*/
package jalview.bin;
-import jalview.datamodel.PDBEntry;
-import jalview.gui.UserDefinedColours;
-import jalview.schemes.ColourSchemeLoader;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureImportSettings;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ColorUtils;
-import jalview.ws.sifts.SiftsSettings;
-
import java.awt.Color;
+import java.awt.Dimension;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.net.URL;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Collections;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+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;
+
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* list entries are separated by '|' symbols unless otherwise stated (|) clauses
* @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 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
};
/** Default file is ~/.jalview_properties */
- static String propertiesFile;
+ // BH 2020 private, not static
+ private 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()
{
*/
public static void loadProperties(String propsFile)
{
+ getInstance().loadPropertiesImpl(propsFile);
+ }
+
+ private void loadPropertiesImpl(String propsFile)
+ {
propertiesFile = propsFile;
- if (propsFile == null)
+ if (propsFile == null && !propsAreReadOnly)
{
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
+ Platform.readInfoProperties(JS_PROPERTY_PREFIX,
+ applicationProperties);
}
else
{
- // don't corrupt the file we've been given.
- propsAreReadOnly = true;
- }
-
- try
- {
- InputStream fis;
try
{
- fis = new java.net.URL(propertiesFile).openStream();
- System.out.println(
- "Loading jalview properties from : " + propertiesFile);
- System.out.println(
- "Disabling Jalview writing to user's local properties file.");
- propsAreReadOnly = true;
+ 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.clear();
- applicationProperties.load(fis);
-
- // remove any old build properties
-
- deleteBuildProperties();
- fis.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading properties file: " + ex);
}
-
if (getDefault("USE_PROXY", false))
{
String proxyServer = getDefault("PROXY_SERVER", ""),
}
// LOAD THE AUTHORS FROM THE authors.props file
+ String authorDetails = (Platform.isJS() ? null
+ : 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);
+ authorDetails = null;
+ }
+ if (authorDetails == null)
+ {
applicationProperties.remove("AUTHORS");
applicationProperties.remove("AUTHORFNAMES");
applicationProperties.remove("YEAR");
jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
- IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
+ IdOrgSettings.setUrl(getDefault(Preferences.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));
+ .getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
{
-
- class VersionChecker extends Thread
+ new Thread()
{
@Override
public void run()
setProperty("LATEST_VERSION", remoteVersion);
}
- }
-
- VersionChecker vc = new VersionChecker();
- vc.start();
+ }.start();
}
else
{
}
// LOAD USERDEFINED COLOURS
- jalview.bin.Cache
- .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+ 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
+ /**
+ * construct a resource URL for the given absolute resource pathname
+ *
+ * @param resourcePath
+ * @return
+ */
+ private static String resolveResourceURLFor(String resourcePath)
{
- String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/.build_properties"));
-
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+ 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;
+ }
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
+ public static void loadBuildProperties(boolean reportVersion)
{
- System.out.println("Error reading build details: " + ex);
- applicationProperties.remove("VERSION");
+ 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();
+ getInstance().applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading build details: " + ex);
+ getInstance().applicationProperties.remove("VERSION");
}
String codeVersion = getProperty("VERSION");
codeInstallation = getProperty("INSTALLATION");
}
setProperty("VERSION", codeVersion);
new BuildDetails(codeVersion, null, codeInstallation);
- if (printV && reportVersion)
+ if (printVersion && reportVersion)
{
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
}
}
- private static void deleteBuildProperties()
+ // BH 2020 was static
+ 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);
+
+// old, original idea:
+// String prop = applicationProperties.getProperty(key);
+// if (prop == null && Platform.isJS())
+// {
+// prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+// + "_" + JS_PROPERTY_PREFIX + key);
+// }
+// return prop;
+
}
+
+ //These methods are used when checking if the saved preference is different
+ // to the default setting
+
/**
- * 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, boolean def)
{
String string = getProperty(property);
- if (string != null)
- {
- def = Boolean.valueOf(string).booleanValue();
- }
-
- return def;
+ // BH simplification only
+ return string == null ? def : Boolean.parseBoolean(string);
}
+ /**
+ * 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, int def)
{
String string = getProperty(property);
{
try
{
- def = Integer.parseInt(string);
+ // BH simplification only
+
+ return Integer.parseInt(string);
} catch (NumberFormatException e)
{
System.out.println("Error parsing int property '" + property
}
/**
- * These methods are used when checking if the saved preference is different
- * to the default setting
+ * 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, String def)
{
- String string = getProperty(property);
- if (string != null)
- {
- return string;
- }
-
- return def;
+ String value = getProperty(property);
+ return value == null ? def : value;
}
/**
*/
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.
+ *
+ * Replaces direct call to Cache.applicationProperties.setProperty
+ *
+ * Used extensively in AppletParams and Preferences.ok_actionPerformed
+ *
+ *
+ * @param key
+ * @param 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
{
oldValue = applicationProperties.setProperty(key, obj);
- if (propertiesFile != null && !propsAreReadOnly)
+ if (andSave && !propsAreReadOnly && propertiesFile != null)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
}
/**
- * 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.
+ *
+ * Called by Preferences.ok_actionPerformed specifically for SEQUENCE_LINKS and STORED_LINKS.
+ *
+ *
+ * @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
{
{
jalview.bin.Cache.log.debug(
"Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
- vamsasJarsArePresent = 1;
+ vamsasJarsArePresent = TRUE;
Logger lvclient = Logger.getLogger("uk.ac.vamsas");
lvclient.setLevel(Level.toLevel(Cache
.getDefault("logs.Vamsas.Level", Level.INFO.toString())));
}
} 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
{
{
jalview.bin.Cache.log.debug(
"Found Groovy (groovy.lang.GroovyObject can be loaded)");
- groovyJarsArePresent = 1;
+ groovyJarsArePresent = TRUE;
Logger lgclient = Logger.getLogger("groovy");
lgclient.setLevel(Level.toLevel(Cache
.getDefault("logs.Groovy.Level", Level.INFO.toString())));
}
} 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)
}
/**
- * 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
}
/**
+ * Stores a colour as a Jalview property, converted to hex values for rgb.
+ * Properties are not saved to file.
+ *
+ *
+ *
+ * Used extensively in Preferences.ok_actionPerformed
+ *
+ * @param property
+ * @param colour
+ */
+ public static void setColourPropertyNoSave(String property, Color colour)
+ {
+ setPropertyNoSave(property, jalview.util.Format.getHexString(colour));
+ }
+
+ /**
* store a colour as a Jalview user default property
*
* @param property
/**
* Stores a formatted date in a jalview property, using a fixed locale.
+ * Updated properties are written out to the properties file.
*
* @param propertyName
* @param date
}
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);
}
}
{
if (coloursFound.toString().length() > 1)
{
- setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
+ // BH moved to Preferences for consistency
+ setProperty(Preferences.USER_DEFINED_COLOURS,
coloursFound.toString());
}
else
{
- applicationProperties
- .remove(UserDefinedColours.USER_DEFINED_COLOURS);
+ // BH moved to Preferences for consistency
+ getInstance().applicationProperties
+ .remove(Preferences.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
*/
sb.append("\n");
sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version"));
sb.append("\n");
- System.out.println("Install4j version: "
- + System.getProperty("sys.install4jVersion"));
- System.out.println("Install4j template version: "
- + System.getProperty("installer_template_version"));
- System.out.println(
- "Launcher version: " + System.getProperty("launcher_version"));
-
+ 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")) {
- sb.append("Getdown appdir: " + System.getProperty("getdownappdir"));
- sb.append("\n");
- sb.append("Java home: " + System.getProperty("java.home"));
- sb.append("\n");
+ appendIfNotNull(sb, "Getdown appdir: ",
+ System.getProperty("getdownappdir"), "\n", null);
+ appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
+ "\n", "unknown");
}
return sb.toString();
}
// eg 'built from Source' or update channel
return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
}
+
+ /**
+ * 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;
+ }
+
+
}
git://source.jalview.org / jalview.git / blobdiff