
}
if (err != null)
{
- System.err
- .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+ System.err.println(
+ "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+ vrs);
err.printStackTrace();
}
@@ -801,19 +958,11 @@ public class Cache
{
return defcolour;
}
- Color col = jalview.schemes.ColourSchemeProperty
- .getAWTColorFromName(colprop);
+ Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- try
- {
- col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
- } catch (Exception ex)
- {
- log.warn("Couldn't parse '" + colprop + "' as a colour for "
- + property);
- col = null;
- }
+ log.warn("Couldn't parse '" + colprop + "' as a colour for "
+ + property);
}
return (col == null) ? defcolour : col;
}
@@ -829,30 +978,31 @@ public class Cache
setProperty(property, jalview.util.Format.getHexString(colour));
}
- public static final DateFormat date_format = SimpleDateFormat
- .getDateTimeInstance();
-
/**
- * store a date in a jalview property
+ * Stores a formatted date in a jalview property, using a fixed locale.
*
- * @param string
- * @param time
+ * @param propertyName
+ * @param date
+ * @return the formatted date string
*/
- public static void setDateProperty(String property, Date time)
+ public static String setDateProperty(String propertyName, Date date)
{
- setProperty(property, date_format.format(time));
+ String formatted = date_format.format(date);
+ setProperty(propertyName, formatted);
+ return formatted;
}
/**
- * read a date stored in a jalview property
+ * 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 property
- * @return valid date as stored by setDateProperty, or null
+ * @param propertyName
+ * @return
*
*/
- public static Date getDateProperty(String property)
+ public static Date getDateProperty(String propertyName)
{
- String val = getProperty(property);
+ String val = getProperty(propertyName);
if (val != null)
{
try
@@ -861,7 +1011,7 @@ public class Cache
} catch (Exception ex)
{
System.err.println("Invalid or corrupt date in property '"
- + property + "' : value was '" + val + "'");
+ + propertyName + "' : value was '" + val + "'");
}
}
return null;
@@ -891,19 +1041,140 @@ public class Cache
return null;
}
- private static DasSourceRegistryI sourceRegistry = 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)
+ {
+ System.out.println("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);
+ }
+ }
+ }
/**
- * initialise and ..
+ * Initial logging information helper for various versions output
*
- * @return instance of the das source registry
+ * @param prefix
+ * @param value
+ * @param defaultValue
*/
- public static DasSourceRegistryI getDasSourceRegistry()
+ private static void appendIfNotNull(StringBuilder sb, String prefix,
+ String value, String suffix, String defaultValue)
{
- if (sourceRegistry == null)
+ if (value == null && defaultValue == null)
{
- sourceRegistry = new DasSourceRegistry();
+ return;
+ }
+ String line = prefix + (value != null ? value : defaultValue) + suffix;
+ sb.append(line);
+ }
+
+ /**
+ *
+ * @return Jalview version, build details and JVM platform version for console
+ */
+ public static String getVersionDetailsForConsole()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append("\n");
+ sb.append("Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append("\n");
+ sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append("\n");
+ sb.append("Java version: " + System.getProperty("java.version"));
+ sb.append("\n");
+ sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + 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);
+ if (jalview.bin.Cache.getDefault("VERSION", "TEST").equals("DEVELOPMENT")) {
+ appendIfNotNull(sb, "Getdown appdir: ",
+ System.getProperty("getdownappdir"), "\n", null);
+ appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
+ "\n", "unknown");
}
- return sourceRegistry;
+ 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 jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
}
}