2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.awt.Color;
24 import java.io.BufferedReader;
26 import java.io.FileInputStream;
27 import java.io.FileOutputStream;
28 import java.io.InputStream;
29 import java.io.InputStreamReader;
30 import java.io.PrintWriter;
31 import java.io.StringWriter;
32 import java.net.Authenticator;
33 import java.net.PasswordAuthentication;
35 import java.text.DateFormat;
36 import java.text.SimpleDateFormat;
37 import java.util.Arrays;
38 import java.util.Collections;
39 import java.util.Date;
40 import java.util.Enumeration;
41 import java.util.Locale;
42 import java.util.Properties;
43 import java.util.StringTokenizer;
44 import java.util.TreeSet;
45 import java.util.regex.Pattern;
47 import javax.swing.LookAndFeel;
48 import javax.swing.UIManager;
50 import jalview.datamodel.PDBEntry;
51 import jalview.gui.Preferences;
52 import jalview.gui.UserDefinedColours;
53 import jalview.log.JLoggerLog4j;
54 import jalview.schemes.ColourSchemeLoader;
55 import jalview.schemes.ColourSchemes;
56 import jalview.schemes.UserColourScheme;
57 import jalview.structure.StructureImportSettings;
58 import jalview.urls.IdOrgSettings;
59 import jalview.util.ChannelProperties;
60 import jalview.util.ColorUtils;
61 import jalview.util.MessageManager;
62 import jalview.util.Platform;
63 import jalview.ws.sifts.SiftsSettings;
66 * Stores and retrieves Jalview Application Properties Lists and fields within
67 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
68 * are alternative values for a tag. <br>
70 * Current properties include:
73 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
74 * logging level for axis (used for web services) <br>
76 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
77 * the logging level for castor (used for serialization) <br>
79 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
81 * <li>SCREEN_WIDTH</li>
82 * <li>SCREEN_HEIGHT</li>
83 * <li>SCREEN_Y=285</li>
84 * <li>SCREEN_X=371</li>
85 * <li>SHOW_FULLSCREEN boolean</li>
86 * <li>FONT_NAME java font name for alignment text display</li>
87 * <li>FONT_SIZE size of displayed alignment text</li>
88 * <li>FONT_STYLE style of font displayed (sequence labels are always
90 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
91 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
92 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
93 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
94 * <li>SHOW_IDENTITY show percentage identity annotation</li>
95 * <li>SHOW_QUALITY show alignment quality annotation</li>
96 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
97 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
98 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
99 * LABEL_AND_SEQUENCE</li>
100 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
101 * sequence annotations</li>
102 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
103 * annotation row</li>
104 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
105 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
106 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
107 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
108 * <li>VERSION the version of the jalview build</li>
109 * <li>BUILD_DATE date of this build</li>
110 * <li>LATEST_VERSION the latest jalview version advertised on the
111 * www.jalview.org</li>
112 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
114 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
115 * suffix to file</li>
116 * <li>RECENT_URL list of recently retrieved URLs</li>
117 * <li>RECENT_FILE list of recently opened files</li>
118 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
119 * <li>PROXY_SERVER the proxy</li>
120 * <li>PROXY_PORT</li>
121 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
123 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
125 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
126 * collecting usage statistics</li>
127 * <li>SHOW_OVERVIEW boolean for overview window display</li>
128 * <li>ANTI_ALIAS boolean for smooth fonts</li>
129 * <li>RIGHT_ALIGN_IDS boolean</li>
130 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
131 * <li>PAD_GAPS boolean</li>
132 * <li>ID_ITALICS boolean</li>
133 * <li>SHOW_JV_SUFFIX</li>
134 * <li>WRAP_ALIGNMENT</li>
135 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
137 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
138 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
140 * <li>STORED_LINKS list of name|url pairs which user has entered but are not
142 * <li>DEFAULT_LINK name of single url to be used when user double clicks a
143 * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
144 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
145 * jalview.utils.GroupURLLink for more info</li>
146 * <li>DEFAULT_BROWSER for unix</li>
147 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
149 * <li>VERSION_CHECK (true) check for the latest release version from
150 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
151 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
153 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
155 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
156 * displayed as '.'</li>
157 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
158 * order of a newly displayed tree</li>
159 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
160 * sequence ID strings before attempting retrieval from any datasource</li>
161 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
163 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
164 * in the alignment.</li>
165 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
167 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
169 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
170 * logo normalised to row height rather than histogram height.</li>
171 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
172 * respond to selections made in other alignments containing the same sequences.
174 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
175 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
176 * warning dialog box is displayed.</li>
177 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
178 * when shading by annotation</li>
179 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
180 * when shading by annotation</li>
181 * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
182 * requests to be redirected to a mirror of https://www.jalview.org</li>
183 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
184 * alignment figure to accommodate even the longest sequence ID or annotation
186 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
187 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
188 * will override this).</li>
189 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
191 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
192 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
194 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
196 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
198 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
199 * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
203 * Deprecated settings:
206 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
207 * startup (JWS1 services only)</li>
208 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
209 * (JWS1 services only)</li>
210 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
211 * services in the desktop GUI</li>
212 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
213 * panel in web service preferences</li>
217 * @version $Revision$
222 * property giving log4j level for CASTOR loggers
224 public static final String CASTORLOGLEVEL = "logs.Castor.level";
227 * property giving log4j level for AXIS loggers
229 public static final String AXISLOGLEVEL = "logs.Axis.level";
232 * property giving log4j level for Jalview Log
234 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
239 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
240 .getProperty("user.home") + File.separatorChar
241 + ".sifts_downloads" + File.separatorChar;
243 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
245 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
248 * Identifiers.org download settings
250 private static final String ID_ORG_FILE = System.getProperty("user.home")
251 + File.separatorChar + ".identifiers.org.ids.json";
254 * Allowed values are PDB or mmCIF
256 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
259 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
263 * a date formatter using a fixed (rather than the user's) locale;
264 * this ensures that date properties can be written and re-read successfully
265 * even if the user changes their locale setting
267 private static final DateFormat date_format = SimpleDateFormat
268 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
269 SimpleDateFormat.MEDIUM, Locale.UK);
272 * Initialises the Jalview Application Log
275 public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
277 // save the proxy properties set at startup
278 public final static String[] startupProxyProperties = {
279 System.getProperty("http.proxyHost"),
280 System.getProperty("http.proxyPort"),
281 System.getProperty("https.proxyHost"),
282 System.getProperty("https.proxyPort"),
283 System.getProperty("http.proxyUser"),
284 System.getProperty("http.proxyPassword"),
285 System.getProperty("https.proxyUser"),
286 System.getProperty("https.proxyPassword"),
287 System.getProperty("http.nonProxyHosts") };
289 public final static String PROXYTYPE_NONE = "none";
291 // "false" and "true" for backward compatibility
292 public final static String PROXYTYPE_SYSTEM = "false";
294 public final static String PROXYTYPE_CUSTOM = "true";
296 // in-memory only storage of proxy password, safer to use char array
297 public static char[] proxyAuthPassword = null;
299 /** Jalview Properties */
300 public static Properties applicationProperties = new Properties()
302 // override results in properties output in alphabetical order
304 public synchronized Enumeration<Object> keys()
306 return Collections.enumeration(new TreeSet<>(super.keySet()));
310 /* build Properties (not all saved to .jalview_properties) */
311 public static Properties buildProperties = new Properties();
313 /** Default file is ~/.jalview_properties */
314 static String propertiesFile;
316 private static boolean propsAreReadOnly = Platform.isJS();
318 private final static String JS_PROPERTY_PREFIX = "jalview_";
321 * Loads properties from the given properties file. Any existing properties
324 public static void loadProperties(String propsFile)
326 propertiesFile = propsFile;
327 String releasePropertiesFile = null;
328 boolean defaultProperties = false;
329 if (propsFile == null && !propsAreReadOnly)
331 String channelPrefsFilename = ChannelProperties
332 .getProperty("preferences.filename");
333 String releasePrefsFilename = ".jalview_properties";
334 propertiesFile = System.getProperty("user.home") + File.separatorChar
335 + channelPrefsFilename;
336 releasePropertiesFile = System.getProperty("user.home")
337 + File.separatorChar + releasePrefsFilename;
338 defaultProperties = true;
342 // don't corrupt the file we've been given.
343 propsAreReadOnly = true;
346 if (propertiesFile == null)
348 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
349 applicationProperties);
358 // props file provided as URL
359 fis = new URL(propertiesFile).openStream();
361 "Loading jalview properties from : " + propertiesFile);
363 "Disabling Jalview writing to user's local properties file.");
364 propsAreReadOnly = true;
365 } catch (Exception ex)
371 String readPropertiesFile = propertiesFile;
372 // if we're using the usual properties file and the channel properties
373 // file doesn't exist, read .jalview_properties
374 // (but we'll still save to the channel properties file).
375 if (defaultProperties && (!new File(propertiesFile).exists())
376 && (new File(releasePropertiesFile).exists()))
378 readPropertiesFile = releasePropertiesFile;
380 fis = new FileInputStream(readPropertiesFile);
382 applicationProperties.clear();
383 applicationProperties.load(fis);
385 // remove any old build properties
387 deleteBuildProperties();
389 } catch (Exception ex)
391 System.out.println("Error reading properties file: " + ex);
395 /* TO BE REPLACED WITH PROXY_TYPE SETTINGS
396 if (getDefault("USE_PROXY", false))
398 String proxyServer = getDefault("PROXY_SERVER", ""),
399 proxyPort = getDefault("PROXY_PORT", "8080");
403 // PROXY TYPE settings (now three options "none", "false", "true", but using
404 // backward compatible strings)
405 String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM);
406 // default to upgrading old settings
410 clearProxyProperties();
412 case PROXYTYPE_SYSTEM: // use system settings
413 resetProxyProperties();
415 case PROXYTYPE_CUSTOM: // use specified proxy settings
416 String httpHost = getDefault("PROXY_SERVER", "");
417 String httpPort = getDefault("PROXY_PORT", "8080");
418 String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
419 String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
420 String httpUser = getDefault("PROXY_AUTH_USER", null);
421 // https.proxyUser and https.proxyPassword are not able to be
422 // independently set in Preferences yet (or http.nonProxyHosts)
423 String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
424 setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
425 proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
428 String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
430 Console.warn(message);
433 // LOAD THE AUTHORS FROM THE authors.props file
434 String authorDetails = resolveResourceURLFor("/authors.props");
438 if (authorDetails != null)
440 URL localJarFileURL = new URL(authorDetails);
441 InputStream in = localJarFileURL.openStream();
442 applicationProperties.load(in);
445 } catch (Exception ex)
447 System.out.println("Error reading author details: " + ex);
448 authorDetails = null;
450 if (authorDetails == null)
452 applicationProperties.remove("AUTHORS");
453 applicationProperties.remove("AUTHORFNAMES");
454 applicationProperties.remove("YEAR");
457 loadBuildProperties(false);
460 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
462 SiftsSettings.setSiftDownloadDirectory(Cache
463 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
465 SiftsSettings.setFailSafePIDThreshold(
466 Cache.getDefault("sifts_fail_safe_pid_threshold",
467 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
469 SiftsSettings.setCacheThresholdInDays(
470 Cache.getDefault("sifts_cache_threshold_in_days",
471 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
473 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
474 "https://www.jalview.org/services/identifiers"));
475 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
477 StructureImportSettings.setDefaultStructureFileFormat(
478 Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
479 StructureImportSettings
480 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
481 // StructureImportSettings
482 // .setDefaultPDBFileParser(Cache.getDefault(
483 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
485 String jnlpVersion = System.getProperty("jalview.version");
487 // jnlpVersion will be null if a latest version check for the channel needs
489 // Dont do this check if running in headless mode
491 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
492 && (System.getProperty("java.awt.headless") == null || System
493 .getProperty("java.awt.headless").equals("false")))
496 class VersionChecker extends Thread
502 String remoteBuildPropertiesUrl = Cache
503 .getAppbaseBuildProperties();
505 String orgtimeout = System
506 .getProperty("sun.net.client.defaultConnectTimeout");
507 if (orgtimeout == null)
510 System.out.println("# INFO: Setting default net timeout to "
511 + orgtimeout + " seconds.");
513 String remoteVersion = null;
516 System.setProperty("sun.net.client.defaultConnectTimeout",
518 java.net.URL url = new java.net.URL(remoteBuildPropertiesUrl);
520 BufferedReader in = new BufferedReader(
521 new InputStreamReader(url.openStream()));
523 Properties remoteBuildProperties = new Properties();
524 remoteBuildProperties.load(in);
525 remoteVersion = remoteBuildProperties.getProperty("VERSION");
526 } catch (Exception ex)
529 .println("Non-fatal exception when checking version at "
530 + remoteBuildPropertiesUrl + ":");
531 System.out.println(ex);
532 remoteVersion = getProperty("VERSION");
534 System.setProperty("sun.net.client.defaultConnectTimeout",
537 setProperty("LATEST_VERSION", remoteVersion);
541 VersionChecker vc = new VersionChecker();
546 if (jnlpVersion != null)
548 setProperty("LATEST_VERSION", jnlpVersion);
552 applicationProperties.remove("LATEST_VERSION");
556 // LOAD USERDEFINED COLOURS
557 Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
558 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
563 * construct a resource URL for the given absolute resource pathname
565 * @param resourcePath
568 private static String resolveResourceURLFor(String resourcePath)
571 if (Platform.isJS() || !Cache.class.getProtectionDomain()
572 .getCodeSource().getLocation().toString().endsWith(".jar"))
576 url = Cache.class.getResource(resourcePath).toString();
577 } catch (Exception ex)
579 System.err.println("Failed to resolve resource " + resourcePath
580 + ": " + ex.getMessage());
585 url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
586 .getLocation().toString().concat("!" + resourcePath));
591 public static void loadBuildProperties(boolean reportVersion)
593 String codeInstallation = getProperty("INSTALLATION");
594 boolean printVersion = codeInstallation == null;
597 * read build properties - from the Jalview jar for a Java distribution,
598 * or from codebase file in test or JalviewJS context
602 String buildDetails = resolveResourceURLFor("/.build_properties");
603 URL localJarFileURL = new URL(buildDetails);
604 InputStream in = localJarFileURL.openStream();
605 buildProperties.load(in);
607 if (buildProperties.getProperty("BUILD_DATE", null) != null)
609 applicationProperties.put("BUILD_DATE",
610 buildProperties.getProperty("BUILD_DATE"));
612 if (buildProperties.getProperty("INSTALLATION", null) != null)
614 applicationProperties.put("INSTALLATION",
615 buildProperties.getProperty("INSTALLATION"));
617 if (buildProperties.getProperty("VERSION", null) != null)
619 applicationProperties.put("VERSION",
620 buildProperties.getProperty("VERSION"));
622 } catch (Exception ex)
624 System.out.println("Error reading build details: " + ex);
625 applicationProperties.remove("VERSION");
627 String codeVersion = getProperty("VERSION");
628 codeInstallation = getProperty("INSTALLATION");
630 if (codeVersion == null)
632 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
633 codeVersion = "Test";
634 codeInstallation = "";
638 codeInstallation = " (" + codeInstallation + ")";
640 setProperty("VERSION", codeVersion);
641 new BuildDetails(codeVersion, null, codeInstallation);
642 if (printVersion && reportVersion)
644 System.out.println(ChannelProperties.getProperty("app_name")
645 + " Version: " + codeVersion + codeInstallation);
649 private static void deleteBuildProperties()
651 applicationProperties.remove("LATEST_VERSION");
652 applicationProperties.remove("VERSION");
653 applicationProperties.remove("AUTHORS");
654 applicationProperties.remove("AUTHORFNAMES");
655 applicationProperties.remove("YEAR");
656 applicationProperties.remove("BUILD_DATE");
657 applicationProperties.remove("INSTALLATION");
661 * Gets Jalview application property of given key. Returns null if key not
667 * @return Property value
669 public static String getProperty(String key)
671 String prop = applicationProperties.getProperty(key);
672 if (prop == null && Platform.isJS())
674 prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
675 + "_" + JS_PROPERTY_PREFIX + key);
681 * These methods are used when checking if the saved preference is different
682 * to the default setting
685 public static boolean getDefault(String property, boolean def)
687 String string = getProperty(property);
690 def = Boolean.valueOf(string).booleanValue();
696 public static int getDefault(String property, int def)
698 String string = getProperty(property);
703 def = Integer.parseInt(string);
704 } catch (NumberFormatException e)
706 System.out.println("Error parsing int property '" + property
707 + "' with value '" + string + "'");
715 * Answers the value of the given property, or the supplied default value if
716 * the property is not set
718 public static String getDefault(String property, String def)
720 String value = getProperty(property);
721 return value == null ? def : value;
725 * Stores property in the file "HOME_DIR/.jalview_properties"
730 * String value of property
732 * @return previous value of property (or null)
734 public static Object setProperty(String key, String obj)
736 Object oldValue = null;
739 oldValue = applicationProperties.setProperty(key, obj);
740 if (propertiesFile != null && !propsAreReadOnly)
742 FileOutputStream out = new FileOutputStream(propertiesFile);
743 applicationProperties.store(out, "---JalviewX Properties File---");
746 } catch (Exception ex)
749 "Error setting property: " + key + " " + obj + "\n" + ex);
755 * remove the specified property from the jalview properties file
759 public static void removeProperty(String string)
761 applicationProperties.remove(string);
766 * save the properties to the jalview properties path
768 public static void saveProperties()
770 if (!propsAreReadOnly)
774 FileOutputStream out = new FileOutputStream(propertiesFile);
775 applicationProperties.store(out, "---JalviewX Properties File---");
777 } catch (Exception ex)
779 System.out.println("Error saving properties: " + ex);
785 * internal vamsas class discovery state
787 private static int vamsasJarsArePresent = -1;
790 * Searches for vamsas client classes on class path.
792 * @return true if vamsas client is present on classpath
794 public static boolean vamsasJarsPresent()
796 if (vamsasJarsArePresent == -1)
800 if (jalview.jbgui.GDesktop.class.getClassLoader()
801 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
803 Console.debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
804 vamsasJarsArePresent = 1;
805 JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
806 Console.getCachedLogLevel("logs.Vamsas.Level"));
807 JLoggerLog4j.addAppender(lvclient, Console.log, JALVIEW_LOGGER_NAME);
808 // Tell the user that debug is enabled
809 lvclient.debug(ChannelProperties.getProperty("app_name")
810 + " Vamsas Client Debugging Output Follows.");
812 } catch (Exception e)
814 vamsasJarsArePresent = 0;
815 Console.debug("Vamsas Classes are not present");
818 return (vamsasJarsArePresent > 0);
822 * internal vamsas class discovery state
824 private static int groovyJarsArePresent = -1;
827 * Searches for vamsas client classes on class path.
829 * @return true if vamsas client is present on classpath
831 public static boolean groovyJarsPresent()
833 if (groovyJarsArePresent == -1)
837 if (Cache.class.getClassLoader()
838 .loadClass("groovy.lang.GroovyObject") != null)
840 Console.debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
841 groovyJarsArePresent = 1;
842 JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
843 Console.getCachedLogLevel("logs.Groovy.Level"));
844 JLoggerLog4j.addAppender(lgclient, Console.log, JALVIEW_LOGGER_NAME);
845 // Tell the user that debug is enabled
846 lgclient.debug(ChannelProperties.getProperty("app_name")
847 + " Groovy Client Debugging Output Follows.");
851 groovyJarsArePresent = 0;
852 Console.debug("Groovy Classes are not present", e);
853 } catch (Exception e)
855 groovyJarsArePresent = 0;
856 Console.debug("Groovy Classes are not present");
859 return (groovyJarsArePresent > 0);
863 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
866 protected static Object tracker = null;
868 protected static Class trackerfocus = null;
870 protected static Class jgoogleanalyticstracker = null;
873 * Initialise the google tracker if it is not done already.
875 public static void initGoogleTracker()
879 if (jgoogleanalyticstracker == null)
881 // try to get the tracker class
884 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
885 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
886 trackerfocus = Cache.class.getClassLoader()
887 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
888 } catch (Exception e)
890 Console.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
892 jgoogleanalyticstracker = null;
897 // now initialise tracker
898 Exception re = null, ex = null;
900 String vrs = "No Version Accessible";
903 // Google analytics tracking code for Library Finder
904 tracker = jgoogleanalyticstracker
905 .getConstructor(new Class[]
906 { String.class, String.class, String.class })
907 .newInstance(new Object[]
908 { ChannelProperties.getProperty("app_name") + " Desktop",
909 (vrs = Cache.getProperty("VERSION") + "_"
910 + Cache.getDefault("BUILD_DATE", "unknown")),
912 jgoogleanalyticstracker
913 .getMethod("trackAsynchronously", new Class[]
915 .invoke(tracker, new Object[]
916 { trackerfocus.getConstructor(new Class[] { String.class })
917 .newInstance(new Object[]
918 { "Application Started." }) });
919 } catch (RuntimeException e)
922 } catch (Exception e)
929 if (re != null || ex != null || err != null)
933 Console.debug("Caught runtime exception in googletracker init:", re);
937 Console.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "
942 Console.error("Whilst initing GoogleTracker for Jalview Desktop version "
948 Console.debug("Successfully initialised tracker.");
954 * get the user's default colour if available
960 public static Color getDefaultColour(String property, Color defcolour)
962 String colprop = getProperty(property);
967 Color col = ColorUtils.parseColourString(colprop);
970 Console.warn("Couldn't parse '" + colprop + "' as a colour for " + property);
972 return (col == null) ? defcolour : col;
976 * store a colour as a Jalview user default property
981 public static void setColourProperty(String property, Color colour)
983 setProperty(property, jalview.util.Format.getHexString(colour));
987 * Stores a formatted date in a jalview property, using a fixed locale.
989 * @param propertyName
991 * @return the formatted date string
993 public static String setDateProperty(String propertyName, Date date)
995 String formatted = date_format.format(date);
996 setProperty(propertyName, formatted);
1001 * Reads a date stored in a Jalview property, parses it (using a fixed locale
1002 * format) and returns as a Date, or null if parsing fails
1004 * @param propertyName
1008 public static Date getDateProperty(String propertyName)
1010 String val = getProperty(propertyName);
1015 return date_format.parse(val);
1016 } catch (Exception ex)
1018 System.err.println("Invalid or corrupt date in property '"
1019 + propertyName + "' : value was '" + val + "'");
1026 * get and parse a property as an integer. send any parsing problems to
1030 * @return null or Integer
1032 public static Integer getIntegerProperty(String property)
1034 String val = getProperty(property);
1035 if (val != null && (val = val.trim()).length() > 0)
1039 return Integer.valueOf(val);
1040 } catch (NumberFormatException x)
1042 System.err.println("Invalid integer in property '" + property
1043 + "' (value was '" + val + "')");
1050 * Set the specified value, or remove it if null or empty. Does not save the
1056 public static void setOrRemove(String propName, String value)
1058 if (propName == null)
1062 if (value == null || value.trim().length() < 1)
1064 Cache.applicationProperties.remove(propName);
1068 Cache.applicationProperties.setProperty(propName, value);
1073 * Loads in user colour schemes from files.
1076 * a '|'-delimited list of file paths
1078 public static void initUserColourSchemes(String files)
1080 if (files == null || files.length() == 0)
1085 // In case colours can't be loaded, we'll remove them
1086 // from the default list here.
1087 StringBuffer coloursFound = new StringBuffer();
1088 StringTokenizer st = new StringTokenizer(files, "|");
1089 while (st.hasMoreElements())
1091 String file = st.nextToken();
1094 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1097 if (coloursFound.length() > 0)
1099 coloursFound.append("|");
1101 coloursFound.append(file);
1102 ColourSchemes.getInstance().registerColourScheme(ucs);
1104 } catch (Exception ex)
1106 System.out.println("Error loading User ColourFile\n" + ex);
1109 if (!files.equals(coloursFound.toString()))
1111 if (coloursFound.toString().length() > 1)
1113 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1114 coloursFound.toString());
1118 applicationProperties
1119 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1125 * Initial logging information helper for various versions output
1129 * @param defaultValue
1131 private static void appendIfNotNull(StringBuilder sb, String prefix,
1132 String value, String suffix, String defaultValue)
1134 if (value == null && defaultValue == null)
1138 String line = prefix + (value != null ? value : defaultValue) + suffix;
1144 * @return Jalview version, build details and JVM platform version for console
1146 public static String getVersionDetailsForConsole()
1148 StringBuilder sb = new StringBuilder();
1149 sb.append(ChannelProperties.getProperty("app_name"))
1150 .append(" Version: ");
1151 sb.append(Cache.getDefault("VERSION", "TEST"));
1153 sb.append(ChannelProperties.getProperty("app_name"))
1154 .append(" Installation: ");
1155 sb.append(Cache.getDefault("INSTALLATION", "unknown"));
1157 sb.append("Build Date: ");
1158 sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
1160 sb.append("Java version: ");
1161 sb.append(System.getProperty("java.version"));
1163 sb.append(System.getProperty("os.arch"));
1165 sb.append(System.getProperty("os.name"));
1167 sb.append(System.getProperty("os.version"));
1169 appendIfNotNull(sb, "Install4j version: ",
1170 System.getProperty("sys.install4jVersion"), "\n", null);
1171 appendIfNotNull(sb, "Install4j template version: ",
1172 System.getProperty("installer_template_version"), "\n", null);
1173 appendIfNotNull(sb, "Launcher version: ",
1174 System.getProperty("launcher_version"), "\n", null);
1175 LookAndFeel laf = UIManager.getLookAndFeel();
1176 String lafName = laf == null ? "Not obtained" : laf.getName();
1177 String lafClass = laf == null ? "unknown" : laf.getClass().getName();
1178 sb.append("LookAndFeel: ");
1181 sb.append(lafClass);
1183 // Not displayed in release version ( determined by possible version number
1184 // regex 9[9.]*9[.-_a9]* )
1185 if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
1186 Cache.getDefault("VERSION", "TEST")))
1188 appendIfNotNull(sb, "Getdown appdir: ",
1189 System.getProperty("getdownappdir"), "\n", null);
1190 appendIfNotNull(sb, "Getdown appbase: ",
1191 System.getProperty("getdownappbase"), "\n", null);
1192 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1195 return sb.toString();
1200 * @return build details as reported in splashscreen
1202 public static String getBuildDetailsForSplash()
1204 // consider returning more human friendly info
1205 // eg 'built from Source' or update channel
1206 return Cache.getDefault("INSTALLATION", "unknown");
1209 public static String getStackTraceString(Throwable t)
1211 StringWriter sw = new StringWriter();
1212 PrintWriter pw = new PrintWriter(sw);
1213 t.printStackTrace(pw);
1214 return sw.toString();
1217 // proxy properties methods
1218 public static void clearProxyProperties()
1220 setProxyProperties(null, null, null, null, null, null, null, null,
1224 public static void resetProxyProperties()
1226 setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
1227 startupProxyProperties[2], startupProxyProperties[3],
1228 startupProxyProperties[4],
1229 startupProxyProperties[5] == null ? null
1230 : startupProxyProperties[5].toCharArray(),
1231 startupProxyProperties[6],
1232 startupProxyProperties[7] == null ? null
1233 : startupProxyProperties[7].toCharArray(),
1234 startupProxyProperties[8]);
1235 StringBuilder sb = new StringBuilder();
1236 sb.append("Setting proxy properties to: http.proxyHost=")
1237 .append(startupProxyProperties[0]).append(", http.proxyPort=")
1238 .append(startupProxyProperties[1])
1239 .append(startupProxyProperties[4] != null
1240 && !startupProxyProperties[4].isEmpty()
1241 ? " [" + startupProxyProperties[4] + "]"
1243 .append(", https.proxyHost=").append(startupProxyProperties[2])
1244 .append(", https.proxyPort=").append(startupProxyProperties[3])
1245 .append(startupProxyProperties[6] != null
1246 && !startupProxyProperties[6].isEmpty()
1247 ? " [" + startupProxyProperties[6] + "]"
1250 Console.debug(sb.toString());
1253 public static void setProxyPropertiesFromPreferences()
1255 setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
1258 public static void setProxyPropertiesFromPreferences(
1259 String previousProxyType)
1261 String proxyType = Cache.getDefault("USE_PROXY",
1262 Cache.PROXYTYPE_SYSTEM);
1263 if (previousProxyType != null
1264 && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
1266 && proxyType.equals(previousProxyType))
1273 case Cache.PROXYTYPE_NONE:
1274 if (!previousProxyType.equals(proxyType))
1276 Console.info("Setting no proxy settings");
1277 Cache.setProxyProperties(null, null, null, null, null, null, null,
1281 case Cache.PROXYTYPE_CUSTOM:
1282 // always re-set a custom proxy -- it might have changed, particularly
1284 Console.info("Setting custom proxy settings");
1285 boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
1286 Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
1287 Cache.getDefault("PROXY_PORT", null),
1288 Cache.getDefault("PROXY_SERVER_HTTPS", null),
1289 Cache.getDefault("PROXY_PORT_HTTPS", null),
1290 proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
1292 proxyAuthSet ? Cache.proxyAuthPassword : null,
1293 proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
1295 proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
1297 default: // system proxy settings by default
1298 Console.info("Setting system proxy settings");
1299 Cache.resetProxyProperties();
1303 public static void setProxyProperties(String httpHost, String httpPort,
1304 String httpsHost, String httpsPort, String httpUser,
1305 char[] httpPassword, String httpsUser, char[] httpsPassword,
1306 String nonProxyHosts)
1308 setOrClearSystemProperty("http.proxyHost", httpHost);
1309 setOrClearSystemProperty("http.proxyPort", httpPort);
1310 setOrClearSystemProperty("https.proxyHost", httpsHost);
1311 setOrClearSystemProperty("https.proxyPort", httpsPort);
1312 setOrClearSystemProperty("http.proxyUser", httpUser);
1313 setOrClearSystemProperty("https.proxyUser", httpsUser);
1314 // note: passwords for http.proxyPassword and https.proxyPassword are sent
1315 // via the Authenticator, properties do not need to be set
1317 // are we using a custom proxy (password prompt might be required)?
1318 boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
1319 .equals(PROXYTYPE_CUSTOM);
1322 * A bug in Java means the AuthCache does not get reset, so once it has working credentials,
1323 * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
1324 * is not re-called).
1325 * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
1327 * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
1329 * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
1334 sun.net.www.protocol.http.AuthCacheValue
1335 .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
1336 } catch (Throwable t)
1338 Cache.error(t.getMessage());
1339 Cache.debug(getStackTraceString(t));
1343 if (httpUser != null || httpsUser != null)
1347 char[] displayHttpPw = new char[httpPassword == null ? 0
1348 : httpPassword.length];
1349 Arrays.fill(displayHttpPw, '*');
1350 Console.debug("CACHE Proxy: setting new Authenticator with httpUser='"
1351 + httpUser + "' httpPassword='" + displayHttpPw + "'");
1352 if (!Platform.isJS())
1354 * java.net.Authenticator not implemented in SwingJS yet
1360 Authenticator.setDefault(new Authenticator()
1363 protected PasswordAuthentication getPasswordAuthentication()
1365 if (getRequestorType() == RequestorType.PROXY)
1367 String protocol = getRequestingProtocol();
1368 boolean needProxyPasswordSet = false;
1369 if (customProxySet &&
1370 // we have a username but no password for the scheme being
1372 (protocol.equalsIgnoreCase("http")
1373 && (httpUser != null && httpUser.length() > 0
1374 && (httpPassword == null
1375 || httpPassword.length == 0)))
1376 || (protocol.equalsIgnoreCase("https")
1377 && (httpsUser != null
1378 && httpsUser.length() > 0
1379 && (httpsPassword == null
1380 || httpsPassword.length == 0))))
1382 // open Preferences -> Connections
1383 String message = MessageManager
1384 .getString("label.proxy_password_required");
1385 Preferences.openPreferences(
1386 Preferences.TabRef.CONNECTIONS_TAB, message);
1387 Preferences.getInstance()
1388 .proxyAuthPasswordCheckHighlight(true, true);
1394 if (protocol.equalsIgnoreCase("http")
1395 && getRequestingHost()
1396 .equalsIgnoreCase(httpHost)
1397 && getRequestingPort() == Integer
1401 "AUTHENTICATOR returning PasswordAuthentication(\""
1402 + httpUser + "\", '"
1403 + new String(displayHttpPw) + "')");
1404 return new PasswordAuthentication(httpUser,
1407 if (protocol.equalsIgnoreCase("https")
1408 && getRequestingHost()
1409 .equalsIgnoreCase(httpsHost)
1410 && getRequestingPort() == Integer
1411 .valueOf(httpsPort))
1413 char[] displayHttpsPw = new char[httpPassword.length];
1414 Arrays.fill(displayHttpsPw, '*');
1416 "AUTHENTICATOR returning PasswordAuthentication(\""
1417 + httpsUser + "\", '" + displayHttpsPw
1419 return new PasswordAuthentication(httpsUser,
1422 } catch (NumberFormatException e)
1424 Console.error("Problem with proxy port values [http:"
1425 + httpPort + ", https:" + httpsPort + "]");
1428 "AUTHENTICATOR after trying to get PasswordAuthentication");
1431 // non proxy request
1432 Console.debug("AUTHENTICATOR returning null");
1436 } // end of j2sIgnore for java.net.Authenticator
1438 // required to re-enable basic authentication (should be okay for a
1441 "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
1442 System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
1443 } catch (SecurityException e)
1445 Console.error("Could not set default Authenticator");
1446 Console.debug(getStackTraceString(e));
1451 // reset the Authenticator to protect http.proxyUser and
1452 // http.proxyPassword Just In Case
1453 /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
1454 * has working credentials. No workaround for Java 11.
1456 if (!Platform.isJS())
1458 * java.net.Authenticator not implemented in SwingJS yet
1464 Console.debug("AUTHENTICATOR setting default Authenticator to null");
1465 Authenticator.setDefault(null);
1469 // nonProxyHosts not currently configurable in Preferences
1470 Console.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
1471 + nonProxyHosts + "\"");
1472 setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
1475 public static void setOrClearSystemProperty(String key, char[] value)
1477 setOrClearSystemProperty(key,
1478 (value == null) ? null : new String(value));
1481 public static void setOrClearSystemProperty(String key, String value)
1489 System.clearProperty(key);
1493 System.setProperty(key, value);
1498 * Getdown appbase methods
1501 private static final String releaseAppbase;
1503 private static String getdownAppbase;
1505 private static String getdownDistDir;
1509 if (!Platform.isJS())
1511 Float specversion = Float
1512 .parseFloat(System.getProperty("java.specification.version"));
1513 releaseAppbase = (specversion < 9)
1514 ? "https://www.jalview.org/getdown/release/1.8"
1515 : "https://www.jalview.org/getdown/release/11";
1519 // this value currenly made up, can be changed to URL that will be
1520 // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
1521 releaseAppbase = "https://www.jalview.org/jalview-js";
1522 getdownAppbase = releaseAppbase;
1523 getdownDistDir = "/swingjs/j2s";
1527 // look for properties (passed in by getdown) otherwise default to release
1528 private static void setGetdownAppbase()
1530 if (getdownAppbase != null)
1534 String appbase = System.getProperty("getdownappbase");
1535 String distDir = System.getProperty("getdowndistdir");
1536 if (appbase == null)
1538 appbase = buildProperties.getProperty("GETDOWNAPPBASE");
1539 distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
1541 if (appbase == null)
1543 appbase = releaseAppbase;
1544 distDir = "release";
1546 if (appbase.endsWith("/"))
1548 appbase = appbase.substring(0, appbase.length() - 1);
1550 if (distDir == null)
1552 distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
1554 getdownAppbase = appbase;
1555 getdownDistDir = distDir;
1558 public static String getGetdownAppbase()
1560 setGetdownAppbase();
1561 return getdownAppbase;
1564 public static String getAppbaseBuildProperties()
1566 String appbase = getGetdownAppbase();
1567 return appbase + "/" + getdownDistDir + "/build_properties";