X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=21d5205ebb719d98172708389d0958b278984f59;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=a73481e045d25f116d9e4b7311bce56b7f8183de;hpb=9a5abc55a76fa3d709146f82207f580990a8180a;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index a73481e..21d5205 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,28 +1,47 @@ /* - * 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 2.9) + * Copyright (C) 2015 The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 org.apache.log4j.*; -import org.biojava.dasobert.dasregistry.Das1Source; +import jalview.ws.dbsources.das.api.DasSourceRegistryI; +import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; + +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.Properties; +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 @@ -40,9 +59,6 @@ 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
    • @@ -59,6 +75,10 @@ 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
    • @@ -82,8 +102,8 @@ 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 +118,15 @@ 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 @@ -111,10 +135,60 @@ 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. + *
    • + *
  • 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)
    • * * + * Deprecated settings: + * * * @author $author$ * @version $Revision$ @@ -148,15 +222,32 @@ 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; + 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"); @@ -199,13 +290,37 @@ 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"); + + // remove any old build properties + + deleteBuildProperties(); fis.close(); } catch (Exception ex) { @@ -214,13 +329,34 @@ 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 @@ -229,8 +365,8 @@ 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); @@ -245,19 +381,26 @@ 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 = ""; } - - System.out.println("Jalview Version: " + codeVersion); + else + { + codeInstallation = " (" + codeInstallation + ")"; + } + new BuildDetails(codeVersion, null, codeInstallation); + System.out + .println("Jalview Version: " + codeVersion + codeInstallation); // 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"))) { @@ -279,8 +422,9 @@ 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; @@ -334,6 +478,17 @@ public class Cache 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 @@ -391,12 +546,16 @@ 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 +564,33 @@ 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 +663,10 @@ 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 +677,13 @@ 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 +693,23 @@ 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 +720,22 @@ 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; @@ -597,18 +751,21 @@ 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); + } if (err != null) + { log.error( "Whilst initing GoogleTracker for Jalview Desktop version " + vrs, err); + } } else { @@ -642,4 +799,147 @@ 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; + } + + /** + * 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); + } + } }