*/
package jalview.bin;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
-
import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.io.StringWriter;
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 java.util.regex.Pattern;
+
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+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;
+
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* list entries are separated by '|' symbols unless otherwise stated (|) clauses
* <li>SHOW_FULLSCREEN boolean</li>
* <li>FONT_NAME java font name for alignment text display</li>
* <li>FONT_SIZE size of displayed alignment text</li>
- * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
+ * <li>FONT_STYLE style of font displayed (sequence labels are always
+ * italic)</li>
* <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
* <li>LAST_DIRECTORY last directory for browsing alignment</li>
* <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
* service</li>
* <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
* collecting usage statistics</li>
- * <li>DAS_LOCAL_SOURCE list of local das sources</li>
* <li>SHOW_OVERVIEW boolean for overview window display</li>
* <li>ANTI_ALIAS boolean for smooth fonts</li>
* <li>RIGHT_ALIGN_IDS boolean</li>
* <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
* <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$</li>
+ * <li>STORED_LINKS list of name|url pairs which user has entered but are not
+ * currently used
+ * <li>DEFAULT_LINK name of single url to be used when user double clicks a
+ * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
* <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info</li>
- * <li>DAS_REGISTRY_URL the registry to query</li>
* <li>DEFAULT_BROWSER for unix</li>
- * <li>DAS_ACTIVE_SOURCE list of active sources</li>
* <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)</li>
* <li>VERSION_CHECK (true) check for the latest release version from
* when shading by annotation</li>
* <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
* when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
* <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
* alignment figure to accommodate even the longest sequence ID or annotation
* label.</li>
* <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
* display</li>
* <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
+ * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
+ * </li>
*
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
* </ul>
* Deprecated settings:
* <ul>
*/
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;
+
+ private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
- public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
+ private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
- public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+ /**
+ * 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
@Override
public synchronized Enumeration<Object> keys()
{
- return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+ return Collections.enumeration(new TreeSet<>(super.keySet()));
}
};
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");
// 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);
}
}
- /** 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;
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.");
+ 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 = new FileInputStream(propertiesFile);
}
+ applicationProperties.clear();
applicationProperties.load(fis);
// remove any old build properties
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);
// LOAD THE AUTHORS FROM THE authors.props file
try
{
- String authorDetails = "jar:".concat(Cache.class
- .getProtectionDomain().getCodeSource().getLocation()
- .toString().concat("!/authors.props"));
+ String authorDetails = "jar:"
+ .concat(Cache.class.getProtectionDomain().getCodeSource()
+ .getLocation().toString().concat("!/authors.props"));
java.net.URL localJarFileURL = new java.net.URL(authorDetails);
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"));
+ loadBuildProperties(false);
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", 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.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",
+ "https://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");
- 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);
- System.out
- .println("Jalview Version: " + codeVersion + codeInstallation);
- // jnlpVersion will be null if we're using InstallAnywhere
+ // 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
{
+
+ @Override
public void run()
{
+ String buildPropertiesUrl = Cache.getAppbaseBuildProperties();
+
String orgtimeout = System
.getProperty("sun.net.client.defaultConnectTimeout");
if (orgtimeout == null)
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")
- + "/webstart/jalview.jnlp");
- BufferedReader in = new BufferedReader(new InputStreamReader(
- url.openStream()));
- String line = null;
- while ((line = in.readLine()) != null)
- {
- if (line.indexOf("jalview.version") == -1)
- {
- continue;
- }
-
- line = line.substring(line.indexOf("value=") + 7);
- line = line.substring(0, line.lastIndexOf("\""));
- jnlpVersion = line;
- break;
- }
+ java.net.URL url = new java.net.URL(buildPropertiesUrl);
+
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(url.openStream()));
+
+ Properties remoteBuildProperties = new Properties();
+ remoteBuildProperties.load(in);
+ remoteVersion = remoteBuildProperties.getProperty("VERSION");
} catch (Exception ex)
{
System.out
- .println("Non-fatal exceptions when checking version at www.jalview.org :");
+ .println("Non-fatal exception when checking version at "
+ + buildPropertiesUrl + ":");
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);
}
}
}
}
- setProperty("VERSION", codeVersion);
-
// LOAD USERDEFINED COLOURS
- jalview.gui.UserDefinedColours
+ jalview.bin.Cache
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
false);
}
+ public static void loadBuildProperties(boolean reportVersion)
+ {
+ String codeInstallation = getProperty("INSTALLATION");
+ boolean printV = codeInstallation == null;
+
+ // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+ 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 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 (printV && reportVersion)
+ {
+ System.out.println(
+ "Jalview Version: " + codeVersion + codeInstallation);
+ }
+ }
+
private static void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
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
* @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---");
}
} 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;
}
/**
{
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
{
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
// 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;
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")
- + "_"
- + 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." }) });
+ 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." }) });
} catch (RuntimeException e)
{
re = e;
{
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();
}
{
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;
}
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
} catch (Exception ex)
{
System.err.println("Invalid or corrupt date in property '"
- + property + "' : value was '" + val + "'");
+ + propertyName + "' : value was '" + val + "'");
}
}
return null;
return null;
}
- private static DasSourceRegistryI sourceRegistry = null;
-
- /**
- * initialise and ..
- *
- * @return instance of the das source registry
- */
- public static DasSourceRegistryI getDasSourceRegistry()
- {
- if (sourceRegistry == null)
- {
- sourceRegistry = new DasSourceRegistry();
- }
- return sourceRegistry;
- }
-
/**
* Set the specified value, or remove it if null or empty. Does not save the
* properties file.
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);
+ }
+ }
+ }
+
+ /**
+ * 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;
+ }
+ 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: ");
+ sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append("\n");
+ sb.append("Jalview Installation: ");
+ sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append("\n");
+ sb.append("Build Date: ");
+ sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append("\n");
+ sb.append("Java version: ");
+ sb.append(System.getProperty("java.version"));
+ sb.append("\n");
+ 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");
+ // Not displayed in release version ( determined by possible version number
+ // regex 9[9.]*9[.-_a9]* )
+ if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
+ jalview.bin.Cache.getDefault("VERSION", "TEST")))
+ {
+ appendIfNotNull(sb, "Getdown appdir: ",
+ System.getProperty("getdownappdir"), "\n", null);
+ appendIfNotNull(sb, "Getdown appbase: ",
+ System.getProperty("getdownappbase"), "\n", null);
+ appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
+ "\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 jalview.bin.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();
+ }
+
+ /**
+ * Getdown appbase methods
+ */
+
+ private static final String releaseAppbase;
+
+ private static String getdownAppbase;
+
+ private static String getdownDistDir;
+
+ static
+ {
+ 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";
+ }
+
+ // 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 = 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";
+ }
}
git://source.jalview.org / jalview.git / blobdiff