X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=3c919cb4d2f76b4083ef05177e1315b84320ea9e;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=5692c496de7ac6712c2df13cd427609f8864be40;hpb=63f3c5bdc2ce5540d8f6bfc9ed9af5d454805181;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 5692c49..3c919cb 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,30 +1,57 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 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.util.Platform; +import jalview.ws.sifts.SiftsSettings; + import java.awt.Color; -import java.io.*; +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.*; - -import org.apache.log4j.*; -import org.biojava.dasobert.dasregistry.Das1Source; +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; +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 @@ -49,7 +76,8 @@ 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 +86,10 @@ 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
    • @@ -83,7 +115,6 @@ import org.biojava.dasobert.dasregistry.Das1Source; * 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
    • @@ -97,11 +128,13 @@ 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
    • *
  • 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 @@ -129,25 +162,48 @@ import org.biojava.dasobert.dasregistry.Das1Source; *
  • 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).
    • - *
  • + *
  • 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 $author$ * @version $Revision$ */ @@ -168,11 +224,40 @@ public class Cache */ public static final String JALVIEWLOGLEVEL = "logs.Jalview.level"; - public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE"; + /** + * Sifts settings + */ + public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System + .getProperty("user.home") + File.separatorChar + + ".sifts_downloads" + File.separatorChar; - public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL"; + private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2"; - public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE"; + 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 @@ -180,12 +265,21 @@ public class Cache 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 = /** @j2sNative true || */ + false; public static void initLogger() { @@ -207,8 +301,8 @@ 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"); @@ -217,8 +311,8 @@ 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); @@ -231,7 +325,10 @@ 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; @@ -239,7 +336,9 @@ public class Cache { propertiesFile = System.getProperty("user.home") + File.separatorChar + ".jalview_properties"; - } else { + } + else + { // don't corrupt the file we've been given. propsAreReadOnly = true; } @@ -250,10 +349,10 @@ 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) @@ -264,9 +363,12 @@ 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) { @@ -275,36 +377,49 @@ 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 + boolean ignore = Platform.isJS(); + if (!ignore) 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); 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"); + ignore = true; } + if (ignore) { + applicationProperties.remove("AUTHORS"); + applicationProperties.remove("AUTHORFNAMES"); + 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 + // BH 2019.01.25 switching to Platform.isJS() + ignore = Platform.isJS(); + if (!ignore) try { String buildDetails = "jar:".concat(Cache.class.getProtectionDomain() @@ -319,31 +434,67 @@ public class Cache } catch (Exception ex) { System.out.println("Error reading build details: " + ex); - applicationProperties.remove("VERSION"); + ignore = true; + } + + if (ignore) { + 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); - System.out.println("Jalview Version: " + codeVersion); + 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 + 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 @@ -354,15 +505,16 @@ 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( - Cache.getDefault("www.jalview.org", "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) { @@ -373,20 +525,20 @@ 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); } } @@ -408,12 +560,23 @@ 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 @@ -444,22 +607,35 @@ public class Cache return def; } - /** - * These methods are used when checking if the saved preference is different - * to the default setting - */ - public static String getDefault(String property, String def) + public static int getDefault(String property, int def) { String string = getProperty(property); if (string != null) { - return string; + try + { + def = Integer.parseInt(string); + } catch (NumberFormatException e) + { + System.out.println("Error parsing int property '" + property + + "' with value '" + string + "'"); + } } return def; } /** + * Answers the value of the given property, or the supplied default value if + * the property is not set + */ + public static String getDefault(String property, String def) + { + String value = getProperty(property); + return value == null ? def : value; + } + + /** * Stores property in the file "HOME_DIR/.jalview_properties" * * @param key @@ -467,14 +643,14 @@ 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); @@ -483,10 +659,10 @@ 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; } /** @@ -535,15 +711,15 @@ 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 @@ -574,15 +750,15 @@ 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 @@ -602,46 +778,6 @@ 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. */ @@ -663,15 +799,14 @@ 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; @@ -685,21 +820,22 @@ 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; @@ -715,37 +851,46 @@ 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(); } @@ -760,6 +905,7 @@ public class Cache /** * get the user's default colour if available + * * @param property * @param defcolour * @return @@ -767,83 +913,180 @@ public class Cache public static Color getDefaultColour(String property, Color defcolour) { String colprop = getProperty(property); - if (colprop==null) { + if (colprop == null) + { return defcolour; } - Color col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(colprop); - if (col==null) + 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) ? defcolour : col; } /** * store a colour as a Jalview user default property + * * @param property - * @param colour + * @param colour */ public static void setColourProperty(String property, Color colour) { - setProperty(property, jalview.util.Format - .getHexString(colour)); + setProperty(property, jalview.util.Format.getHexString(colour)); } - public static final DateFormat date_format = SimpleDateFormat.getDateTimeInstance(); - /** - * store a date in a jalview property - * @param string - * @param time + * Stores a formatted date in a jalview property, using a fixed locale. + * + * @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 - * @param property - * @return valid date as stored by setDateProperty, or null + * 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 property) + public static Date getDateProperty(String propertyName) { - String val = getProperty(property); - if (val!=null) + String val = getProperty(propertyName); + if (val != null) { - try { + try + { return date_format.parse(val); } catch (Exception ex) { - System.err.println("Invalid or corrupt date in property '"+property+"' : value was '"+val+"'"); + 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 + * 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) + String val = getProperty(property); + if (val != null && (val = val.trim()).length() > 0) { - try { + try + { return Integer.valueOf(val); } catch (NumberFormatException x) { - System.err.println("Invalid integer in property '"+property+"' (value was '"+val+"')"); + System.err.println("Invalid integer in property '" + property + + "' (value was '" + val + "')"); } } return null; } + + /** + * 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); + } + } + } + + /** + * Add a known domain that implements access-control-allow-origin:* bh 2018 + * + * @param defaultUniprotDomain + */ + public static void addJ2SDirectDatabaseCall(String domain) + { + + /** + * @j2sNative + * + * J2S.addDirectDatabaseCall(domain); + */ + } }