X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=d791cb66761dc78a5cc8ba331e5ba913abcc91f2;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=069589e24b1c48ad60d07fda5842964ac9f156ce;hpb=fe021b84fb9a8a80ac6edd991f43d3bed2a110f7;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 069589e..d791cb6 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,22 +1,26 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 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; @@ -24,7 +28,6 @@ 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 @@ -124,28 +127,42 @@ 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
    • + *
  • 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).
    • + *
  • 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 $Revision$ */ @@ -183,7 +200,7 @@ public class Cache /** Default file is ~/.jalview_properties */ static String propertiesFile; - private static boolean propsAreReadOnly=false; + private static boolean propsAreReadOnly = false; public static void initLogger() { @@ -237,7 +254,9 @@ 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; } @@ -273,11 +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 @@ -337,8 +379,9 @@ 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; @@ -580,46 +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. */ @@ -738,6 +741,7 @@ public class Cache /** * get the user's default colour if available + * * @param property * @param defcolour * @return @@ -745,38 +749,44 @@ 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 */ @@ -784,8 +794,10 @@ 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 * @@ -793,35 +805,57 @@ 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 + * 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) + String val = getProperty(property); + if (val != null && (val = val.trim()).length() > 0) { - try { + try + { return Integer.valueOf(val); } catch (NumberFormatException x) { - System.err.println("Invalid integer in property '"+property+"' (value was '"+val+"')"); + 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; + } }