X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=dcd6546ad8bd27f2210c9261761a56f33cbb46f3;hb=4bb7ef2feb729af8a320e9c090e39aee12028375;hp=75fb61812abb4d10088fcdae067b61574ebdedef;hpb=2f3b33ed7140d07e2bb31960ce5aedfed134dfeb;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 75fb618..dcd6546 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,27 +1,58 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.bin; -import java.io.*; -import java.util.*; +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.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; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.InputStream; +import java.io.InputStreamReader; +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 org.apache.log4j.*; -import org.biojava.dasobert.dasregistry.Das1Source; +import org.apache.log4j.ConsoleAppender; +import org.apache.log4j.Level; +import org.apache.log4j.Logger; +import org.apache.log4j.SimpleLayout; /** * Stores and retrieves Jalview Application Properties Lists and fields within @@ -39,9 +70,6 @@ import org.biojava.dasobert.dasregistry.Das1Source; * *
  • logs.Jalview.Level - Cache.log stringified level.
    *
    • - *
  • DISCOVERY_START - Boolean - controls if discovery services are queried on - * startup
    • - *
  • DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
    • *
  • SCREEN_WIDTH
    • *
  • SCREEN_HEIGHT
    • *
  • SCREEN_Y=285
    • @@ -49,7 +77,8 @@ import org.biojava.dasobert.dasregistry.Das1Source; *
  • 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
    • @@ -58,6 +87,10 @@ import org.biojava.dasobert.dasregistry.Das1Source; *
  • SHOW_QUALITY show alignment quality annotation
    • *
  • SHOW_ANNOTATIONS show alignment annotation rows
    • *
  • SHOW_CONSERVATION show alignment conservation annotation
    • + *
  • SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or + * LABEL_AND_SEQUENCE
    • + *
  • SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above + * sequence annotations
    • *
  • CENTRE_COLUMN_LABELS centre the labels at each column in a displayed * annotation row
    • *
  • DEFAULT_COLOUR default colour scheme to apply for a new alignment
    • @@ -97,6 +130,10 @@ import org.biojava.dasobert.dasregistry.Das1Source; *
  • 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
    • @@ -105,7 +142,7 @@ import org.biojava.dasobert.dasregistry.Das1Source; *
  • SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop * (false)
    • *
  • VERSION_CHECK (true) check for the latest release version from - * www.jalview.org
    • + * www.jalview.org (or the alias given by the www.jalview.org property) *
  • SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence * ID tooltip
    • *
  • SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence @@ -124,16 +161,51 @@ import org.biojava.dasobert.dasregistry.Das1Source; * histogram.
    • *
  • SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence * logo.
    • + *
  • NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence + * logo normalised to row height rather than histogram height.
    • *
  • FOLLOW_SELECTIONS (true) Controls whether a new alignment view should * respond to selections made in other alignments containing the same sequences. *
    • + *
  • JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services
    • *
  • SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery * warning dialog box is displayed.
    • + *
  • ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation + * when shading by annotation
    • + *
  • ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation + * when shading by annotation
    • + *
  • www.jalview.org (http://www.jalview.org) a property enabling all HTTP + * requests to be redirected to a mirror of http://www.jalview.org
    • + *
  • FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported + * alignment figure to accommodate even the longest sequence ID or annotation + * label.
    • + *
  • FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column + * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true + * will override this).
    • + *
  • STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB + * record
    • + *
  • USE_RNAVIEW (false) use RNAViewer to derive secondary structure
    • + *
  • ADD_SS_ANN (false) add secondary structure annotation to alignment + * display
    • + *
  • ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment + * display
    • + *
  • 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: + * * * @author $author$ @@ -163,17 +235,60 @@ public class Cache 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 + + ".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 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 */ public static Logger log; /** Jalview Properties */ - public static Properties applicationProperties = new Properties(); + public static Properties applicationProperties = new Properties() + { + // override results in properties output in alphabetical order + @Override + public synchronized Enumeration keys() + { + return Collections.enumeration(new TreeSet<>(super.keySet())); + } + }; /** Default file is ~/.jalview_properties */ static String propertiesFile; - private static boolean propsAreReadOnly=false; + private static boolean propsAreReadOnly = false; public static void initLogger() { @@ -195,8 +310,8 @@ 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"); @@ -205,8 +320,8 @@ 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()))); + 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); @@ -219,7 +334,10 @@ 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; @@ -228,6 +346,11 @@ public class Cache propertiesFile = System.getProperty("user.home") + File.separatorChar + ".jalview_properties"; } + else + { + // don't corrupt the file we've been given. + propsAreReadOnly = true; + } try { @@ -235,10 +358,10 @@ 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) @@ -249,9 +372,12 @@ public class Cache { fis = new FileInputStream(propertiesFile); } + applicationProperties.clear(); applicationProperties.load(fis); - applicationProperties.remove("LATEST_VERSION"); - applicationProperties.remove("VERSION"); + + // remove any old build properties + + deleteBuildProperties(); fis.close(); } catch (Exception ex) { @@ -260,11 +386,34 @@ public class Cache if (getDefault("USE_PROXY", false)) { - System.out.println("Using proxyServer: " - + getDefault("PROXY_SERVER", null) + " proxyPort: " - + getDefault("PROXY_PORT", null)); - System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null)); - System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null)); + String proxyServer = getDefault("PROXY_SERVER", ""), + proxyPort = getDefault("PROXY_PORT", "8080"); + + System.out.println("Using proxyServer: " + proxyServer + + " proxyPort: " + proxyPort); + + System.setProperty("http.proxyHost", proxyServer); + System.setProperty("http.proxyPort", proxyPort); + } + + // LOAD THE AUTHORS FROM THE authors.props file + 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(); + } catch (Exception ex) + { + System.out.println("Error reading author details: " + ex); + applicationProperties.remove("AUTHORS"); + applicationProperties.remove("AUTHORFNAMES"); + applicationProperties.remove("YEAR"); } // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar @@ -289,26 +438,58 @@ public class Cache 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); + + SiftsSettings + .setMapWithSifts(Cache.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", + DEFAULT_FAIL_SAFE_PID_THRESHOLD)); + + SiftsSettings.setCacheThresholdInDays( + jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days", + DEFAULT_CACHE_THRESHOLD_IN_DAYS)); + + IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL", + "http://www.jalview.org/services/identifiers")); + IdOrgSettings.setDownloadLocation(ID_ORG_FILE); - System.out.println("Jalview Version: " + codeVersion); + System.out + .println("Jalview Version: " + codeVersion + codeInstallation); + StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache + .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); + StructureImportSettings + .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); + // StructureImportSettings + // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( + // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); // jnlpVersion will be null if we're using InstallAnywhere // Dont do this check if running in headless mode - if (jnlpVersion == null - && getDefault("VERSION_CHECK", true) + if (jnlpVersion == null && getDefault("VERSION_CHECK", true) && (System.getProperty("java.awt.headless") == null || System .getProperty("java.awt.headless").equals("false"))) { class VersionChecker extends Thread { + @Override public void run() { String orgtimeout = System @@ -319,15 +500,16 @@ public class Cache System.out.println("# INFO: Setting default net timeout to " + orgtimeout + " seconds."); } - String jnlpVersion = null; + String remoteVersion = null; try { System.setProperty("sun.net.client.defaultConnectTimeout", "5000"); - java.net.URL url = new java.net.URL( - "http://www.jalview.org/webstart/jalview.jnlp"); - BufferedReader in = new BufferedReader(new InputStreamReader( - url.openStream())); + 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())); String line = null; while ((line = in.readLine()) != null) { @@ -338,20 +520,20 @@ public class Cache line = line.substring(line.indexOf("value=") + 7); line = line.substring(0, line.lastIndexOf("\"")); - jnlpVersion = line; + remoteVersion = line; break; } } catch (Exception ex) { - System.out - .println("Non-fatal exceptions when checking version at www.jalview.org :"); + System.out.println( + "Non-fatal exception when checking version at www.jalview.org :"); System.out.println(ex); - jnlpVersion = getProperty("VERSION"); + remoteVersion = getProperty("VERSION"); } System.setProperty("sun.net.client.defaultConnectTimeout", orgtimeout); - setProperty("LATEST_VERSION", jnlpVersion); + setProperty("LATEST_VERSION", remoteVersion); } } @@ -373,12 +555,23 @@ 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); } + private static void deleteBuildProperties() + { + applicationProperties.remove("LATEST_VERSION"); + applicationProperties.remove("VERSION"); + applicationProperties.remove("AUTHORS"); + applicationProperties.remove("AUTHORFNAMES"); + applicationProperties.remove("YEAR"); + applicationProperties.remove("BUILD_DATE"); + applicationProperties.remove("INSTALLATION"); + } + /** * Gets Jalview application property of given key. Returns null if key not * found @@ -432,14 +625,14 @@ 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); + oldValue = applicationProperties.setProperty(key, obj); if (!propsAreReadOnly) { FileOutputStream out = new FileOutputStream(propertiesFile); @@ -448,10 +641,10 @@ 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; } /** @@ -500,15 +693,15 @@ 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 @@ -539,15 +732,15 @@ 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 @@ -567,46 +760,6 @@ public class Cache } /** - * generate Das1Sources from the local das source list - * - * @return Vector of Das1Sources - */ - public static Vector getLocalDasSources() - { - Vector localSources = new Vector(); - String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE"); - if (local != null) - { - StringTokenizer st = new StringTokenizer(local, "\t"); - while (st.hasMoreTokens()) - { - String token = st.nextToken(); - int bar = token.indexOf("|"); - Das1Source source = new Das1Source(); - source.setUrl(token.substring(bar + 1)); - if (source.getUrl().startsWith("sequence:")) - { - source.setUrl(source.getUrl().substring(9)); - // this source also serves sequences as well as features - source.setCapabilities(new String[] - { "sequence", "features" }); - } - else - { - // default is that all user added sources serve features - source.setCapabilities(new String[] - { "features" }); - } - - source.setNickname(token.substring(0, bar)); - - localSources.addElement(source); - } - } - return localSources; - } - - /** * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not * enabled. */ @@ -628,15 +781,14 @@ 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; @@ -650,21 +802,22 @@ 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") - + "_" + 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." }) }); + "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; @@ -680,37 +833,46 @@ public class Cache if (log != null) { 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(); } @@ -723,4 +885,191 @@ public class Cache } } + /** + * get the user's default colour if available + * + * @param property + * @param defcolour + * @return + */ + public static Color getDefaultColour(String property, Color defcolour) + { + String colprop = getProperty(property); + if (colprop == null) + { + return defcolour; + } + Color col = ColorUtils.parseColourString(colprop); + if (col == null) + { + log.warn("Couldn't parse '" + colprop + "' as a colour for " + + property); + } + return (col == null) ? defcolour : col; + } + + /** + * store a colour as a Jalview user default property + * + * @param property + * @param colour + */ + public static void setColourProperty(String property, Color colour) + { + setProperty(property, jalview.util.Format.getHexString(colour)); + } + + /** + * Stores a formatted date in a jalview property, using a fixed locale. + * + * @param propertyName + * @param date + * @return the formatted date string + */ + public static String setDateProperty(String propertyName, Date date) + { + String formatted = date_format.format(date); + setProperty(propertyName, formatted); + return formatted; + } + + /** + * 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 propertyName + * @return + * + */ + public static Date getDateProperty(String propertyName) + { + String val = getProperty(propertyName); + if (val != null) + { + try + { + return date_format.parse(val); + } catch (Exception ex) + { + System.err.println("Invalid or corrupt date in property '" + + propertyName + "' : value was '" + val + "'"); + } + } + return null; + } + + /** + * get and parse a property as an integer. send any parsing problems to + * System.err + * + * @param property + * @return null or Integer + */ + public static Integer getIntegerProperty(String property) + { + String val = getProperty(property); + if (val != null && (val = val.trim()).length() > 0) + { + try + { + return Integer.valueOf(val); + } catch (NumberFormatException x) + { + System.err.println("Invalid integer in property '" + property + + "' (value was '" + val + "')"); + } + } + 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. + * + * @param propName + * @param value + */ + public static void setOrRemove(String propName, String value) + { + if (propName == null) + { + return; + } + if (value == null || value.trim().length() < 1) + { + Cache.applicationProperties.remove(propName); + } + else + { + 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); + } + } + } }