X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=141470af33d9296afddd224d70ce7d0bb503a8ed;hb=d0b386f1c8c27a08c8b65bd23603f3d23f241670;hp=a73481e045d25f116d9e4b7311bce56b7f8183de;hpb=9a5abc55a76fa3d709146f82207f580990a8180a;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index a73481e..141470a 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,28 +1,32 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 . */ package jalview.bin; +import jalview.ws.dbsources.das.api.DasSourceRegistryI; +import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; + +import java.awt.Color; import java.io.*; +import java.text.DateFormat; +import java.text.SimpleDateFormat; import java.util.*; import org.apache.log4j.*; -import org.biojava.dasobert.dasregistry.Das1Source; /** * Stores and retrieves Jalview Application Properties Lists and fields within @@ -40,9 +44,6 @@ 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
    • @@ -82,8 +83,8 @@ import org.biojava.dasobert.dasregistry.Das1Source; * service *
  • QUESTIONNAIRE last questionnaire:responder id string from questionnaire * service
    • - *
  • USAGESTATS (true) Enable google analytics tracker for collecting usage - * statistics
    • + *
  • 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
    • @@ -98,11 +99,15 @@ 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 * $SEQUENCE_ID$
    • + *
  • 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 + * 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 @@ -111,11 +116,40 @@ import org.biojava.dasobert.dasregistry.Das1Source; * displayed as '.'
    • *
  • SORT_BY_TREE (false) sort the current alignment view according to the * order of a newly displayed tree
    • + *
  • DBFETCH_USEPICR (false) use PICR to recover valid DB references from + * sequence ID strings before attempting retrieval from any datasource
    • + *
  • SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the + * alignment.
    • + *
  • SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups + * in the alignment.
    • + *
  • SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's + * 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. + *
    • + *
  • 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).
    • *
  • * * - * + * Deprecated settings: + * * @author $author$ * @version $Revision$ */ @@ -153,10 +187,19 @@ public class Cache /** Default file is ~/.jalview_properties */ static String propertiesFile; + private static boolean propsAreReadOnly=false; + public static void initLogger() { + if (log != null) + { + return; + } try { + // TODO: redirect stdout and stderr here in order to grab the output of + // the log + ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(), "System.err"); ap.setName("JalviewLogger"); @@ -198,11 +241,31 @@ 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 { - FileInputStream fis = new FileInputStream(propertiesFile); + InputStream fis; + try + { + fis = new java.net.URL(propertiesFile).openStream(); + System.out.println("Loading jalview properties from : " + + propertiesFile); + System.out + .println("Disabling Jalview writing to user's local properties file."); + propsAreReadOnly = true; + + } catch (Exception ex) + { + fis = null; + } + if (fis == null) + { + fis = new FileInputStream(propertiesFile); + } applicationProperties.load(fis); applicationProperties.remove("LATEST_VERSION"); applicationProperties.remove("VERSION"); @@ -214,13 +277,34 @@ public class Cache if (getDefault("USE_PROXY", false)) { + String proxyServer=getDefault("PROXY_SERVER", ""), proxyPort=getDefault("PROXY_PORT", "8080"); + 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)); + + 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 @@ -229,8 +313,8 @@ public class Cache try { String buildDetails = "jar:".concat(Cache.class.getProtectionDomain() - .getCodeSource().getLocation().toString().concat( - "!/.build_properties")); + .getCodeSource().getLocation().toString() + .concat("!/.build_properties")); java.net.URL localJarFileURL = new java.net.URL(buildDetails); @@ -258,6 +342,7 @@ public class Cache // jnlpVersion will be null if we're using InstallAnywhere // Dont do this check if running in headless mode if (jnlpVersion == null + && getDefault("VERSION_CHECK", true) && (System.getProperty("java.awt.headless") == null || System .getProperty("java.awt.headless").equals("false"))) { @@ -280,7 +365,7 @@ public class Cache System.setProperty("sun.net.client.defaultConnectTimeout", "5000"); java.net.URL url = new java.net.URL( - "http://www.jalview.org/webstart/jalview.jnlp"); + Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/webstart/jalview.jnlp"); BufferedReader in = new BufferedReader(new InputStreamReader( url.openStream())); String line = null; @@ -391,12 +476,16 @@ public class Cache */ public static String setProperty(String key, String obj) { + try { - FileOutputStream out = new FileOutputStream(propertiesFile); applicationProperties.setProperty(key, obj); - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); + if (!propsAreReadOnly) + { + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); + } } catch (Exception ex) { System.out.println("Error setting property: " + key + " " + obj @@ -405,16 +494,33 @@ public class Cache return obj; } + /** + * remove the specified property from the jalview properties file + * + * @param string + */ + public static void removeProperty(String string) + { + applicationProperties.remove(string); + saveProperties(); + } + + /** + * save the properties to the jalview properties path + */ public static void saveProperties() { - try + if (!propsAreReadOnly) { - FileOutputStream out = new FileOutputStream(propertiesFile); - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); - } catch (Exception ex) - { - System.out.println("Error saving properties: " + ex); + try + { + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); + } catch (Exception ex) + { + System.out.println("Error saving properties: " + ex); + } } } @@ -487,6 +593,10 @@ public class Cache // Tell the user that debug is enabled lgclient.debug("Jalview Groovy Client Debugging Output Follows."); } + } catch (Error e) + { + groovyJarsArePresent = 0; + jalview.bin.Cache.log.debug("Groovy Classes are not present", e); } catch (Exception e) { groovyJarsArePresent = 0; @@ -497,50 +607,13 @@ 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. + * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not + * enabled. */ protected static Object tracker = null; + protected static Class trackerfocus = null; + protected static Class jgoogleanalyticstracker = null; /** @@ -550,20 +623,23 @@ public class Cache { if (tracker == null) { - if (jgoogleanalyticstracker==null) + if (jgoogleanalyticstracker == null) { // try to get the tracker class - try { - jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass( - "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker"); + try + { + jgoogleanalyticstracker = Cache.class + .getClassLoader() + .loadClass( + "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker"); trackerfocus = Cache.class.getClassLoader().loadClass( - "com.boxysystems.jgoogleanalytics.FocusPoint"); + "com.boxysystems.jgoogleanalytics.FocusPoint"); } catch (Exception e) { log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled."); tracker = null; - jgoogleanalyticstracker=null; - trackerfocus=null; + jgoogleanalyticstracker = null; + trackerfocus = null; return; } } @@ -574,14 +650,21 @@ public class Cache try { // Google analytics tracking code for Library Finder - tracker = jgoogleanalyticstracker.getConstructor(new Class[] { String.class,String.class,String.class}).newInstance(new Object[] { "Jalview Desktop", - (vrs = jalview.bin.Cache.getProperty("VERSION") - + "_" - + jalview.bin.Cache.getDefault("BUILD_DATE", - "unknown")), "UA-9060947-1"}); - jgoogleanalyticstracker.getMethod("trackAsynchronously", new Class[] { trackerfocus }) - .invoke(tracker, new Object[] { trackerfocus.getConstructor( - new Class[] { String.class}).newInstance(new Object[] { "Application Started." })}); + tracker = jgoogleanalyticstracker.getConstructor(new Class[] + { String.class, String.class, String.class }).newInstance( + new Object[] + { + "Jalview Desktop", + (vrs = jalview.bin.Cache.getProperty("VERSION") + + "_" + + 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; @@ -597,10 +680,7 @@ 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 " @@ -642,4 +722,107 @@ 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 = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(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; + } + } + 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)); + } + + public static final DateFormat date_format = SimpleDateFormat.getDateTimeInstance(); + + /** + * store a date in a jalview property + * @param string + * @param time + */ + public static void setDateProperty(String property, Date time) + { + setProperty(property, date_format.format(time)); + } + /** + * read a date stored in a jalview property + * @param property + * @return valid date as stored by setDateProperty, or null + * + */ + public static Date getDateProperty(String property) + { + String val = getProperty(property); + if (val!=null) + { + try { + return date_format.parse(val); + } catch (Exception ex) + { + System.err.println("Invalid or corrupt date in property '"+property+"' : 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; + } }