X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=07e346f6a2c977f2b8323353f9f2bcbf0a29ff3f;hb=76f9992a5fd8e818f8051130e25c6aefb4ef51ad;hp=b2f6e95271f8338d6fff2987740a925929395b6c;hpb=5721b73c6d5de84b21a989a8734e4c161f5dc630;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index b2f6e95..07e346f 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -20,8 +20,9 @@ */ package jalview.bin; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; import jalview.datamodel.PDBEntry; -import jalview.gui.UserDefinedColours; +import jalview.gui.Preferences; import jalview.schemes.ColourSchemeLoader; import jalview.schemes.ColourSchemes; import jalview.schemes.UserColourScheme; @@ -32,6 +33,7 @@ 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; @@ -204,13 +206,14 @@ import org.apache.log4j.SimpleLayout; * panel in web service preferences * * - * @author $author$ - * @version $Revision$ */ -public class Cache +public class Cache implements ApplicationSingletonI { - static Cache instance; + private Cache() + { + // private singleton + } /** * In Java, this will be a static field instance, which will be @@ -221,36 +224,7 @@ public class Cache */ public static Cache getInstance() { - - // BH 2019.05.08 need to isolate static fields in JavaScript - - Cache i = instance; - @SuppressWarnings("unused") - ThreadGroup g = null; - if (Platform.isJS()) - { - g = Thread.currentThread().getThreadGroup(); - /** - * @j2sNative i = g._jalviewCacheInstance; - * - */ - } - if (i == null) - { - i = new Cache(); - if (Platform.isJS()) - { - /** - * @j2sNative g._jalviewCacheInstance = i; - * - */ - } - else - { - instance = i; - } - } - return i; + return (Cache) ApplicationSingletonProvider.getInstance(Cache.class); } /** @@ -308,15 +282,10 @@ public class Cache */ public static Logger log; - private Cache() - { - // inaccessible - } - /** Jalview Properties */ // BH 2019.05.08 was static @SuppressWarnings("serial") - private Properties applicationProperties = new Properties() + public Properties applicationProperties = new Properties() { // override results in properties output in alphabetical order @Override @@ -327,8 +296,7 @@ public class Cache }; /** Default file is ~/.jalview_properties */ - // BH 2019.05.07 note: Instances of Jalview will share this file. - static String propertiesFile; + private String propertiesFile; /** * flag to possibly allow properties to be written to a property file @@ -358,14 +326,14 @@ public class Cache 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()))); + 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()))); @@ -528,21 +496,20 @@ public class Cache } 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.setFailSafePIDThreshold( - jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold", + getDefault("sifts_fail_safe_pid_threshold", DEFAULT_FAIL_SAFE_PID_THRESHOLD)); SiftsSettings.setCacheThresholdInDays( - jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days", + 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); @@ -550,11 +517,11 @@ public class Cache .println("Jalview Version: " + codeVersion + codeInstallation); 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 - // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( + // .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 @@ -630,13 +597,9 @@ public class Cache setProperty("VERSION", codeVersion); // LOAD USERDEFINED COLOURS - jalview.bin.Cache - .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); - jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", - false); + initUserColourSchemes(getProperty(Preferences.USER_DEFINED_COLOURS)); } - private void deleteBuildProperties() { applicationProperties.remove("LATEST_VERSION"); @@ -659,59 +622,93 @@ public class Cache */ public static String getProperty(String key) { - return getInstance().getPropertyImpl(key); + return getInstance().applicationProperties.getProperty(key); } - private String getPropertyImpl(String key) + /** + * 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 prop = applicationProperties.getProperty(key); - if (prop == null && Platform.isJS()) - { - prop = applicationProperties.getProperty(Platform.getUniqueAppletID() - + "_" + JS_PROPERTY_PREFIX + key); - } - return prop; + String string = getProperty(property); + return string == null ? def : Boolean.parseBoolean(string); } /** - * These methods are used when checking if the saved preference is different - * to the default setting + * 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 boolean getDefault(String property, boolean def) + 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; } - public static int getDefault(String property, int def) + /** + * retrieve a dimension, such as for Jmol + * + * @param property + * @param def + * @return + */ + public static Dimension getDefaultDim(String property, Dimension def) { - String string = getProperty(property); - if (string != null) + String s = getProperty(property); + if (s != null) { + if (s.indexOf(',') < 0) + { + s = s.trim().replace(' ', ','); + if (s.indexOf(',') < 0) + { + s += "," + s; + } + } try { - def = Integer.parseInt(string); + 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 int property '" + property - + "' with value '" + string + "'"); + 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 + * 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) + public static String getDefault(String property, final String def) { String value = getProperty(property); return value == null ? def : value; @@ -732,18 +729,34 @@ public class Cache 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 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 (andSave && !propsAreReadOnly) + if (andSave && !propsAreReadOnly && propertiesFile != null) { FileOutputStream out = new FileOutputStream(propertiesFile); applicationProperties.store(out, "---JalviewX Properties File---"); @@ -758,7 +771,7 @@ public class Cache } /** - * remove the specified property from the jalview properties file + * Removes the specified property from the jalview properties file * * @param key */ @@ -767,11 +780,24 @@ public class Cache getInstance().removePropertyImpl(key, true); } + /** + * 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); @@ -781,6 +807,9 @@ public class Cache } } + /** + * Saves the current properties to file + */ public static void saveProperties() { getInstance().savePropertiesImpl(); @@ -947,8 +976,7 @@ public class Cache .newInstance(new Object[] { "Jalview Desktop", (vrs = jalview.bin.Cache.getProperty("VERSION") + "_" - + jalview.bin.Cache.getDefault("BUILD_DATE", - "unknown")), + + getDefault("BUILD_DATE", "unknown")), "UA-9060947-1" }); jgoogleanalyticstracker .getMethod("trackAsynchronously", new Class[] @@ -1025,18 +1053,24 @@ public class Cache } /** - * 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 = ColorUtils.parseColourString(colprop); if (col == null) @@ -1044,22 +1078,24 @@ public class Cache 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)); } /** * 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 @@ -1185,13 +1221,13 @@ public class Cache { if (coloursFound.toString().length() > 1) { - setProperty(UserDefinedColours.USER_DEFINED_COLOURS, + setProperty(Preferences.USER_DEFINED_COLOURS, coloursFound.toString()); } else { getInstance().applicationProperties - .remove(UserDefinedColours.USER_DEFINED_COLOURS); + .remove(Preferences.USER_DEFINED_COLOURS); } } }