*/
package jalview.bin;
-import jalview.datamodel.DBRefSource;
-import jalview.structure.StructureViewSettings;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.PDBEntry;
+import jalview.gui.Preferences;
+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.awt.Dimension;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
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;
* <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
* <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>
*
* </ul>
* Deprecated settings:
* panel in web service preferences</li>
* </ul>
*
- * @author $author$
- * @version $Revision$
*/
-public class Cache
+public class Cache implements ApplicationSingletonI
{
+
+ private Cache()
+ {
+ // private singleton
+ }
+
+ /**
+ * In Java, this will be a static field instance, which will be
+ * application-specific; in JavaScript it will be an applet-specific instance
+ * tied to the applet's ThreadGroup.
+ *
+ * @return
+ */
+ public static Cache getInstance()
+ {
+ return (Cache) ApplicationSingletonProvider.getInstance(Cache.class);
+ }
+
/**
* property giving log4j level for CASTOR loggers
*/
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
- public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
-
- public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
-
- public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
-
+ /**
+ * Sifts settings
+ */
public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
- .getProperty("user.home")
- + File.separatorChar
+ .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";
- private final static String DEFAULT_STRUCTURE_FORMAT = DBRefSource.PDB;
+ /**
+ * 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()
+ // BH 2019.05.08 was static
+ @SuppressWarnings("serial")
+ public Properties applicationProperties = new Properties()
{
// override results in properties output in alphabetical order
@Override
public synchronized Enumeration<Object> keys()
{
- return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+ return Collections.enumeration(new TreeSet<>(super.keySet()));
}
};
/** Default file is ~/.jalview_properties */
- static String propertiesFile;
+ private String propertiesFile;
- private static boolean propsAreReadOnly = false;
+ /**
+ * flag to possibly allow properties to be written to a property file
+ */
+ private boolean propsAreReadOnly = Platform.isJS();
+
+ private final static String JS_PROPERTY_PREFIX = "jalview_";
public static void initLogger()
{
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())));
+ laxis.setLevel(Level.toLevel(
+ getDefault("logs.Axis.Level", Level.INFO.toString())));
+ lcastor.setLevel(Level.toLevel(
+ 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.setLevel(Level.toLevel(
+ getDefault("logs.Castor.Level", Level.INFO.toString())));
// lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
- // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ // lcastor.setLevel(Level.toLevel(getDefault("logs.Castor.Level",
// Level.INFO.toString())));
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Jalview.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);
}
}
- /** Called when Jalview is started */
+ /**
+ * Loads properties from the given properties file. Any existing properties
+ * are first cleared.
+ */
public static void loadProperties(String propsFile)
{
+ getInstance().loadPropertiesImpl(propsFile);
+ }
+
+ private void loadPropertiesImpl(String propsFile)
+ {
propertiesFile = propsFile;
- if (propsFile == null)
- {
- propertiesFile = System.getProperty("user.home") + File.separatorChar
- + ".jalview_properties";
- }
- else
+ if (!propsAreReadOnly)
{
- // don't corrupt the file we've been given.
- propsAreReadOnly = true;
+ // Java only
+ 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
+ if (propertiesFile == null)
+ { // BH 2019 read properties from the Info object associated with this
+ // applet
+ 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;
- }
- if (fis == null)
- {
- fis = new FileInputStream(propertiesFile);
+ System.out.println("Error reading properties file: " + ex);
}
- 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);
}
// LOAD THE AUTHORS FROM THE authors.props file
+ String authorDetails = (Platform.isJS() ? null
+ : "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/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)
+ {
+ 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);
+ authorDetails = null;
+ }
+ if (authorDetails == null)
+ {
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 = (Platform.isJS() ? null
+ : "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/.build_properties")));
+ if (buildDetails != null)
{
- 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)
+ try
+ {
+ 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);
+ buildDetails = null;
+ }
+ }
+ if (buildDetails == null)
{
- 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");
}
new BuildDetails(codeVersion, null, codeInstallation);
- SiftsSettings
- .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+ SiftsSettings.setMapWithSifts(getDefault("MAP_WITH_SIFTS", false));
- SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
- "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+ 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.setFailSafePIDThreshold(
+ 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));
+ SiftsSettings.setCacheThresholdInDays(
+ getDefault("sifts_cache_threshold_in_days",
+ DEFAULT_CACHE_THRESHOLD_IN_DAYS));
+
+ IdOrgSettings.setUrl(getDefault(Preferences.ID_ORG_HOSTURL,
+ "http://www.jalview.org/services/identifiers"));
+ IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
- StructureViewSettings.setCurrentDefaultFormat(jalview.bin.Cache
- .getDefault(
- "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
+ StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
+ .getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT));
+ StructureImportSettings
+ .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(jalview.bin.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")))
+ if (jnlpVersion == null && !Jalview.isHeadlessMode()
+ && getDefault("VERSION_CHECK", true))
{
class VersionChecker extends Thread
{
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)
{
}
} catch (Exception ex)
{
- System.out
- .println("Non-fatal exception when checking version at www.jalview.org :");
+ System.out.println(
+ "Non-fatal exception when checking version at www.jalview.org :");
System.out.println(ex);
remoteVersion = getProperty("VERSION");
}
setProperty("VERSION", codeVersion);
// LOAD USERDEFINED COLOURS
- jalview.gui.UserDefinedColours
- .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
- jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
- false);
+ initUserColourSchemes(getProperty(Preferences.USER_DEFINED_COLOURS));
}
- private static void deleteBuildProperties()
+ private void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
applicationProperties.remove("VERSION");
*/
public static String getProperty(String key)
{
- return applicationProperties.getProperty(key);
+ return getInstance().applicationProperties.getProperty(key);
}
/**
- * These methods are used when checking if the saved preference is different
- * to the default setting
+ * Returns the boolean property value for the given property name. If the
+ * value is absent then the default value is returned instead.
+ *
+ * @param property
+ * @param def
+ * @return
*/
+ public static boolean getDefault(String property, final boolean def)
+ {
+ String string = getProperty(property);
+ return string == null ? def : Boolean.parseBoolean(string);
+ }
- public static boolean getDefault(String property, boolean def)
+ /**
+ * Returns the integer property value for the given property name. If the
+ * value is absent, or malformed (not an integer), then the default value is
+ * returned instead.
+ *
+ * @param property
+ * @param def
+ * @return
+ */
+ public static int getDefault(String property, final int def)
{
String string = getProperty(property);
if (string != null)
{
- def = Boolean.valueOf(string).booleanValue();
+ try
+ {
+ return 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
+ * retrieve a dimension, such as for Jmol
+ *
+ * @param property
+ * @param def
+ * @return
*/
- public static String getDefault(String property, String def)
+ public static Dimension getDefaultDim(String property, Dimension def)
{
- String string = getProperty(property);
- if (string != null)
+ String s = getProperty(property);
+ if (s != null)
{
- return string;
+ if (s.indexOf(',') < 0)
+ {
+ s = s.trim().replace(' ', ',');
+ if (s.indexOf(',') < 0)
+ {
+ s += "," + s;
+ }
+ }
+ try
+ {
+ int pt = s.indexOf(",");
+ return new Dimension(Integer.parseInt(s.substring(0, pt)),
+ Integer.parseInt(s.substring(pt + 1)));
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Error parsing Dimension property '" + property
+ + "' with value '" + s + "'");
+ }
}
-
return def;
}
/**
+ * Returns the value of the given property, or the supplied default value if
+ * the property is not set
+ *
+ * @param property
+ * @param def
+ * @return
+ */
+ public static String getDefault(String property, final String def)
+ {
+ String value = getProperty(property);
+ return value == null ? def : value;
+ }
+
+ /**
* Stores property in the file "HOME_DIR/.jalview_properties"
*
* @param key
* @param obj
* String value of property
*
- * @return String value of property
+ * @return previous value of property (or null)
+ */
+ public static Object setProperty(String key, String obj)
+ {
+ return getInstance().setPropertyImpl(key, obj, true);
+ }
+
+ /**
+ * Sets a property value for the running application, without saving it to the
+ * properties file
+ *
+ * @param key
+ * @param obj
*/
- public static String setProperty(String key, String obj)
+ public static void setPropertyNoSave(String key, String obj)
{
+ getInstance().setPropertyImpl(key, obj, false);
+ }
+ /**
+ * Sets a property value, and optionally also saves the current properties to
+ * file
+ *
+ * @param key
+ * @param obj
+ * @param andSave
+ * @return
+ */
+ private Object setPropertyImpl(String key, String obj, boolean andSave)
+ {
+ Object oldValue = null;
try
{
- applicationProperties.setProperty(key, obj);
- if (!propsAreReadOnly)
+ oldValue = applicationProperties.setProperty(key, obj);
+ if (andSave && !propsAreReadOnly && propertiesFile != null)
{
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;
}
/**
- * remove the specified property from the jalview properties file
+ * Removes the specified property from the jalview properties file
*
- * @param string
+ * @param key
*/
- public static void removeProperty(String string)
+ public static void removeProperty(String key)
{
- applicationProperties.remove(string);
- saveProperties();
+ getInstance().removePropertyImpl(key, true);
}
/**
- * save the properties to the jalview properties path
+ * Removes the named property for the running application, without saving the
+ * properties file
+ *
+ * @param key
+ */
+ public static void removePropertyNoSave(String key)
+ {
+ getInstance().removePropertyImpl(key, false);
+ }
+
+ /**
+ * Removes the named property, and optionally saves the current properties to
+ * file
+ *
+ * @param key
+ * @param andSave
+ */
+ private void removePropertyImpl(String key, boolean andSave)
+ {
+ applicationProperties.remove(key);
+ if (andSave)
+ {
+ savePropertiesImpl();
+ }
+ }
+
+ /**
+ * Saves the current properties to file
*/
public static void saveProperties()
{
+ getInstance().savePropertiesImpl();
+ }
+
+ /**
+ * save the properties to the jalview properties path
+ */
+ private void savePropertiesImpl()
+ {
if (!propsAreReadOnly)
{
try
}
}
+ private final static int UNTESTED = -1;
+
+ private final static int TRUE = 1;
+
+ private final static int FALSE = 0;
+
/**
* internal vamsas class discovery state
*/
- private static int vamsasJarsArePresent = -1;
+ private static int vamsasJarsArePresent = (Platform.isJS() ? FALSE
+ : UNTESTED);
/**
* Searches for vamsas client classes on class path.
*/
public static boolean vamsasJarsPresent()
{
- if (vamsasJarsArePresent == -1)
+ if (vamsasJarsArePresent == UNTESTED)
{
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)");
- vamsasJarsArePresent = 1;
+ jalview.bin.Cache.log.debug(
+ "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ vamsasJarsArePresent = TRUE;
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
}
} catch (Exception e)
{
- vamsasJarsArePresent = 0;
+ vamsasJarsArePresent = FALSE;
jalview.bin.Cache.log.debug("Vamsas Classes are not present");
}
}
- return (vamsasJarsArePresent > 0);
+ return (vamsasJarsArePresent == TRUE);
}
/**
* internal vamsas class discovery state
*/
- private static int groovyJarsArePresent = -1;
+ private static int groovyJarsArePresent = (Platform.isJS() ? FALSE
+ : UNTESTED);
/**
* Searches for vamsas client classes on class path.
*/
public static boolean groovyJarsPresent()
{
- if (groovyJarsArePresent == -1)
+ if (groovyJarsArePresent == UNTESTED)
{
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)");
- groovyJarsArePresent = 1;
+ jalview.bin.Cache.log.debug(
+ "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ groovyJarsArePresent = TRUE;
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
}
} catch (Error e)
{
- groovyJarsArePresent = 0;
+ groovyJarsArePresent = FALSE;
jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
- groovyJarsArePresent = 0;
+ groovyJarsArePresent = FALSE;
jalview.bin.Cache.log.debug("Groovy Classes are not present");
}
}
- return (groovyJarsArePresent > 0);
+ return (groovyJarsArePresent == TRUE);
}
/**
*/
protected static Object tracker = null;
- protected static Class trackerfocus = null;
+ protected static Class<?> trackerfocus = null;
- protected static Class jgoogleanalyticstracker = null;
+ protected static Class<?> jgoogleanalyticstracker = null;
/**
* Initialise the google tracker if it is not done already.
*/
public static void initGoogleTracker()
{
+
+ // TODO: SwingJS JavaScript tracker?
+
if (tracker == null)
{
if (jgoogleanalyticstracker == null)
// 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") + "_"
+ + 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();
}
}
/**
- * get the user's default colour if available
+ * Returns the Color value of the given property's value, or the supplied
+ * default colour if no property is found, or it cannot be parsed to a colour.
+ * Colours are normally saved as hex rgb values, though other formats may be
+ * parseable.
*
* @param property
- * @param defcolour
+ * @param defaultColour
* @return
+ * @see Cache#setColourPropertyNoSave(String, Color)
+ * @see ColorUtils#parseColourString(String)
*/
- public static Color getDefaultColour(String property, Color defcolour)
+ public static Color getDefaultColour(String property,
+ final Color defaultColour)
{
String colprop = getProperty(property);
if (colprop == null)
{
- return defcolour;
+ return defaultColour;
}
- 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;
+ return (col == null) ? defaultColour : col;
}
/**
- * store a colour as a Jalview user default property
+ * Stores a colour as a Jalview property, converted to hex values for rgb.
+ * Properties are not saved to file.
*
* @param property
* @param colour
*/
- public static void setColourProperty(String property, Color colour)
+ public static void setColourPropertyNoSave(String property, Color colour)
{
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.
+ * Updated properties are written out to the properties file.
*
- * @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.
}
if (value == null || value.trim().length() < 1)
{
- Cache.applicationProperties.remove(propName);
+ getInstance().applicationProperties.remove(propName);
}
else
{
- Cache.applicationProperties.setProperty(propName, value);
+ getInstance().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(Preferences.USER_DEFINED_COLOURS,
+ coloursFound.toString());
+ }
+ else
+ {
+ getInstance().applicationProperties
+ .remove(Preferences.USER_DEFINED_COLOURS);
+ }
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff