X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=21d5205ebb719d98172708389d0958b278984f59;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=5dbf5bc83ac034a2c2ed97ce7ff1cd287d0816e5;hpb=bbfdb203ce3a889600caa52478478b75ab03809f;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 5dbf5bc..21d5205 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,30 +1,47 @@ /* - * 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 2.9) + * Copyright (C) 2015 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.ws.dbsources.das.api.DasSourceRegistryI; +import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; + 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 java.util.Collections; +import java.util.Date; +import java.util.Enumeration; +import java.util.Properties; +import java.util.TreeSet; -import org.apache.log4j.*; -import org.biojava.dasobert.dasregistry.Das1Source; +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 @@ -58,6 +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
    • @@ -129,23 +150,46 @@ 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
    • - * - *
  • + *
  • 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 $Revision$ */ @@ -178,12 +222,20 @@ 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 = false; public static void initLogger() { @@ -237,7 +289,9 @@ 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; } @@ -263,8 +317,10 @@ public class Cache 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) { @@ -273,19 +329,22 @@ 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")); + String authorDetails = "jar:".concat(Cache.class + .getProtectionDomain().getCodeSource().getLocation() + .toString().concat("!/authors.props")); java.net.URL localJarFileURL = new java.net.URL(authorDetails); @@ -322,15 +381,21 @@ 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 @@ -357,8 +422,9 @@ 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")+"/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; @@ -412,6 +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 @@ -600,46 +677,6 @@ 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. */ @@ -683,21 +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" }); + 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." }) }); + new Class[] { trackerfocus }).invoke( + tracker, + new Object[] { trackerfocus.getConstructor( + new Class[] { String.class }).newInstance( + new Object[] { "Application Started." }) }); } catch (RuntimeException e) { re = e; @@ -713,15 +751,21 @@ public class Cache if (log != null) { if (re != null) + { 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 { @@ -758,6 +802,7 @@ public class Cache /** * get the user's default colour if available + * * @param property * @param defcolour * @return @@ -765,38 +810,44 @@ 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 = jalview.schemes.ColourSchemeProperty + .getAWTColorFromName(colprop); + if (col == null) { - try { + 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); + col = null; } } - 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(); + public static final DateFormat date_format = SimpleDateFormat + .getDateTimeInstance(); /** * store a date in a jalview property + * * @param string * @param time */ @@ -804,8 +855,10 @@ public class Cache { 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 * @@ -813,15 +866,80 @@ public class Cache public static Date getDateProperty(String property) { String val = getProperty(property); - if (val!=null) + 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 '" + + 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); + } + } }