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
201 * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
202 * <li>NOHTMLTEMPLATES - when set, the
203 * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
204 * not downloaded automatically</li>
205 * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
206 * available URL linkouts via www.jalview.org/services/identifiers</li>
209 * Deprecated settings:
212 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
213 * startup (JWS1 services only)</li>
214 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
215 * (JWS1 services only)</li>
216 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
217 * services in the desktop GUI</li>
218 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
219 * panel in web service preferences</li>
223 * @version $Revision$
228 * property giving log4j level for CASTOR loggers
230 public static final String CASTORLOGLEVEL = "logs.Castor.level";
233 * property giving log4j level for AXIS loggers
235 public static final String AXISLOGLEVEL = "logs.Axis.level";
238 * property giving log4j level for Jalview Log
240 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
245 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
246 .getProperty("user.home") + File.separatorChar
247 + ".sifts_downloads" + File.separatorChar;
249 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
251 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
254 * Identifiers.org download settings
256 private static final String ID_ORG_FILE = System.getProperty("user.home")
257 + File.separatorChar + ".identifiers.org.ids.json";
260 * Allowed values are PDB or mmCIF
262 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
265 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
269 * a date formatter using a fixed (rather than the user's) locale;
270 * this ensures that date properties can be written and re-read successfully
271 * even if the user changes their locale setting
273 private static final DateFormat date_format = SimpleDateFormat
274 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
275 SimpleDateFormat.MEDIUM, Locale.UK);
278 * Initialises the Jalview Application Log
281 public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
283 // save the proxy properties set at startup
284 public final static String[] startupProxyProperties = {
285 System.getProperty("http.proxyHost"),
286 System.getProperty("http.proxyPort"),
287 System.getProperty("https.proxyHost"),
288 System.getProperty("https.proxyPort"),
289 System.getProperty("http.proxyUser"),
290 System.getProperty("http.proxyPassword"),
291 System.getProperty("https.proxyUser"),
292 System.getProperty("https.proxyPassword"),
293 System.getProperty("http.nonProxyHosts") };
295 public final static String PROXYTYPE_NONE = "none";
297 // "false" and "true" for backward compatibility
298 public final static String PROXYTYPE_SYSTEM = "false";
300 public final static String PROXYTYPE_CUSTOM = "true";
302 // in-memory only storage of proxy password, safer to use char array
303 public static char[] proxyAuthPassword = null;
305 /** Jalview Properties */
306 public static Properties applicationProperties = new Properties()
308 // override results in properties output in alphabetical order
310 public synchronized Enumeration<Object> keys()
312 return Collections.enumeration(new TreeSet<>(super.keySet()));
316 /* build Properties (not all saved to .jalview_properties) */
317 public static Properties buildProperties = new Properties();
319 /** Default file is ~/.jalview_properties */
320 static String propertiesFile;
322 private static boolean propsAreReadOnly = Platform.isJS();
324 private final static String JS_PROPERTY_PREFIX = "jalview_";
327 * Loads properties from the given properties file. Any existing properties
330 public static void loadProperties(String propsFile)
332 propertiesFile = propsFile;
333 String releasePropertiesFile = null;
334 boolean defaultProperties = false;
335 if (propsFile == null && !propsAreReadOnly)
337 String channelPrefsFilename = ChannelProperties
338 .getProperty("preferences.filename");
339 String releasePrefsFilename = ".jalview_properties";
340 propertiesFile = System.getProperty("user.home") + File.separatorChar
341 + channelPrefsFilename;
342 releasePropertiesFile = System.getProperty("user.home")
343 + File.separatorChar + releasePrefsFilename;
344 defaultProperties = true;
348 // don't corrupt the file we've been given.
349 propsAreReadOnly = true;
352 if (propertiesFile == null)
354 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
355 applicationProperties);
364 // props file provided as URL
365 fis = new URL(propertiesFile).openStream();
367 "Loading jalview properties from : " + propertiesFile);
369 "Disabling Jalview writing to user's local properties file.");
370 propsAreReadOnly = true;
371 } catch (Exception ex)
377 String readPropertiesFile = propertiesFile;
378 // if we're using the usual properties file and the channel properties
379 // file doesn't exist, read .jalview_properties
380 // (but we'll still save to the channel properties file).
381 if (defaultProperties && (!new File(propertiesFile).exists())
382 && (new File(releasePropertiesFile).exists()))
384 readPropertiesFile = releasePropertiesFile;
386 fis = new FileInputStream(readPropertiesFile);
388 applicationProperties.clear();
389 applicationProperties.load(fis);
391 // remove any old build properties
393 deleteBuildProperties();
395 } catch (Exception ex)
397 System.out.println("Error reading properties file: " + ex);
401 /* TO BE REPLACED WITH PROXY_TYPE SETTINGS
402 if (getDefault("USE_PROXY", false))
404 String proxyServer = getDefault("PROXY_SERVER", ""),
405 proxyPort = getDefault("PROXY_PORT", "8080");
409 // PROXY TYPE settings (now three options "none", "false", "true", but using
410 // backward compatible strings)
411 String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM);
412 // default to upgrading old settings
416 clearProxyProperties();
418 case PROXYTYPE_SYSTEM: // use system settings
419 resetProxyProperties();
421 case PROXYTYPE_CUSTOM: // use specified proxy settings
422 String httpHost = getDefault("PROXY_SERVER", "");
423 String httpPort = getDefault("PROXY_PORT", "8080");
424 String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
425 String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
426 String httpUser = getDefault("PROXY_AUTH_USER", null);
427 // https.proxyUser and https.proxyPassword are not able to be
428 // independently set in Preferences yet (or http.nonProxyHosts)
429 String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
430 setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
431 proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
434 String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
436 Console.warn(message);
439 // LOAD THE AUTHORS FROM THE authors.props file
440 String authorDetails = resolveResourceURLFor("/authors.props");
444 if (authorDetails != null)
446 URL localJarFileURL = new URL(authorDetails);
447 InputStream in = localJarFileURL.openStream();
448 applicationProperties.load(in);
451 } catch (Exception ex)
453 System.out.println("Error reading author details: " + ex);
454 authorDetails = null;
456 if (authorDetails == null)
458 applicationProperties.remove("AUTHORS");
459 applicationProperties.remove("AUTHORFNAMES");
460 applicationProperties.remove("YEAR");
463 loadBuildProperties(false);
466 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
468 SiftsSettings.setSiftDownloadDirectory(Cache
469 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
471 SiftsSettings.setFailSafePIDThreshold(
472 Cache.getDefault("sifts_fail_safe_pid_threshold",
473 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
475 SiftsSettings.setCacheThresholdInDays(
476 Cache.getDefault("sifts_cache_threshold_in_days",
477 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
479 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
480 "https://www.jalview.org/services/identifiers"));
481 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
483 StructureImportSettings.setDefaultStructureFileFormat(
484 Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
485 StructureImportSettings
486 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
487 // StructureImportSettings
488 // .setDefaultPDBFileParser(Cache.getDefault(
489 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
491 String jnlpVersion = System.getProperty("jalview.version");
493 // jnlpVersion will be null if a latest version check for the channel needs
495 // Dont do this check if running in headless mode
497 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
498 && (System.getProperty("java.awt.headless") == null || System
499 .getProperty("java.awt.headless").equals("false")))
502 class VersionChecker extends Thread
508 String remoteBuildPropertiesUrl = Cache
509 .getAppbaseBuildProperties();
511 String orgtimeout = System
512 .getProperty("sun.net.client.defaultConnectTimeout");
513 if (orgtimeout == null)
516 System.out.println("# INFO: Setting default net timeout to "
517 + orgtimeout + " seconds.");
519 String remoteVersion = null;
522 System.setProperty("sun.net.client.defaultConnectTimeout",
524 java.net.URL url = new java.net.URL(remoteBuildPropertiesUrl);
526 BufferedReader in = new BufferedReader(
527 new InputStreamReader(url.openStream()));
529 Properties remoteBuildProperties = new Properties();
530 remoteBuildProperties.load(in);
531 remoteVersion = remoteBuildProperties.getProperty("VERSION");
532 } catch (Exception ex)
535 .println("Non-fatal exception when checking version at "
536 + remoteBuildPropertiesUrl + ":");
537 System.out.println(ex);
538 remoteVersion = getProperty("VERSION");
540 System.setProperty("sun.net.client.defaultConnectTimeout",
543 setProperty("LATEST_VERSION", remoteVersion);
547 VersionChecker vc = new VersionChecker();
552 if (jnlpVersion != null)
554 setProperty("LATEST_VERSION", jnlpVersion);
558 applicationProperties.remove("LATEST_VERSION");
562 // LOAD USERDEFINED COLOURS
563 Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
564 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
569 * construct a resource URL for the given absolute resource pathname
571 * @param resourcePath
574 private static String resolveResourceURLFor(String resourcePath)
577 if (Platform.isJS() || !Cache.class.getProtectionDomain()
578 .getCodeSource().getLocation().toString().endsWith(".jar"))
582 url = Cache.class.getResource(resourcePath).toString();
583 } catch (Exception ex)
585 System.err.println("Failed to resolve resource " + resourcePath
586 + ": " + ex.getMessage());
591 url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
592 .getLocation().toString().concat("!" + resourcePath));
597 public static void loadBuildProperties(boolean reportVersion)
599 String codeInstallation = getProperty("INSTALLATION");
600 boolean printVersion = codeInstallation == null;
603 * read build properties - from the Jalview jar for a Java distribution,
604 * or from codebase file in test or JalviewJS context
608 String buildDetails = resolveResourceURLFor("/.build_properties");
609 URL localJarFileURL = new URL(buildDetails);
610 InputStream in = localJarFileURL.openStream();
611 buildProperties.load(in);
613 if (buildProperties.getProperty("BUILD_DATE", null) != null)
615 applicationProperties.put("BUILD_DATE",
616 buildProperties.getProperty("BUILD_DATE"));
618 if (buildProperties.getProperty("INSTALLATION", null) != null)
620 applicationProperties.put("INSTALLATION",
621 buildProperties.getProperty("INSTALLATION"));
623 if (buildProperties.getProperty("VERSION", null) != null)
625 applicationProperties.put("VERSION",
626 buildProperties.getProperty("VERSION"));
628 } catch (Exception ex)
630 System.out.println("Error reading build details: " + ex);
631 applicationProperties.remove("VERSION");
633 String codeVersion = getProperty("VERSION");
634 codeInstallation = getProperty("INSTALLATION");
636 if (codeVersion == null)
638 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
639 codeVersion = "Test";
640 codeInstallation = "";
644 codeInstallation = " (" + codeInstallation + ")";
646 setProperty("VERSION", codeVersion);
647 new BuildDetails(codeVersion, null, codeInstallation);
648 if (printVersion && reportVersion)
650 System.out.println(ChannelProperties.getProperty("app_name")
651 + " Version: " + codeVersion + codeInstallation);
655 private static void deleteBuildProperties()
657 applicationProperties.remove("LATEST_VERSION");
658 applicationProperties.remove("VERSION");
659 applicationProperties.remove("AUTHORS");
660 applicationProperties.remove("AUTHORFNAMES");
661 applicationProperties.remove("YEAR");
662 applicationProperties.remove("BUILD_DATE");
663 applicationProperties.remove("INSTALLATION");
667 * Gets Jalview application property of given key. Returns null if key not
673 * @return Property value
675 public static String getProperty(String key)
677 String prop = applicationProperties.getProperty(key);
678 if (prop == null && Platform.isJS())
680 prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
681 + "_" + JS_PROPERTY_PREFIX + key);
687 * These methods are used when checking if the saved preference is different
688 * to the default setting
691 public static boolean getDefault(String property, boolean def)
693 String string = getProperty(property);
696 def = Boolean.valueOf(string).booleanValue();
702 public static int getDefault(String property, int def)
704 String string = getProperty(property);
709 def = Integer.parseInt(string);
710 } catch (NumberFormatException e)
712 System.out.println("Error parsing int property '" + property
713 + "' with value '" + string + "'");
721 * Answers the value of the given property, or the supplied default value if
722 * the property is not set
724 public static String getDefault(String property, String def)
726 String value = getProperty(property);
727 return value == null ? def : value;
731 * Stores property in the file "HOME_DIR/.jalview_properties"
736 * String value of property
738 * @return previous value of property (or null)
740 public static Object setProperty(String key, String obj)
742 Object oldValue = null;
745 oldValue = applicationProperties.setProperty(key, obj);
746 if (propertiesFile != null && !propsAreReadOnly)
748 FileOutputStream out = new FileOutputStream(propertiesFile);
749 applicationProperties.store(out, "---JalviewX Properties File---");
752 } catch (Exception ex)
755 "Error setting property: " + key + " " + obj + "\n" + ex);
761 * remove the specified property from the jalview properties file
765 public static void removeProperty(String string)
767 applicationProperties.remove(string);
772 * save the properties to the jalview properties path
774 public static void saveProperties()
776 if (!propsAreReadOnly)
780 FileOutputStream out = new FileOutputStream(propertiesFile);
781 applicationProperties.store(out, "---JalviewX Properties File---");
783 } catch (Exception ex)
785 System.out.println("Error saving properties: " + ex);
791 * internal vamsas class discovery state
793 private static int vamsasJarsArePresent = -1;
796 * Searches for vamsas client classes on class path.
798 * @return true if vamsas client is present on classpath
800 public static boolean vamsasJarsPresent()
802 if (vamsasJarsArePresent == -1)
806 if (jalview.jbgui.GDesktop.class.getClassLoader()
807 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
809 Console.debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
810 vamsasJarsArePresent = 1;
811 JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
812 Console.getCachedLogLevel("logs.Vamsas.Level"));
813 JLoggerLog4j.addAppender(lvclient, Console.log, JALVIEW_LOGGER_NAME);
814 // Tell the user that debug is enabled
815 lvclient.debug(ChannelProperties.getProperty("app_name")
816 + " Vamsas Client Debugging Output Follows.");
818 } catch (Exception e)
820 vamsasJarsArePresent = 0;
821 Console.debug("Vamsas Classes are not present");
824 return (vamsasJarsArePresent > 0);
828 * internal vamsas class discovery state
830 private static int groovyJarsArePresent = -1;
833 * Searches for vamsas client classes on class path.
835 * @return true if vamsas client is present on classpath
837 public static boolean groovyJarsPresent()
839 if (groovyJarsArePresent == -1)
843 if (Cache.class.getClassLoader()
844 .loadClass("groovy.lang.GroovyObject") != null)
846 Console.debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
847 groovyJarsArePresent = 1;
848 JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
849 Console.getCachedLogLevel("logs.Groovy.Level"));
850 JLoggerLog4j.addAppender(lgclient, Console.log, JALVIEW_LOGGER_NAME);
851 // Tell the user that debug is enabled
852 lgclient.debug(ChannelProperties.getProperty("app_name")
853 + " Groovy Client Debugging Output Follows.");
857 groovyJarsArePresent = 0;
858 Console.debug("Groovy Classes are not present", e);
859 } catch (Exception e)
861 groovyJarsArePresent = 0;
862 Console.debug("Groovy Classes are not present");
865 return (groovyJarsArePresent > 0);
869 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
872 protected static Object tracker = null;
874 protected static Class trackerfocus = null;
876 protected static Class jgoogleanalyticstracker = null;
879 * Initialise the google tracker if it is not done already.
881 public static void initGoogleTracker()
885 if (jgoogleanalyticstracker == null)
887 // try to get the tracker class
890 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
891 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
892 trackerfocus = Cache.class.getClassLoader()
893 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
894 } catch (Exception e)
896 Console.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
898 jgoogleanalyticstracker = null;
903 // now initialise tracker
904 Exception re = null, ex = null;
906 String vrs = "No Version Accessible";
909 // Google analytics tracking code for Library Finder
910 tracker = jgoogleanalyticstracker
911 .getConstructor(new Class[]
912 { String.class, String.class, String.class })
913 .newInstance(new Object[]
914 { ChannelProperties.getProperty("app_name") + " Desktop",
915 (vrs = Cache.getProperty("VERSION") + "_"
916 + Cache.getDefault("BUILD_DATE", "unknown")),
918 jgoogleanalyticstracker
919 .getMethod("trackAsynchronously", new Class[]
921 .invoke(tracker, new Object[]
922 { trackerfocus.getConstructor(new Class[] { String.class })
923 .newInstance(new Object[]
924 { "Application Started." }) });
925 } catch (RuntimeException e)
928 } catch (Exception e)
935 if (re != null || ex != null || err != null)
939 Console.debug("Caught runtime exception in googletracker init:", re);
943 Console.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "
948 Console.error("Whilst initing GoogleTracker for Jalview Desktop version "
954 Console.debug("Successfully initialised tracker.");
960 * get the user's default colour if available
966 public static Color getDefaultColour(String property, Color defcolour)
968 String colprop = getProperty(property);
973 Color col = ColorUtils.parseColourString(colprop);
976 Console.warn("Couldn't parse '" + colprop + "' as a colour for " + property);
978 return (col == null) ? defcolour : col;
982 * store a colour as a Jalview user default property
987 public static void setColourProperty(String property, Color colour)
989 setProperty(property, jalview.util.Format.getHexString(colour));
993 * Stores a formatted date in a jalview property, using a fixed locale.
995 * @param propertyName
997 * @return the formatted date string
999 public static String setDateProperty(String propertyName, Date date)
1001 String formatted = date_format.format(date);
1002 setProperty(propertyName, formatted);
1007 * Reads a date stored in a Jalview property, parses it (using a fixed locale
1008 * format) and returns as a Date, or null if parsing fails
1010 * @param propertyName
1014 public static Date getDateProperty(String propertyName)
1016 String val = getProperty(propertyName);
1021 return date_format.parse(val);
1022 } catch (Exception ex)
1024 System.err.println("Invalid or corrupt date in property '"
1025 + propertyName + "' : value was '" + val + "'");
1032 * get and parse a property as an integer. send any parsing problems to
1036 * @return null or Integer
1038 public static Integer getIntegerProperty(String property)
1040 String val = getProperty(property);
1041 if (val != null && (val = val.trim()).length() > 0)
1045 return Integer.valueOf(val);
1046 } catch (NumberFormatException x)
1048 System.err.println("Invalid integer in property '" + property
1049 + "' (value was '" + val + "')");
1056 * Set the specified value, or remove it if null or empty. Does not save the
1062 public static void setOrRemove(String propName, String value)
1064 if (propName == null)
1068 if (value == null || value.trim().length() < 1)
1070 Cache.applicationProperties.remove(propName);
1074 Cache.applicationProperties.setProperty(propName, value);
1079 * Loads in user colour schemes from files.
1082 * a '|'-delimited list of file paths
1084 public static void initUserColourSchemes(String files)
1086 if (files == null || files.length() == 0)
1091 // In case colours can't be loaded, we'll remove them
1092 // from the default list here.
1093 StringBuffer coloursFound = new StringBuffer();
1094 StringTokenizer st = new StringTokenizer(files, "|");
1095 while (st.hasMoreElements())
1097 String file = st.nextToken();
1100 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1103 if (coloursFound.length() > 0)
1105 coloursFound.append("|");
1107 coloursFound.append(file);
1108 ColourSchemes.getInstance().registerColourScheme(ucs);
1110 } catch (Exception ex)
1112 System.out.println("Error loading User ColourFile\n" + ex);
1115 if (!files.equals(coloursFound.toString()))
1117 if (coloursFound.toString().length() > 1)
1119 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1120 coloursFound.toString());
1124 applicationProperties
1125 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1131 * Initial logging information helper for various versions output
1135 * @param defaultValue
1137 private static void appendIfNotNull(StringBuilder sb, String prefix,
1138 String value, String suffix, String defaultValue)
1140 if (value == null && defaultValue == null)
1144 String line = prefix + (value != null ? value : defaultValue) + suffix;
1150 * @return Jalview version, build details and JVM platform version for console
1152 public static String getVersionDetailsForConsole()
1154 StringBuilder sb = new StringBuilder();
1155 sb.append(ChannelProperties.getProperty("app_name"))
1156 .append(" Version: ");
1157 sb.append(Cache.getDefault("VERSION", "TEST"));
1159 sb.append(ChannelProperties.getProperty("app_name"))
1160 .append(" Installation: ");
1161 sb.append(Cache.getDefault("INSTALLATION", "unknown"));
1163 sb.append("Build Date: ");
1164 sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
1166 sb.append("Java version: ");
1167 sb.append(System.getProperty("java.version"));
1169 sb.append(System.getProperty("os.arch"));
1171 sb.append(System.getProperty("os.name"));
1173 sb.append(System.getProperty("os.version"));
1175 appendIfNotNull(sb, "Install4j version: ",
1176 System.getProperty("sys.install4jVersion"), "\n", null);
1177 appendIfNotNull(sb, "Install4j template version: ",
1178 System.getProperty("installer_template_version"), "\n", null);
1179 appendIfNotNull(sb, "Launcher version: ",
1180 System.getProperty("launcher_version"), "\n", null);
1181 LookAndFeel laf = UIManager.getLookAndFeel();
1182 String lafName = laf == null ? "Not obtained" : laf.getName();
1183 String lafClass = laf == null ? "unknown" : laf.getClass().getName();
1184 sb.append("LookAndFeel: ");
1187 sb.append(lafClass);
1189 // Not displayed in release version ( determined by possible version number
1190 // regex 9[9.]*9[.-_a9]* )
1191 if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
1192 Cache.getDefault("VERSION", "TEST")))
1194 appendIfNotNull(sb, "Getdown appdir: ",
1195 System.getProperty("getdownappdir"), "\n", null);
1196 appendIfNotNull(sb, "Getdown appbase: ",
1197 System.getProperty("getdownappbase"), "\n", null);
1198 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1201 return sb.toString();
1206 * @return build details as reported in splashscreen
1208 public static String getBuildDetailsForSplash()
1210 // consider returning more human friendly info
1211 // eg 'built from Source' or update channel
1212 return Cache.getDefault("INSTALLATION", "unknown");
1215 public static String getStackTraceString(Throwable t)
1217 StringWriter sw = new StringWriter();
1218 PrintWriter pw = new PrintWriter(sw);
1219 t.printStackTrace(pw);
1220 return sw.toString();
1223 // proxy properties methods
1224 public static void clearProxyProperties()
1226 setProxyProperties(null, null, null, null, null, null, null, null,
1230 public static void resetProxyProperties()
1232 setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
1233 startupProxyProperties[2], startupProxyProperties[3],
1234 startupProxyProperties[4],
1235 startupProxyProperties[5] == null ? null
1236 : startupProxyProperties[5].toCharArray(),
1237 startupProxyProperties[6],
1238 startupProxyProperties[7] == null ? null
1239 : startupProxyProperties[7].toCharArray(),
1240 startupProxyProperties[8]);
1241 StringBuilder sb = new StringBuilder();
1242 sb.append("Setting proxy properties to: http.proxyHost=")
1243 .append(startupProxyProperties[0]).append(", http.proxyPort=")
1244 .append(startupProxyProperties[1])
1245 .append(startupProxyProperties[4] != null
1246 && !startupProxyProperties[4].isEmpty()
1247 ? " [" + startupProxyProperties[4] + "]"
1249 .append(", https.proxyHost=").append(startupProxyProperties[2])
1250 .append(", https.proxyPort=").append(startupProxyProperties[3])
1251 .append(startupProxyProperties[6] != null
1252 && !startupProxyProperties[6].isEmpty()
1253 ? " [" + startupProxyProperties[6] + "]"
1256 Console.debug(sb.toString());
1259 public static void setProxyPropertiesFromPreferences()
1261 setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
1264 public static void setProxyPropertiesFromPreferences(
1265 String previousProxyType)
1267 String proxyType = Cache.getDefault("USE_PROXY",
1268 Cache.PROXYTYPE_SYSTEM);
1269 if (previousProxyType != null
1270 && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
1272 && proxyType.equals(previousProxyType))
1279 case Cache.PROXYTYPE_NONE:
1280 if (!previousProxyType.equals(proxyType))
1282 Console.info("Setting no proxy settings");
1283 Cache.setProxyProperties(null, null, null, null, null, null, null,
1287 case Cache.PROXYTYPE_CUSTOM:
1288 // always re-set a custom proxy -- it might have changed, particularly
1290 Console.info("Setting custom proxy settings");
1291 boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
1292 Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
1293 Cache.getDefault("PROXY_PORT", null),
1294 Cache.getDefault("PROXY_SERVER_HTTPS", null),
1295 Cache.getDefault("PROXY_PORT_HTTPS", null),
1296 proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
1298 proxyAuthSet ? Cache.proxyAuthPassword : null,
1299 proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
1301 proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
1303 default: // system proxy settings by default
1304 Console.info("Setting system proxy settings");
1305 Cache.resetProxyProperties();
1309 public static void setProxyProperties(String httpHost, String httpPort,
1310 String httpsHost, String httpsPort, String httpUser,
1311 char[] httpPassword, String httpsUser, char[] httpsPassword,
1312 String nonProxyHosts)
1314 setOrClearSystemProperty("http.proxyHost", httpHost);
1315 setOrClearSystemProperty("http.proxyPort", httpPort);
1316 setOrClearSystemProperty("https.proxyHost", httpsHost);
1317 setOrClearSystemProperty("https.proxyPort", httpsPort);
1318 setOrClearSystemProperty("http.proxyUser", httpUser);
1319 setOrClearSystemProperty("https.proxyUser", httpsUser);
1320 // note: passwords for http.proxyPassword and https.proxyPassword are sent
1321 // via the Authenticator, properties do not need to be set
1323 // are we using a custom proxy (password prompt might be required)?
1324 boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
1325 .equals(PROXYTYPE_CUSTOM);
1328 * A bug in Java means the AuthCache does not get reset, so once it has working credentials,
1329 * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
1330 * is not re-called).
1331 * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
1333 * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
1335 * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
1340 sun.net.www.protocol.http.AuthCacheValue
1341 .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
1342 } catch (Throwable t)
1344 Cache.error(t.getMessage());
1345 Cache.debug(getStackTraceString(t));
1349 if (httpUser != null || httpsUser != null)
1353 char[] displayHttpPw = new char[httpPassword == null ? 0
1354 : httpPassword.length];
1355 Arrays.fill(displayHttpPw, '*');
1356 Console.debug("CACHE Proxy: setting new Authenticator with httpUser='"
1357 + httpUser + "' httpPassword='" + displayHttpPw + "'");
1358 if (!Platform.isJS())
1360 * java.net.Authenticator not implemented in SwingJS yet
1366 Authenticator.setDefault(new Authenticator()
1369 protected PasswordAuthentication getPasswordAuthentication()
1371 if (getRequestorType() == RequestorType.PROXY)
1373 String protocol = getRequestingProtocol();
1374 boolean needProxyPasswordSet = false;
1375 if (customProxySet &&
1376 // we have a username but no password for the scheme being
1378 (protocol.equalsIgnoreCase("http")
1379 && (httpUser != null && httpUser.length() > 0
1380 && (httpPassword == null
1381 || httpPassword.length == 0)))
1382 || (protocol.equalsIgnoreCase("https")
1383 && (httpsUser != null
1384 && httpsUser.length() > 0
1385 && (httpsPassword == null
1386 || httpsPassword.length == 0))))
1388 // open Preferences -> Connections
1389 String message = MessageManager
1390 .getString("label.proxy_password_required");
1391 Preferences.openPreferences(
1392 Preferences.TabRef.CONNECTIONS_TAB, message);
1393 Preferences.getInstance()
1394 .proxyAuthPasswordCheckHighlight(true, true);
1400 if (protocol.equalsIgnoreCase("http")
1401 && getRequestingHost()
1402 .equalsIgnoreCase(httpHost)
1403 && getRequestingPort() == Integer
1407 "AUTHENTICATOR returning PasswordAuthentication(\""
1408 + httpUser + "\", '"
1409 + new String(displayHttpPw) + "')");
1410 return new PasswordAuthentication(httpUser,
1413 if (protocol.equalsIgnoreCase("https")
1414 && getRequestingHost()
1415 .equalsIgnoreCase(httpsHost)
1416 && getRequestingPort() == Integer
1417 .valueOf(httpsPort))
1419 char[] displayHttpsPw = new char[httpPassword.length];
1420 Arrays.fill(displayHttpsPw, '*');
1422 "AUTHENTICATOR returning PasswordAuthentication(\""
1423 + httpsUser + "\", '" + displayHttpsPw
1425 return new PasswordAuthentication(httpsUser,
1428 } catch (NumberFormatException e)
1430 Console.error("Problem with proxy port values [http:"
1431 + httpPort + ", https:" + httpsPort + "]");
1434 "AUTHENTICATOR after trying to get PasswordAuthentication");
1437 // non proxy request
1438 Console.debug("AUTHENTICATOR returning null");
1442 } // end of j2sIgnore for java.net.Authenticator
1444 // required to re-enable basic authentication (should be okay for a
1447 "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
1448 System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
1449 } catch (SecurityException e)
1451 Console.error("Could not set default Authenticator");
1452 Console.debug(getStackTraceString(e));
1457 // reset the Authenticator to protect http.proxyUser and
1458 // http.proxyPassword Just In Case
1459 /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
1460 * has working credentials. No workaround for Java 11.
1462 if (!Platform.isJS())
1464 * java.net.Authenticator not implemented in SwingJS yet
1470 Console.debug("AUTHENTICATOR setting default Authenticator to null");
1471 Authenticator.setDefault(null);
1475 // nonProxyHosts not currently configurable in Preferences
1476 Console.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
1477 + nonProxyHosts + "\"");
1478 setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
1481 public static void setOrClearSystemProperty(String key, char[] value)
1483 setOrClearSystemProperty(key,
1484 (value == null) ? null : new String(value));
1487 public static void setOrClearSystemProperty(String key, String value)
1495 System.clearProperty(key);
1499 System.setProperty(key, value);
1504 * Getdown appbase methods
1507 private static final String releaseAppbase;
1509 private static String getdownAppbase;
1511 private static String getdownDistDir;
1515 if (!Platform.isJS())
1517 Float specversion = Float
1518 .parseFloat(System.getProperty("java.specification.version"));
1519 releaseAppbase = (specversion < 9)
1520 ? "https://www.jalview.org/getdown/release/1.8"
1521 : "https://www.jalview.org/getdown/release/11";
1525 // this value currenly made up, can be changed to URL that will be
1526 // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
1527 releaseAppbase = "https://www.jalview.org/jalview-js";
1528 getdownAppbase = releaseAppbase;
1529 getdownDistDir = "/swingjs/j2s";
1533 // look for properties (passed in by getdown) otherwise default to release
1534 private static void setGetdownAppbase()
1536 if (getdownAppbase != null)
1540 String appbase = System.getProperty("getdownappbase");
1541 String distDir = System.getProperty("getdowndistdir");
1542 if (appbase == null)
1544 appbase = buildProperties.getProperty("GETDOWNAPPBASE");
1545 distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
1547 if (appbase == null)
1549 appbase = releaseAppbase;
1550 distDir = "release";
1552 if (appbase.endsWith("/"))
1554 appbase = appbase.substring(0, appbase.length() - 1);
1556 if (distDir == null)
1558 distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
1560 getdownAppbase = appbase;
1561 getdownDistDir = distDir;
1564 public static String getGetdownAppbase()
1566 setGetdownAppbase();
1567 return getdownAppbase;
1570 public static String getAppbaseBuildProperties()
1572 String appbase = getGetdownAppbase();
1573 return appbase + "/" + getdownDistDir + "/build_properties";