*/
package jalview.bin;
-import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.datamodel.PDBEntry;
-import jalview.gui.Preferences;
+import jalview.gui.UserDefinedColours;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.UserColourScheme;
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;
* @author $author$
* @version $Revision$
*/
-public class Cache implements ApplicationSingletonI
+public class Cache
{
-
- 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
- */
- private static Cache getInstance()
- {
- return (Cache) ApplicationSingletonProvider.getInstance(Cache.class);
- }
-
/**
* property giving log4j level for CASTOR loggers
*/
public static Logger log;
/** Jalview Properties */
- // BH 2019.05.08 was static
- @SuppressWarnings("serial")
- private Properties applicationProperties = new Properties()
+ public static Properties applicationProperties = new Properties()
{
// override results in properties output in alphabetical order
@Override
};
/** Default file is ~/.jalview_properties */
- private String propertiesFile;
+ static String propertiesFile;
- /**
- * flag to possibly allow properties to be written to a property file
- */
- private boolean propsAreReadOnly = Platform.isJS();
+ private static boolean propsAreReadOnly = Platform.isJS();
private final static String JS_PROPERTY_PREFIX = "jalview_";
jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
laxis.setLevel(Level.toLevel(
- getDefault("logs.Axis.Level", Level.INFO.toString())));
- lcastor.setLevel(Level.toLevel(
- getDefault("logs.Castor.Level", Level.INFO.toString())));
+ 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(
- getDefault("logs.Castor.Level", Level.INFO.toString())));
+ lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ Level.INFO.toString())));
// lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
- // lcastor.setLevel(Level.toLevel(getDefault("logs.Castor.Level",
+ // 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())));
*/
public static void loadProperties(String propsFile)
{
- getInstance().loadPropertiesImpl(propsFile);
- }
-
- private void loadPropertiesImpl(String propsFile)
- {
propertiesFile = propsFile;
- if (!propsAreReadOnly)
+ if (propsFile == null && !propsAreReadOnly)
{
- // 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;
- }
+ propertiesFile = System.getProperty("user.home") + File.separatorChar
+ + ".jalview_properties";
+ }
+ else
+ {
+ // don't corrupt the file we've been given.
+ propsAreReadOnly = true;
}
if (propertiesFile == null)
- { // BH 2019 read properties from the Info object associated with this
- // applet
+ { // BH 2019
Platform.readInfoProperties(JS_PROPERTY_PREFIX,
applicationProperties);
}
}
if (authorDetails == null)
{
- applicationProperties.remove("AUTHORS");
- applicationProperties.remove("AUTHORFNAMES");
- applicationProperties.remove("YEAR");
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
}
// FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
}
if (buildDetails == null)
{
- applicationProperties.remove("VERSION");
+ applicationProperties.remove("VERSION");
}
String jnlpVersion = System.getProperty("jalview.version");
String codeVersion = getProperty("VERSION");
}
new BuildDetails(codeVersion, null, codeInstallation);
- SiftsSettings.setMapWithSifts(getDefault("MAP_WITH_SIFTS", false));
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
.getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setFailSafePIDThreshold(
- getDefault("sifts_fail_safe_pid_threshold",
+ jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
DEFAULT_FAIL_SAFE_PID_THRESHOLD));
SiftsSettings.setCacheThresholdInDays(
- getDefault("sifts_cache_threshold_in_days",
+ jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
- IdOrgSettings.setUrl(getDefault(Preferences.ID_ORG_HOSTURL,
+ IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
"http://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
.println("Jalview Version: " + codeVersion + codeInstallation);
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
- .getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT));
+ .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
- // .setDefaultPDBFileParser(jalview.bin.getDefault(
+ // .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 && !Jalview.isHeadlessMode()
- && 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
setProperty("VERSION", codeVersion);
// LOAD USERDEFINED COLOURS
- initUserColourSchemes(getProperty(Preferences.USER_DEFINED_COLOURS));
+ jalview.bin.Cache
+ .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+ jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+ false);
}
- private void deleteBuildProperties()
+
+ private static void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
applicationProperties.remove("VERSION");
*/
public static String getProperty(String key)
{
- return getInstance().applicationProperties.getProperty(key);
+ String prop = applicationProperties.getProperty(key);
+ if (prop == null && Platform.isJS())
+ {
+ prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+ + "_" + JS_PROPERTY_PREFIX + key);
+ }
+ return prop;
}
/**
}
/**
- * retrieve a dimension, such as for Jmol
- *
- * @param property
- * @param def
- * @return
- */
- public static Dimension getDefaultDim(String property, Dimension def)
- {
- String s = getProperty(property);
- if (s != null)
- {
- 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;
- }
-
- /**
* Answers the value of the given property, or the supplied default value if
* the property is not set
*/
*/
public static Object setProperty(String key, String obj)
{
- return getInstance().setPropertyImpl(key, obj, true);
- }
-
- public static void setPropertyNoSave(String key, String obj)
- {
- getInstance().setPropertyImpl(key, obj, false);
- }
-
- private Object setPropertyImpl(String key, String obj, boolean andSave)
- {
Object oldValue = null;
try
{
oldValue = applicationProperties.setProperty(key, obj);
- if (andSave && !propsAreReadOnly && propertiesFile != null)
+ if (!propsAreReadOnly)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
/**
* remove the specified property from the jalview properties file
*
- * @param key
+ * @param string
*/
- public static void removeProperty(String key)
+ public static void removeProperty(String string)
{
- getInstance().removePropertyImpl(key, true);
- }
-
- public static void removePropertyNoSave(String key)
- {
- getInstance().removePropertyImpl(key, false);
- }
-
- private void removePropertyImpl(String key, boolean andSave)
- {
- applicationProperties.remove(key);
- if (andSave)
- {
- savePropertiesImpl();
- }
- }
-
- public static void saveProperties()
- {
- getInstance().savePropertiesImpl();
+ applicationProperties.remove(string);
+ saveProperties();
}
/**
* save the properties to the jalview properties path
*/
- private void savePropertiesImpl()
+ public static void saveProperties()
{
if (!propsAreReadOnly)
{
}
}
- 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 = (Platform.isJS() ? FALSE
- : UNTESTED);
+ private static int vamsasJarsArePresent = -1;
/**
* Searches for vamsas client classes on class path.
*/
public static boolean vamsasJarsPresent()
{
- if (vamsasJarsArePresent == UNTESTED)
+ if (vamsasJarsArePresent == -1)
{
try
{
{
jalview.bin.Cache.log.debug(
"Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
- vamsasJarsArePresent = TRUE;
+ vamsasJarsArePresent = 1;
Logger lvclient = Logger.getLogger("uk.ac.vamsas");
lvclient.setLevel(Level.toLevel(Cache
.getDefault("logs.Vamsas.Level", Level.INFO.toString())));
}
} catch (Exception e)
{
- vamsasJarsArePresent = FALSE;
+ vamsasJarsArePresent = 0;
jalview.bin.Cache.log.debug("Vamsas Classes are not present");
}
}
- return (vamsasJarsArePresent == TRUE);
+ return (vamsasJarsArePresent > 0);
}
/**
* internal vamsas class discovery state
*/
- private static int groovyJarsArePresent = (Platform.isJS() ? FALSE
- : UNTESTED);
+ private static int groovyJarsArePresent = -1;
/**
* Searches for vamsas client classes on class path.
*/
public static boolean groovyJarsPresent()
{
- if (groovyJarsArePresent == UNTESTED)
+ if (groovyJarsArePresent == -1)
{
try
{
{
jalview.bin.Cache.log.debug(
"Found Groovy (groovy.lang.GroovyObject can be loaded)");
- groovyJarsArePresent = TRUE;
+ groovyJarsArePresent = 1;
Logger lgclient = Logger.getLogger("groovy");
lgclient.setLevel(Level.toLevel(Cache
.getDefault("logs.Groovy.Level", Level.INFO.toString())));
}
} catch (Error e)
{
- groovyJarsArePresent = FALSE;
+ groovyJarsArePresent = 0;
jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
- groovyJarsArePresent = FALSE;
+ groovyJarsArePresent = 0;
jalview.bin.Cache.log.debug("Groovy Classes are not present");
}
}
- return (groovyJarsArePresent == TRUE);
+ return (groovyJarsArePresent > 0);
}
/**
*/
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)
.newInstance(new Object[]
{ "Jalview Desktop",
(vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
- + getDefault("BUILD_DATE", "unknown")),
+ + jalview.bin.Cache.getDefault("BUILD_DATE",
+ "unknown")),
"UA-9060947-1" });
jgoogleanalyticstracker
.getMethod("trackAsynchronously", new Class[]
}
if (value == null || value.trim().length() < 1)
{
- getInstance().applicationProperties.remove(propName);
+ Cache.applicationProperties.remove(propName);
}
else
{
- getInstance().applicationProperties.setProperty(propName, value);
+ Cache.applicationProperties.setProperty(propName, value);
}
}
{
if (coloursFound.toString().length() > 1)
{
- setProperty(Preferences.USER_DEFINED_COLOURS,
+ setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
coloursFound.toString());
}
else
{
- getInstance().applicationProperties
- .remove(Preferences.USER_DEFINED_COLOURS);
+ applicationProperties
+ .remove(UserDefinedColours.USER_DEFINED_COLOURS);
}
}
}
git://source.jalview.org / jalview.git / blobdiff