X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=ba2871749d5b59f446ee84f2858399acdcbf0f8c;hb=4977df097c88bac7b47babefd3cb749b6f811d8b;hp=4be78302bbacc10b62ed83a86438be1a081c927d;hpb=65c671b0263c0c692a4a0a0905a4acc2fc6b1065;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 4be7830..ba28717 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -20,12 +20,6 @@ */ package jalview.bin; -import jalview.datamodel.PDBEntry; -import jalview.structure.StructureImportSettings; -import jalview.ws.dbsources.das.api.DasSourceRegistryI; -import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; -import jalview.ws.sifts.SiftsSettings; - import java.awt.Color; import java.io.BufferedReader; import java.io.File; @@ -33,19 +27,37 @@ import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.InputStream; import java.io.InputStreamReader; +import java.io.PrintWriter; +import java.io.StringWriter; import java.text.DateFormat; 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 java.util.regex.Pattern; + +import javax.swing.LookAndFeel; +import javax.swing.UIManager; import org.apache.log4j.ConsoleAppender; import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.apache.log4j.SimpleLayout; +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; + /** * Stores and retrieves Jalview Application Properties Lists and fields within * list entries are separated by '|' symbols unless otherwise stated (|) clauses @@ -69,7 +81,8 @@ 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
    • @@ -107,7 +120,6 @@ 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
    • @@ -121,11 +133,13 @@ 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 @@ -178,6 +192,8 @@ 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: @@ -213,30 +229,41 @@ 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"; - + + /** + * 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 DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.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 */ @@ -249,7 +276,7 @@ public class Cache @Override public synchronized Enumeration keys() { - return Collections.enumeration(new TreeSet(super.keySet())); + return Collections.enumeration(new TreeSet<>(super.keySet())); } }; @@ -278,8 +305,8 @@ 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()))); + laxis.setLevel(Level.toLevel( + 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"); @@ -288,8 +315,11 @@ public class Cache // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller"); // 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()))); + // we shouldn't need to do this + org.apache.log4j.Logger.getRootLogger().setLevel(org.apache.log4j.Level.INFO); + + 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); @@ -302,7 +332,10 @@ 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) { propertiesFile = propsFile; @@ -323,10 +356,10 @@ public class Cache 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."); + 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) @@ -337,6 +370,7 @@ public class Cache { fis = new FileInputStream(propertiesFile); } + applicationProperties.clear(); applicationProperties.load(fis); // remove any old build properties @@ -350,8 +384,8 @@ public class Cache 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); @@ -363,9 +397,9 @@ public class Cache // LOAD THE AUTHORS FROM THE authors.props file try { - String authorDetails = "jar:".concat(Cache.class - .getProtectionDomain().getCodeSource().getLocation() - .toString().concat("!/authors.props")); + String authorDetails = "jar:" + .concat(Cache.class.getProtectionDomain().getCodeSource() + .getLocation().toString().concat("!/authors.props")); java.net.URL localJarFileURL = new java.net.URL(authorDetails); @@ -380,69 +414,41 @@ public class Cache 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 = "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) - { - 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"); - if (codeVersion == null) - { - // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! - codeVersion = "Test"; - jnlpVersion = "Test"; - codeInstallation = ""; - } - else - { - codeInstallation = " (" + codeInstallation + ")"; - } - new BuildDetails(codeVersion, null, codeInstallation); + loadBuildProperties(false); SiftsSettings .setMapWithSifts(Cache.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( + jalview.bin.Cache.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( + jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days", + DEFAULT_CACHE_THRESHOLD_IN_DAYS)); - System.out - .println("Jalview Version: " + codeVersion + codeInstallation); + IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL", + "http://www.jalview.org/services/identifiers")); + IdOrgSettings.setDownloadLocation(ID_ORG_FILE); StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache - .getDefault( - "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT)); + .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); StructureImportSettings - .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( - "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); - // jnlpVersion will be null if we're using InstallAnywhere + .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); + // StructureImportSettings + // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( + // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); + + String jnlpVersion = System.getProperty("jalview.version"); + + // jnlpVersion will be null if a latest version check for the channel needs + // to be done // Dont do this check if running in headless mode - if (jnlpVersion == null - && getDefault("VERSION_CHECK", true) + + if (jnlpVersion == null && getDefault("VERSION_CHECK", true) && (System.getProperty("java.awt.headless") == null || System .getProperty("java.awt.headless").equals("false"))) { @@ -465,11 +471,11 @@ 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) { @@ -485,8 +491,8 @@ 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"); } @@ -512,15 +518,57 @@ public class Cache } } - setProperty("VERSION", codeVersion); - // LOAD USERDEFINED COLOURS - jalview.gui.UserDefinedColours + jalview.bin.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 + { + 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) + { + System.out.println("Error reading build details: " + ex); + applicationProperties.remove("VERSION"); + } + String codeVersion = getProperty("VERSION"); + codeInstallation = getProperty("INSTALLATION"); + + if (codeVersion == null) + { + // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! + codeVersion = "Test"; + codeInstallation = ""; + } + else + { + codeInstallation = " (" + codeInstallation + ")"; + } + setProperty("VERSION", codeVersion); + new BuildDetails(codeVersion, null, codeInstallation); + if (printV && reportVersion) + { + System.out.println( + "Jalview Version: " + codeVersion + codeInstallation); + } + } + private static void deleteBuildProperties() { applicationProperties.remove("LATEST_VERSION"); @@ -562,6 +610,24 @@ public class Cache return def; } + public static int getDefault(String property, int def) + { + String string = getProperty(property); + if (string != null) + { + try + { + def = 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 @@ -585,15 +651,15 @@ public class Cache * @param obj * String value of property * - * @return String value of property + * @return previous value of property (or null) */ - public static String setProperty(String key, String obj) + public static Object setProperty(String key, String obj) { - + Object oldValue = null; try { - applicationProperties.setProperty(key, obj); - if (!propsAreReadOnly) + oldValue = applicationProperties.setProperty(key, obj); + if (propertiesFile != null && !propsAreReadOnly) { FileOutputStream out = new FileOutputStream(propertiesFile); applicationProperties.store(out, "---JalviewX Properties File---"); @@ -601,10 +667,10 @@ 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; } /** @@ -653,15 +719,15 @@ public class Cache { 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)"); + jalview.bin.Cache.log.debug( + "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)"); vamsasJarsArePresent = 1; 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 @@ -692,15 +758,15 @@ public class Cache { 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)"); + jalview.bin.Cache.log.debug( + "Found Groovy (groovy.lang.GroovyObject can be loaded)"); groovyJarsArePresent = 1; 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 @@ -741,15 +807,14 @@ 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; @@ -763,22 +828,22 @@ 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") + "_" + + 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." }) }); } catch (RuntimeException e) { re = e; @@ -795,42 +860,45 @@ 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(); } @@ -857,19 +925,11 @@ public class Cache { return defcolour; } - 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; } @@ -885,30 +945,31 @@ public class Cache 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. * - * @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 @@ -917,7 +978,7 @@ 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; @@ -947,22 +1008,6 @@ 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. @@ -985,4 +1030,145 @@ public class Cache Cache.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(UserDefinedColours.USER_DEFINED_COLOURS, + coloursFound.toString()); + } + else + { + applicationProperties + .remove(UserDefinedColours.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 + */ + public static String getVersionDetailsForConsole() + { + StringBuilder sb = new StringBuilder(); + sb.append("Jalview Version: "); + sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST")); + sb.append("\n"); + sb.append("Jalview Installation: "); + sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown")); + sb.append("\n"); + sb.append("Build Date: "); + sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); + sb.append("\n"); + sb.append("Java version: "); + sb.append(System.getProperty("java.version")); + sb.append("\n"); + sb.append(System.getProperty("os.arch")); + sb.append(" "); + sb.append(System.getProperty("os.name")); + sb.append(" "); + sb.append(System.getProperty("os.version")); + sb.append("\n"); + 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); + LookAndFeel laf = UIManager.getLookAndFeel(); + String lafName = laf == null ? "Not obtained" : laf.getName(); + String lafClass = laf == null ? "unknown" : laf.getClass().getName(); + sb.append("LookAndFeel: "); + sb.append(lafName); + sb.append(" ("); + sb.append(lafClass); + sb.append(")\n"); + // Not displayed in release version ( determined by possible version number + // regex 9[9.]*9[.-_a9]* ) + if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$", + jalview.bin.Cache.getDefault("VERSION", "TEST"))) + { + appendIfNotNull(sb, "Getdown appdir: ", + System.getProperty("getdownappdir"), "\n", null); + appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"), + "\n", "unknown"); + } + return sb.toString(); + } + + /** + * + * @return build details as reported in splashscreen + */ + public static String getBuildDetailsForSplash() + { + // consider returning more human friendly info + // eg 'built from Source' or update channel + return jalview.bin.Cache.getDefault("INSTALLATION", "unknown"); + } + + public static String getStackTraceString(Throwable t) + { + StringWriter sw = new StringWriter(); + PrintWriter pw = new PrintWriter(sw); + t.printStackTrace(pw); + return sw.toString(); + } }