X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=dc5084347e9bc01cab00b33cf6a8a44479085053;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=a7c002c85a315726cc993ae61dab38a1057a23d8;hpb=1e085f14ae2f19adfac0153c437ee891f0ad07bc;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index a7c002c..dc50843 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,8 +20,17 @@ */ 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.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; @@ -35,7 +44,9 @@ 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; @@ -66,7 +77,8 @@ 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
    • @@ -118,6 +130,10 @@ 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
    • @@ -175,6 +191,8 @@ 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: @@ -217,6 +235,41 @@ 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; @@ -257,8 +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"); @@ -267,8 +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); @@ -302,10 +355,10 @@ 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) @@ -329,8 +382,8 @@ 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); @@ -342,9 +395,9 @@ 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); @@ -394,19 +447,45 @@ public class Cache 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 + 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 @@ -422,11 +501,11 @@ 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) { @@ -442,8 +521,8 @@ 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"); } @@ -472,7 +551,7 @@ 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); @@ -558,8 +637,8 @@ 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; } @@ -610,15 +689,15 @@ 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 @@ -649,15 +728,15 @@ 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 @@ -698,15 +777,14 @@ 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; @@ -720,22 +798,22 @@ 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; @@ -752,42 +830,45 @@ 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(); } @@ -814,19 +895,11 @@ 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; } @@ -842,30 +915,31 @@ 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 @@ -874,7 +948,7 @@ 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; @@ -942,4 +1016,56 @@ 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); + } + } + } }