X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=07e346f6a2c977f2b8323353f9f2bcbf0a29ff3f;hb=76f9992a5fd8e818f8051130e25c6aefb4ef51ad;hp=23277a42bb7552ec6ab286bf5c1b2c2a434c0b6e;hpb=0555b298d22be533a0a67a3cd0ce2db883bae8bd;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 23277a4..07e346f 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -20,12 +20,20 @@ */ package jalview.bin; +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.ws.dbsources.das.api.DasSourceRegistryI; -import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; +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; @@ -37,7 +45,9 @@ 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 org.apache.log4j.ConsoleAppender; @@ -68,7 +78,8 @@ import org.apache.log4j.SimpleLayout; *
  • SHOW_FULLSCREEN boolean
    • *
  • FONT_NAME java font name for alignment text display
    • *
  • FONT_SIZE size of displayed alignment text
    • - *
  • FONT_STYLE style of font displayed (sequence labels are always italic)
    • + *
  • FONT_STYLE style of font displayed (sequence labels are always + * italic)
    • *
  • GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
    • *
  • LAST_DIRECTORY last directory for browsing alignment
    • *
  • USER_DEFINED_COLOURS list of user defined colour scheme files
    • @@ -106,7 +117,6 @@ import org.apache.log4j.SimpleLayout; * service *
  • USAGESTATS (false - user prompted) Enable google analytics tracker for * collecting usage statistics
    • - *
  • DAS_LOCAL_SOURCE list of local das sources
    • *
  • SHOW_OVERVIEW boolean for overview window display
    • *
  • ANTI_ALIAS boolean for smooth fonts
    • *
  • RIGHT_ALIGN_IDS boolean
    • @@ -120,11 +130,13 @@ import org.apache.log4j.SimpleLayout; *
  • SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
    • *
  • SEQUENCE_LINKS list of name|URL pairs for opening a url with * $SEQUENCE_ID$
    • + *
  • STORED_LINKS list of name|url pairs which user has entered but are not + * currently used + *
  • DEFAULT_LINK name of single url to be used when user double clicks a + * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS) *
  • GROUP_LINKS list of name|URL[|<separator>] tuples - see * jalview.utils.GroupURLLink for more info
    • - *
  • DAS_REGISTRY_URL the registry to query
    • *
  • DEFAULT_BROWSER for unix
    • - *
  • DAS_ACTIVE_SOURCE list of active sources
    • *
  • SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop * (false)
    • *
  • VERSION_CHECK (true) check for the latest release version from @@ -177,6 +189,8 @@ import org.apache.log4j.SimpleLayout; *
  • STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure * display
    • *
  • CHIMERA_PATH specify full path to Chimera program (if non-standard)
    • + *
  • ID_ORG_HOSTURL location of jalview service providing identifiers.org urls + *
    • * * * Deprecated settings: @@ -192,11 +206,27 @@ import org.apache.log4j.SimpleLayout; * panel in web service preferences * * - * @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 */ @@ -212,24 +242,40 @@ public class Cache */ 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 = StructureImportSettings.MMCIF; - - private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.JMOL_PARSER; + /** + * 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 @@ -237,20 +283,27 @@ public class Cache 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 keys() { - return Collections.enumeration(new TreeSet(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() { @@ -272,18 +325,18 @@ public class Cache 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); @@ -296,56 +349,77 @@ public class Cache } } - /** 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); @@ -355,20 +429,27 @@ public class Cache } // 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"); @@ -377,23 +458,28 @@ public class Cache // 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"); @@ -410,37 +496,37 @@ 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.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); StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache - .getDefault( - "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT)); + .getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT)); StructureImportSettings - .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( - "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); - StructureImportSettings.setProcessHETATMs(jalview.bin.Cache.getDefault( - "PROCESS_HETATM", false)); + .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 @@ -461,11 +547,11 @@ public class Cache { 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) { @@ -481,8 +567,8 @@ public class Cache } } 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"); } @@ -511,13 +597,10 @@ public class Cache 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"); @@ -539,41 +622,99 @@ public class Cache */ 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 @@ -581,15 +722,41 @@ public class Cache * @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---"); @@ -597,28 +764,62 @@ public class Cache } } 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 @@ -633,10 +834,17 @@ public class Cache } } + 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. @@ -645,19 +853,19 @@ public class Cache */ 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 @@ -665,17 +873,18 @@ public class Cache } } 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. @@ -684,19 +893,19 @@ public class Cache */ 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 @@ -704,15 +913,15 @@ public class Cache } } 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); } /** @@ -721,15 +930,18 @@ public class Cache */ 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) @@ -737,15 +949,14 @@ public class Cache // 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; @@ -759,22 +970,21 @@ public class Cache 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; @@ -791,42 +1001,45 @@ public class Cache { 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(); } @@ -840,71 +1053,72 @@ 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 = 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 @@ -913,7 +1127,7 @@ public class Cache } catch (Exception ex) { System.err.println("Invalid or corrupt date in property '" - + property + "' : value was '" + val + "'"); + + propertyName + "' : value was '" + val + "'"); } } return null; @@ -943,22 +1157,6 @@ public class Cache 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. @@ -974,11 +1172,64 @@ public class Cache } 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); + } } } + }