X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=9363c233c17ebe530e8ee62cf39f80a809a01a5b;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=a3950937e94cc35d907da9f791c9658192eb1586;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index a395093..9363c23 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,33 +1,56 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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.datamodel.PDBEntry; +import jalview.gui.UserDefinedColours; +import jalview.schemes.ColourSchemes; +import jalview.schemes.UserColourScheme; +import jalview.structure.StructureImportSettings; +import jalview.util.ColorUtils; import jalview.ws.dbsources.das.api.DasSourceRegistryI; import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; +import jalview.ws.sifts.SiftsSettings; 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 org.apache.log4j.*; +import java.util.Collections; +import java.util.Date; +import java.util.Enumeration; +import java.util.Locale; +import java.util.Properties; +import java.util.StringTokenizer; +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 @@ -61,6 +84,10 @@ import org.apache.log4j.*; *
  • 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
    • @@ -132,6 +159,7 @@ import org.apache.log4j.*; *
  • 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 @@ -140,14 +168,22 @@ import org.apache.log4j.*; * 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: @@ -189,13 +225,48 @@ public class Cache public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE"; + public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System + .getProperty("user.home") + + File.separatorChar + + ".sifts_downloads" + File.separatorChar; + + private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2"; + + private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30"; + + /** + * Allowed values are PDB or mmCIF + */ + private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF + .toString(); + + private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER + .toString(); + + /* + * a date formatter using a fixed (rather than the user's) locale; + * this ensures that date properties can be written and re-read successfully + * even if the user changes their locale setting + */ + private static final DateFormat date_format = SimpleDateFormat + .getDateTimeInstance(SimpleDateFormat.MEDIUM, + SimpleDateFormat.MEDIUM, Locale.UK); + /** * Initialises the Jalview Application Log */ 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; @@ -282,8 +353,10 @@ 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) { @@ -344,16 +417,44 @@ 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 = ""; } + else + { + codeInstallation = " (" + codeInstallation + ")"; + } + new BuildDetails(codeVersion, null, codeInstallation); + + SiftsSettings + .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); - System.out.println("Jalview Version: " + codeVersion); + SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault( + "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); + SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault( + "sifts_fail_safe_pid_threshold", + DEFAULT_FAIL_SAFE_PID_THRESHOLD)); + + SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault( + "sifts_cache_threshold_in_days", + DEFAULT_CACHE_THRESHOLD_IN_DAYS)); + + System.out + .println("Jalview Version: " + codeVersion + codeInstallation); + + StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache + .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); + StructureImportSettings + .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); + // StructureImportSettings + // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( + // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); // jnlpVersion will be null if we're using InstallAnywhere // Dont do this check if running in headless mode if (jnlpVersion == null @@ -364,6 +465,7 @@ public class Cache class VersionChecker extends Thread { + @Override public void run() { String orgtimeout = System @@ -374,7 +476,7 @@ public class Cache System.out.println("# INFO: Setting default net timeout to " + orgtimeout + " seconds."); } - String jnlpVersion = null; + String remoteVersion = null; try { System.setProperty("sun.net.client.defaultConnectTimeout", @@ -394,20 +496,20 @@ public class Cache line = line.substring(line.indexOf("value=") + 7); line = line.substring(0, line.lastIndexOf("\"")); - jnlpVersion = line; + remoteVersion = line; break; } } catch (Exception ex) { System.out - .println("Non-fatal exceptions when checking version at www.jalview.org :"); + .println("Non-fatal exception when checking version at www.jalview.org :"); System.out.println(ex); - jnlpVersion = getProperty("VERSION"); + remoteVersion = getProperty("VERSION"); } System.setProperty("sun.net.client.defaultConnectTimeout", orgtimeout); - setProperty("LATEST_VERSION", jnlpVersion); + setProperty("LATEST_VERSION", remoteVersion); } } @@ -429,12 +531,23 @@ public class Cache setProperty("VERSION", codeVersion); // LOAD USERDEFINED COLOURS - jalview.gui.UserDefinedColours + jalview.bin.Cache .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", 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 @@ -666,21 +779,22 @@ 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; @@ -696,15 +810,21 @@ 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 { @@ -753,19 +873,11 @@ public class Cache { return defcolour; } - Color col = jalview.schemes.ColourSchemeProperty - .getAWTColorFromName(colprop); + Color col = ColorUtils.parseColourString(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; - } + log.warn("Couldn't parse '" + colprop + "' as a colour for " + + property); } return (col == null) ? defcolour : col; } @@ -781,30 +893,31 @@ public class Cache setProperty(property, jalview.util.Format.getHexString(colour)); } - public static final DateFormat date_format = SimpleDateFormat - .getDateTimeInstance(); - /** - * store a date in a jalview property + * Stores a formatted date in a jalview property, using a fixed locale. * - * @param string - * @param time + * @param propertyName + * @param date + * @return the formatted date string */ - public static void setDateProperty(String property, Date time) + public static String setDateProperty(String propertyName, Date date) { - setProperty(property, date_format.format(time)); + String formatted = date_format.format(date); + setProperty(propertyName, formatted); + return formatted; } /** - * read a date stored in a jalview property + * Reads a date stored in a Jalview property, parses it (using a fixed locale + * format) and returns as a Date, or null if parsing fails * - * @param property - * @return valid date as stored by setDateProperty, or null + * @param propertyName + * @return * */ - public static Date getDateProperty(String property) + public static Date getDateProperty(String propertyName) { - String val = getProperty(property); + String val = getProperty(propertyName); if (val != null) { try @@ -813,7 +926,7 @@ public class Cache } catch (Exception ex) { System.err.println("Invalid or corrupt date in property '" - + property + "' : value was '" + val + "'"); + + propertyName + "' : value was '" + val + "'"); } } return null; @@ -858,4 +971,77 @@ public class Cache } 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); + } + } + + /** + * Loads in user colour schemes from files. + * + * @param files + * a '|'-delimited list of file paths + */ + public static void initUserColourSchemes(String files) + { + if (files == null || files.length() == 0) + { + return; + } + + // In case colours can't be loaded, we'll remove them + // from the default list here. + StringBuffer coloursFound = new StringBuffer(); + StringTokenizer st = new StringTokenizer(files, "|"); + while (st.hasMoreElements()) + { + String file = st.nextToken(); + try + { + UserColourScheme ucs = ColourSchemes.loadColourScheme(file); + if (ucs != null) + { + if (coloursFound.length() > 0) + { + coloursFound.append("|"); + } + coloursFound.append(file); + ColourSchemes.getInstance().registerColourScheme(ucs); + } + } catch (Exception ex) + { + System.out.println("Error loading User ColourFile\n" + ex); + } + } + if (!files.equals(coloursFound.toString())) + { + if (coloursFound.toString().length() > 1) + { + setProperty(UserDefinedColours.USER_DEFINED_COLOURS, coloursFound.toString()); + } + else + { + applicationProperties.remove(UserDefinedColours.USER_DEFINED_COLOURS); + } + } + } }