X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=d791cb66761dc78a5cc8ba331e5ba913abcc91f2;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=cebb50414d00c84864a3e39439865d0010bc716e;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index cebb504..d791cb6 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,27 +1,33 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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. - * + * * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ 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 @@ -39,9 +45,6 @@ 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
    • @@ -105,7 +108,7 @@ 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 @@ -124,11 +127,40 @@ 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. + *
    • + *
  • 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 $author$ @@ -168,8 +200,14 @@ 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 @@ -217,10 +255,32 @@ 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"); @@ -232,13 +292,34 @@ 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 @@ -247,8 +328,8 @@ 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); @@ -298,8 +379,9 @@ 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"); + 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; @@ -410,12 +492,16 @@ 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 @@ -440,14 +526,17 @@ public class Cache */ 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); + } } } @@ -534,46 +623,6 @@ 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. */ @@ -603,8 +652,7 @@ public class Cache "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; @@ -648,10 +696,7 @@ 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 " @@ -694,4 +739,123 @@ 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; + } }