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.FileNotFoundException;
28 import java.io.FileOutputStream;
29 import java.io.IOException;
30 import java.io.InputStream;
31 import java.io.InputStreamReader;
32 import java.io.PrintWriter;
33 import java.io.StringWriter;
34 import java.net.Authenticator;
35 import java.net.PasswordAuthentication;
37 import java.text.DateFormat;
38 import java.text.SimpleDateFormat;
39 import java.util.ArrayList;
40 import java.util.Arrays;
41 import java.util.Collection;
42 import java.util.Collections;
43 import java.util.Date;
44 import java.util.Enumeration;
45 import java.util.HashMap;
46 import java.util.List;
47 import java.util.Locale;
49 import java.util.Properties;
50 import java.util.StringTokenizer;
51 import java.util.TreeSet;
53 import javax.swing.LookAndFeel;
54 import javax.swing.UIManager;
56 import jalview.analytics.Plausible;
57 import jalview.bin.argparser.Arg;
58 import jalview.bin.argparser.ArgParser;
59 import jalview.datamodel.PDBEntry;
60 import jalview.gui.Preferences;
61 import jalview.gui.UserDefinedColours;
62 import jalview.log.JLoggerLog4j;
63 import jalview.schemes.ColourSchemeLoader;
64 import jalview.schemes.ColourSchemes;
65 import jalview.schemes.UserColourScheme;
66 import jalview.structure.StructureImportSettings;
67 import jalview.urls.IdOrgSettings;
68 import jalview.util.ChannelProperties;
69 import jalview.util.ColorUtils;
70 import jalview.util.HttpUtils;
71 import jalview.util.MessageManager;
72 import jalview.util.Platform;
73 import jalview.ws.sifts.SiftsSettings;
76 * Stores and retrieves Jalview Application Properties Lists and fields within
77 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
78 * are alternative values for a tag. <br>
80 * Current properties include:
83 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
84 * logging level for axis (used for web services) <br>
86 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
87 * the logging level for castor (used for serialization) <br>
89 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
91 * <li>SCREEN_WIDTH</li>
92 * <li>SCREEN_HEIGHT</li>
93 * <li>SCREEN_Y=285</li>
94 * <li>SCREEN_X=371</li>
95 * <li>SHOW_FULLSCREEN boolean</li>
96 * <li>FONT_NAME java font name for alignment text display</li>
97 * <li>FONT_SIZE size of displayed alignment text</li>
98 * <li>FONT_STYLE style of font displayed (sequence labels are always
100 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
101 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
102 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
103 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
104 * <li>SHOW_IDENTITY show percentage identity annotation</li>
105 * <li>SHOW_QUALITY show alignment quality annotation</li>
106 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
107 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
108 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
109 * LABEL_AND_SEQUENCE</li>
110 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
111 * sequence annotations</li>
112 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
113 * annotation row</li>
114 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
115 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
116 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
117 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
118 * <li>VERSION the version of the jalview build</li>
119 * <li>BUILD_DATE date of this build</li>
120 * <li>LATEST_VERSION the latest jalview version advertised on the
121 * www.jalview.org</li>
122 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
124 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
125 * suffix to file</li>
126 * <li>RECENT_URL list of recently retrieved URLs</li>
127 * <li>RECENT_FILE list of recently opened files</li>
128 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
129 * <li>PROXY_SERVER the proxy</li>
130 * <li>PROXY_PORT</li>
131 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
133 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
135 * <li>USAGESTATS (false - user prompted) Enable analytics tracker for
136 * collecting usage statistics</li>
137 * <li>SHOW_OVERVIEW boolean for overview window display</li>
138 * <li>ANTI_ALIAS boolean for smooth fonts</li>
139 * <li>RIGHT_ALIGN_IDS boolean</li>
140 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
141 * <li>PAD_GAPS boolean</li>
142 * <li>ID_ITALICS boolean</li>
143 * <li>SHOW_JV_SUFFIX</li>
144 * <li>WRAP_ALIGNMENT</li>
145 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
147 * <li>BITMAP_SCALE - scale factor for PNG export - default 0.0 - native
149 * <li>BITMAP_HEIGHT - height bound for PNG export or 0 for unbound</li>
150 * <li>BITMAP_WIDTH - width bound for PNG export or 0 for unbound</li>
151 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
152 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
154 * <li>STORED_LINKS list of name|url pairs which user has entered but are not
156 * <li>DEFAULT_LINK name of single url to be used when user double clicks a
157 * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
158 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
159 * jalview.utils.GroupURLLink for more info</li>
160 * <li>DEFAULT_BROWSER for unix</li>
161 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
163 * <li>VERSION_CHECK (true) check for the latest release version from
164 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
165 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
167 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
169 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
170 * displayed as '.'</li>
171 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
172 * order of a newly displayed tree</li>
173 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
174 * sequence ID strings before attempting retrieval from any datasource</li>
175 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
177 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
178 * in the alignment.</li>
179 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
181 * <li>SHOW_SSCONSENSUS_HISTOGRAM (false) Show secondary structure consensus annotation row's
183 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
185 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
186 * logo normalised to row height rather than histogram height.</li>
187 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
188 * respond to selections made in other alignments containing the same sequences.
190 * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
191 * auto-discover JABAWS services</li>
192 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
193 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
194 * warning dialog box is displayed.</li>
195 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
196 * when shading by annotation</li>
197 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
198 * when shading by annotation</li>
199 * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
200 * requests to be redirected to a mirror of https://www.jalview.org</li>
201 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
202 * alignment figure to accommodate even the longest sequence ID or annotation
204 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
205 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
206 * will override this).</li>
207 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
209 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
210 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
212 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
214 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
216 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
217 * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
219 * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
220 * <li>NOHTMLTEMPLATES - when set, the
221 * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
222 * not downloaded automatically</li>
223 * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
224 * available URL linkouts via www.jalview.org/services/identifiers</li>
227 * Deprecated settings:
230 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
231 * startup (JWS1 services only)</li>
232 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
233 * (JWS1 services only)</li>
234 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
235 * services in the desktop GUI</li>
236 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
237 * panel in web service preferences</li>
241 * @version $Revision$
246 * property giving log4j level for CASTOR loggers
248 public static final String CASTORLOGLEVEL = "logs.Castor.level";
251 * property giving log4j level for AXIS loggers
253 public static final String AXISLOGLEVEL = "logs.Axis.level";
256 * property giving log4j level for Jalview Log
258 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
261 public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
266 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
267 .getProperty("user.home") + File.separatorChar
268 + ".sifts_downloads" + File.separatorChar;
270 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
272 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
275 * Identifiers.org download settings
277 private static final String ID_ORG_FILE = System.getProperty("user.home")
278 + File.separatorChar + ".identifiers.org.ids.json";
281 * Allowed values are PDB or mmCIF
283 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
286 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
290 * a date formatter using a fixed (rather than the user's) locale;
291 * this ensures that date properties can be written and re-read successfully
292 * even if the user changes their locale setting
294 private static final DateFormat date_format = SimpleDateFormat
295 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
296 SimpleDateFormat.MEDIUM, Locale.UK);
299 * Initialises the Jalview Application Log
302 public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
304 // save the proxy properties set at startup
305 public final static String[] startupProxyProperties = {
306 System.getProperty("http.proxyHost"),
307 System.getProperty("http.proxyPort"),
308 System.getProperty("https.proxyHost"),
309 System.getProperty("https.proxyPort"),
310 System.getProperty("http.proxyUser"),
311 System.getProperty("http.proxyPassword"),
312 System.getProperty("https.proxyUser"),
313 System.getProperty("https.proxyPassword"),
314 System.getProperty("http.nonProxyHosts") };
316 public final static String PROXYTYPE_NONE = "none";
318 // "false" and "true" for backward compatibility
319 public final static String PROXYTYPE_SYSTEM = "false";
321 public final static String PROXYTYPE_CUSTOM = "true";
323 // in-memory only storage of proxy password, safer to use char array
324 public static char[] proxyAuthPassword = null;
327 * Session properties, set by command line, try not to affect stored
330 private static Map<String, String> sessionProperties = new HashMap<>();
332 private static boolean bypassSessionProperties = false;
334 public static void enableSessionProperties()
336 bypassSessionProperties = false;
339 public static void disableSessionProperties()
341 bypassSessionProperties = true;
344 /** Jalview Properties */
345 public static Properties applicationProperties = new Properties()
347 // override results in properties output in alphabetical order
349 public synchronized Enumeration<Object> keys()
351 return Collections.enumeration(new TreeSet<>(super.keySet()));
355 /* build Properties (not all saved to .jalview_properties) */
356 public static Properties buildProperties = new Properties();
358 /** Default file is ~/.jalview_properties */
359 static String propertiesFile;
361 private static final String fallbackPropertiesFile = ".jalview_properties";
363 private static boolean propsAreReadOnly = Platform.isJS();
365 public static boolean isPropsAreReadOnly()
367 return propsAreReadOnly;
370 public static void setPropsAreReadOnly(boolean propsAreReadOnly)
372 Cache.propsAreReadOnly = propsAreReadOnly;
375 private final static String JS_PROPERTY_PREFIX = "jalview_";
378 * Loads properties from the given properties file. Any existing properties
381 public static void loadProperties(String propsFile)
383 propertiesFile = propsFile;
384 String releasePropertiesFile = null;
385 boolean defaultProperties = false;
386 if (propsFile == null && !propsAreReadOnly)
388 String channelPrefsFilename = ChannelProperties
389 .getProperty("preferences.filename");
390 String releasePrefsFilename = fallbackPropertiesFile;
391 propertiesFile = System.getProperty("user.home") + File.separatorChar
392 + channelPrefsFilename;
393 releasePropertiesFile = System.getProperty("user.home")
394 + File.separatorChar + releasePrefsFilename;
395 defaultProperties = true;
399 // don't corrupt the file we've been given.
400 propsAreReadOnly = true;
403 if (propertiesFile == null)
405 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
406 applicationProperties);
415 // props file provided as URL
416 fis = HttpUtils.openStream(new URL(propertiesFile));
417 if (!Jalview.quiet())
419 jalview.bin.Console.outPrintln(
420 "Loading jalview properties from : " + propertiesFile);
421 jalview.bin.Console.outPrintln(
422 "Disabling Jalview writing to user's local properties file.");
424 propsAreReadOnly = true;
425 } catch (Exception ex)
431 String readPropertiesFile = propertiesFile;
432 // if we're using the usual properties file and the channel properties
433 // file doesn't exist, read .jalview_properties
434 // (but we'll still save to the channel properties file).
435 if (defaultProperties && (!new File(propertiesFile).exists())
436 && (new File(releasePropertiesFile).exists()))
438 readPropertiesFile = releasePropertiesFile;
440 fis = new FileInputStream(readPropertiesFile);
442 applicationProperties.clear();
443 applicationProperties.load(fis);
445 // remove any old build properties
447 deleteBuildProperties();
449 } catch (Exception ex)
451 if (!Jalview.quiet())
453 .outPrintln("Error reading properties file: " + ex);
457 /* TO BE REPLACED WITH PROXY_TYPE SETTINGS
458 if (getDefault("USE_PROXY", false))
460 String proxyServer = getDefault("PROXY_SERVER", ""),
461 proxyPort = getDefault("PROXY_PORT", "8080");
465 // PROXY TYPE settings (now three options "none", "false", "true", but using
466 // backward compatible strings)
467 String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM);
468 // default to upgrading old settings
472 clearProxyProperties();
474 case PROXYTYPE_SYSTEM: // use system settings
475 resetProxyProperties();
477 case PROXYTYPE_CUSTOM: // use specified proxy settings
478 String httpHost = getDefault("PROXY_SERVER", "");
479 String httpPort = getDefault("PROXY_PORT", "8080");
480 String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
481 String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
482 String httpUser = getDefault("PROXY_AUTH_USER", null);
483 // https.proxyUser and https.proxyPassword are not able to be
484 // independently set in Preferences yet (or http.nonProxyHosts)
485 String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
486 setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
487 proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
490 String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
492 Console.warn(message);
495 // LOAD THE AUTHORS FROM THE authors.props file
496 String authorDetails = resolveResourceURLFor("/authors.props");
500 if (authorDetails != null)
502 URL localJarFileURL = new URL(authorDetails);
503 InputStream in = localJarFileURL.openStream();
504 applicationProperties.load(in);
507 } catch (Exception ex)
509 if (!Jalview.quiet())
511 .outPrintln("Error reading author details: " + ex);
512 authorDetails = null;
514 if (authorDetails == null)
516 applicationProperties.remove("AUTHORS");
517 applicationProperties.remove("AUTHORFNAMES");
518 applicationProperties.remove("YEAR");
521 loadBuildProperties(false);
524 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
526 SiftsSettings.setSiftDownloadDirectory(Cache
527 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
529 SiftsSettings.setFailSafePIDThreshold(
530 Cache.getDefault("sifts_fail_safe_pid_threshold",
531 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
533 SiftsSettings.setCacheThresholdInDays(
534 Cache.getDefault("sifts_cache_threshold_in_days",
535 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
537 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
538 "https://www.jalview.org/services/identifiers"));
539 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
541 StructureImportSettings.setDefaultStructureFileFormat(
542 Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
543 StructureImportSettings
544 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
545 // StructureImportSettings
546 // .setDefaultPDBFileParser(Cache.getDefault(
547 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
549 String jnlpVersion = System.getProperty("jalview.version");
551 // jnlpVersion will be null if a latest version check for the channel needs
553 // Dont do this check if running in headless mode
555 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
556 && (System.getProperty("java.awt.headless") == null || System
557 .getProperty("java.awt.headless").equals("false")))
560 class VersionChecker extends Thread
566 String remoteBuildPropertiesUrl = Cache
567 .getAppbaseBuildProperties();
569 String orgtimeout = System
570 .getProperty("sun.net.client.defaultConnectTimeout");
571 if (orgtimeout == null)
574 Console.debug("Setting default net timeout to " + orgtimeout
577 String remoteVersion = null;
578 if (remoteBuildPropertiesUrl.startsWith("http"))
582 System.setProperty("sun.net.client.defaultConnectTimeout",
585 URL url = new URL(remoteBuildPropertiesUrl);
587 BufferedReader in = new BufferedReader(
588 new InputStreamReader(HttpUtils.openStream(url)));
590 Properties remoteBuildProperties = new Properties();
591 remoteBuildProperties.load(in);
592 remoteVersion = remoteBuildProperties.getProperty("VERSION");
593 } catch (Exception ex)
595 if (!Jalview.quiet())
597 jalview.bin.Console.errPrintln(
598 "Non-fatal exception when checking version at "
599 + remoteBuildPropertiesUrl + ":");
600 jalview.bin.Console.printStackTrace(ex);
602 remoteVersion = getProperty("VERSION");
605 System.setProperty("sun.net.client.defaultConnectTimeout",
608 setProperty("LATEST_VERSION", remoteVersion);
612 VersionChecker vc = new VersionChecker();
617 if (jnlpVersion != null)
619 setProperty("LATEST_VERSION", jnlpVersion);
623 applicationProperties.remove("LATEST_VERSION");
627 // LOAD USERDEFINED COLOURS
628 Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
629 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
634 * construct a resource URL for the given absolute resource pathname
636 * @param resourcePath
639 private static String resolveResourceURLFor(String resourcePath)
642 if (Platform.isJS() || !Cache.class.getProtectionDomain()
643 .getCodeSource().getLocation().toString().endsWith(".jar"))
647 url = Cache.class.getResource(resourcePath).toString();
648 } catch (Exception ex)
650 jalview.bin.Console.errPrintln("Failed to resolve resource "
651 + resourcePath + ": " + ex.getMessage());
656 url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
657 .getLocation().toString().concat("!" + resourcePath));
662 public static void loadBuildProperties(boolean reportVersion)
664 String codeInstallation = getProperty("INSTALLATION");
665 boolean printVersion = codeInstallation == null;
668 * read build properties - from the Jalview jar for a Java distribution,
669 * or from codebase file in test or JalviewJS context
673 String buildDetails = resolveResourceURLFor("/.build_properties");
674 URL localJarFileURL = new URL(buildDetails);
675 InputStream in = localJarFileURL.openStream();
676 buildProperties.load(in);
678 if (buildProperties.getProperty("BUILD_DATE", null) != null)
680 applicationProperties.put("BUILD_DATE",
681 buildProperties.getProperty("BUILD_DATE"));
683 if (buildProperties.getProperty("INSTALLATION", null) != null)
685 applicationProperties.put("INSTALLATION",
686 buildProperties.getProperty("INSTALLATION"));
688 if (buildProperties.getProperty("VERSION", null) != null)
690 applicationProperties.put("VERSION",
691 buildProperties.getProperty("VERSION"));
693 if (buildProperties.getProperty("JAVA_COMPILE_VERSION", null) != null)
695 applicationProperties.put("JAVA_COMPILE_VERSION",
696 buildProperties.getProperty("JAVA_COMPILE_VERSION"));
698 } catch (Exception ex)
700 if (!Jalview.quiet())
702 .outPrintln("Error reading build details: " + ex);
703 applicationProperties.remove("VERSION");
705 String codeVersion = getProperty("VERSION");
706 codeInstallation = getProperty("INSTALLATION");
708 if (codeVersion == null)
710 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
711 codeVersion = "Test";
712 codeInstallation = "";
716 codeInstallation = " (" + codeInstallation + ")";
718 setProperty("VERSION", codeVersion);
719 new BuildDetails(codeVersion, null, codeInstallation);
720 if (printVersion && reportVersion)
723 .outPrintln(ChannelProperties.getProperty("app_name")
724 + " version: " + codeVersion + codeInstallation);
728 private static void deleteBuildProperties()
730 applicationProperties.remove("LATEST_VERSION");
731 applicationProperties.remove("VERSION");
732 applicationProperties.remove("AUTHORS");
733 applicationProperties.remove("AUTHORFNAMES");
734 applicationProperties.remove("YEAR");
735 applicationProperties.remove("BUILD_DATE");
736 applicationProperties.remove("INSTALLATION");
740 * Gets Jalview application property of given key. Returns null if key not
746 * @return Property value
748 public static String getProperty(String key)
750 return getProperty(key, false);
753 public static String getProperty(String key,
754 boolean skipSessionProperties)
757 if (!(skipSessionProperties || bypassSessionProperties))
759 prop = getSessionProperty(key);
763 prop = applicationProperties.getProperty(key);
765 if (prop == null && Platform.isJS())
767 prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
768 + "_" + JS_PROPERTY_PREFIX + key);
774 * These methods are used when checking if the saved preference is different
775 * to the default setting
778 public static boolean getDefault(String property, boolean def)
780 String string = getProperty(property);
783 def = Boolean.valueOf(string).booleanValue();
789 public static int getDefault(String property, int def)
791 String string = getProperty(property);
796 def = Integer.parseInt(string);
797 } catch (NumberFormatException e)
799 if (!Jalview.quiet())
800 jalview.bin.Console.errPrintln("Error parsing int property '"
801 + property + "' with value '" + string + "'");
808 public static float getDefault(String property, float def)
810 String string = getProperty(property);
815 def = Float.parseFloat(string);
816 } catch (NumberFormatException e)
818 if (!Jalview.quiet())
819 jalview.bin.Console.errPrintln("Error parsing float property '"
820 + property + "' with value '" + string + "'");
828 * Answers the value of the given property, or the supplied default value if
829 * the property is not set
831 public static String getDefault(String property, String def)
833 String value = getProperty(property);
834 return value == null ? def : value;
838 * Stores property in the file "HOME_DIR/.jalview_properties"
843 * String value of property
845 * @return previous value of property (or null)
847 public static Object setProperty(String key, String obj)
849 Object oldValue = null;
852 oldValue = applicationProperties.setProperty(key, obj);
853 if (propertiesFile != null && !propsAreReadOnly
854 // don't rewrite if new value is same as old value
855 && !((obj == null && oldValue == null)
856 || (obj != null && obj.equals(oldValue))))
858 // reset the session property too
859 if (sessionProperties.containsKey(key))
861 sessionProperties.remove(key);
863 FileOutputStream out = new FileOutputStream(propertiesFile);
864 applicationProperties.store(out, "---JalviewX Properties File---");
867 } catch (Exception ex)
869 if (!Jalview.quiet())
870 jalview.bin.Console.errPrintln(
871 "Error setting property: " + key + " " + obj + "\n" + ex);
877 * remove the specified property from the jalview properties file
881 public static void removeProperty(String string)
883 applicationProperties.remove(string);
888 * save the properties to the jalview properties path
890 public static void saveProperties()
892 if (!propsAreReadOnly)
896 FileOutputStream out = new FileOutputStream(propertiesFile);
897 applicationProperties.store(out, "---JalviewX Properties File---");
899 } catch (Exception ex)
901 if (!Jalview.quiet())
902 jalview.bin.Console.errPrintln("Error saving properties: " + ex);
908 * internal vamsas class discovery state
910 private static int vamsasJarsArePresent = -1;
913 * Searches for vamsas client classes on class path.
915 * @return true if vamsas client is present on classpath
917 public static boolean vamsasJarsPresent()
919 if (vamsasJarsArePresent == -1)
923 if (jalview.jbgui.GDesktop.class.getClassLoader()
924 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
927 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
928 vamsasJarsArePresent = 1;
929 JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
930 Console.getCachedLogLevel("logs.Vamsas.Level"));
931 JLoggerLog4j.addAppender(lvclient, Console.log,
932 JALVIEW_LOGGER_NAME);
933 // Tell the user that debug is enabled
934 lvclient.debug(ChannelProperties.getProperty("app_name")
935 + " Vamsas Client Debugging Output Follows.");
937 } catch (Exception e)
939 vamsasJarsArePresent = 0;
940 Console.debug("Vamsas Classes are not present");
943 return (vamsasJarsArePresent > 0);
947 * internal vamsas class discovery state
949 private static int groovyJarsArePresent = -1;
952 * Searches for vamsas client classes on class path.
954 * @return true if vamsas client is present on classpath
956 public static boolean groovyJarsPresent()
958 if (groovyJarsArePresent == -1)
962 if (Cache.class.getClassLoader()
963 .loadClass("groovy.lang.GroovyObject") != null)
966 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
967 groovyJarsArePresent = 1;
968 JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
969 Console.getCachedLogLevel("logs.Groovy.Level"));
970 JLoggerLog4j.addAppender(lgclient, Console.log,
971 JALVIEW_LOGGER_NAME);
972 // Tell the user that debug is enabled
973 lgclient.debug(ChannelProperties.getProperty("app_name")
974 + " Groovy Client Debugging Output Follows.");
978 groovyJarsArePresent = 0;
979 Console.debug("Groovy Classes are not present", e);
980 } catch (Exception e)
982 groovyJarsArePresent = 0;
983 Console.debug("Groovy Classes are not present");
986 return (groovyJarsArePresent > 0);
990 * Initialise the tracker if it is not done already.
992 public static void initAnalytics()
994 Plausible.setEnabled(true);
996 String appName = ChannelProperties.getProperty("app_name") + " Desktop";
997 String version = Cache.getProperty("VERSION") + "_"
998 + Cache.getDefault("BUILD_DATE", "unknown");
1000 /* we don't want to encode ':' as "%3A" for backward compatibility with the UA setup
1003 path = "/" + String.join("/", URLEncoder.encode(appName, "UTF-8"),
1004 URLEncoder.encode(version, "UTF-8"),
1005 URLEncoder.encode(APPLICATION_STARTED, "UTF-8"));
1006 } catch (UnsupportedEncodingException e)
1009 List<String> pathParts = new ArrayList<>();
1010 pathParts.add(appName);
1011 pathParts.add(version);
1012 pathParts.add(APPLICATION_STARTED);
1013 path = ("/" + String.join("/", pathParts)).replace(' ', '+');
1017 Plausible plausible = Plausible.getInstance();
1019 // This will send a new "application_launch" event with parameters
1020 // including the old-style "path", the channel name and version
1021 plausible.sendEvent("application_launch", path, true);
1024 private static final String APPLICATION_STARTED = "Application Started";
1027 * get the user's default colour if available
1033 public static Color getDefaultColour(String property, Color defcolour)
1035 String colprop = getProperty(property);
1036 if (colprop == null)
1040 Color col = ColorUtils.parseColourString(colprop);
1043 Console.warn("Couldn't parse '" + colprop + "' as a colour for "
1046 return (col == null) ? defcolour : col;
1050 * store a colour as a Jalview user default property
1055 public static void setColourProperty(String property, Color colour)
1057 setProperty(property, jalview.util.Format.getHexString(colour));
1061 * Stores a formatted date in a jalview property, using a fixed locale.
1063 * @param propertyName
1065 * @return the formatted date string
1067 public static String setDateProperty(String propertyName, Date date)
1069 String formatted = date_format.format(date);
1070 setProperty(propertyName, formatted);
1075 * Reads a date stored in a Jalview property, parses it (using a fixed locale
1076 * format) and returns as a Date, or null if parsing fails
1078 * @param propertyName
1082 public static Date getDateProperty(String propertyName)
1084 String val = getProperty(propertyName);
1089 return date_format.parse(val);
1090 } catch (Exception ex)
1093 .errPrintln("Invalid or corrupt date in property '"
1094 + propertyName + "' : value was '" + val + "'");
1101 * get and parse a property as an integer. send any parsing problems to
1105 * @return null or Integer
1107 public static Integer getIntegerProperty(String property)
1109 String val = getProperty(property);
1110 if (val != null && (val = val.trim()).length() > 0)
1114 return Integer.valueOf(val);
1115 } catch (NumberFormatException x)
1117 jalview.bin.Console.errPrintln("Invalid integer in property '"
1118 + property + "' (value was '" + val + "')");
1125 * Set the specified value, or remove it if null or empty. Does not save the
1131 public static void setOrRemove(String propName, String value)
1133 if (propName == null)
1137 if (value == null || value.trim().length() < 1)
1139 Cache.applicationProperties.remove(propName);
1143 Cache.applicationProperties.setProperty(propName, value);
1148 * Loads in user colour schemes from files.
1151 * a '|'-delimited list of file paths
1153 public static void initUserColourSchemes(String files)
1155 if (files == null || files.length() == 0)
1160 // In case colours can't be loaded, we'll remove them
1161 // from the default list here.
1162 StringBuffer coloursFound = new StringBuffer();
1163 StringTokenizer st = new StringTokenizer(files, "|");
1164 while (st.hasMoreElements())
1166 String file = st.nextToken();
1169 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1172 if (coloursFound.length() > 0)
1174 coloursFound.append("|");
1176 coloursFound.append(file);
1177 ColourSchemes.getInstance().registerColourScheme(ucs);
1179 } catch (Exception ex)
1181 if (!Jalview.quiet())
1183 .outPrintln("Error loading User ColourFile\n" + ex);
1186 if (!files.equals(coloursFound.toString()))
1188 if (coloursFound.toString().length() > 1)
1190 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1191 coloursFound.toString());
1195 applicationProperties
1196 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1202 * Initial logging information helper for various versions output
1206 * @param defaultValue
1208 private static void appendIfNotNull(StringBuilder sb, String prefix,
1209 String value, String suffix, String defaultValue)
1211 if (value == null && defaultValue == null)
1217 sb.append(value == null ? defaultValue : value);
1224 * @return Jalview version, build details and JVM platform version for console
1226 public static String getVersionDetailsForConsole()
1228 StringBuilder sb = new StringBuilder();
1229 sb.append(ChannelProperties.getProperty("app_name"))
1230 .append(" Version: ");
1231 sb.append(Cache.getDefault("VERSION", "TEST"));
1233 sb.append(ChannelProperties.getProperty("app_name"))
1234 .append(" Installation: ");
1235 sb.append(Cache.getDefault("INSTALLATION", "unknown"));
1237 sb.append("Build Date: ");
1238 sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
1240 sb.append("Java version: ");
1241 sb.append(System.getProperty("java.version"));
1243 sb.append("Java platform: ");
1244 sb.append(System.getProperty("os.arch"));
1246 sb.append(System.getProperty("os.name"));
1248 sb.append(System.getProperty("os.version"));
1250 appendIfNotNull(sb, "Install4j version: ",
1251 System.getProperty("sys.install4jVersion"), "\n", null);
1252 appendIfNotNull(sb, "Install4j template version: ",
1253 System.getProperty("installer_template_version"), "\n", null);
1254 appendIfNotNull(sb, "Launcher version: ",
1255 System.getProperty("launcher_version"), "\n", null);
1256 LookAndFeel laf = UIManager.getLookAndFeel();
1257 String lafName = laf == null ? "Not obtained" : laf.getName();
1258 String lafClass = laf == null ? "unknown" : laf.getClass().getName();
1259 sb.append("LookAndFeel: ");
1262 sb.append(lafClass);
1264 appendIfNotNull(sb, "Channel: ",
1265 ChannelProperties.getProperty("channel"), "\n", null);
1266 if (Console.isDebugEnabled()
1267 || !"release".equals(ChannelProperties.getProperty("channel")))
1269 appendIfNotNull(sb, "Getdown appdir: ",
1270 System.getProperty("getdowninstanceappdir"), "\n", null);
1271 appendIfNotNull(sb, "Getdown appbase: ",
1272 System.getProperty("getdowninstanceappbase"), "\n", null);
1273 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1275 appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n",
1278 return sb.toString();
1283 * @return build details as reported in splashscreen
1285 public static String getBuildDetailsForSplash()
1287 // consider returning more human friendly info
1288 // eg 'built from Source' or update channel
1289 return Cache.getDefault("INSTALLATION", "unknown");
1292 public static String getStackTraceString(Throwable t)
1294 StringWriter sw = new StringWriter();
1295 PrintWriter pw = new PrintWriter(sw);
1296 t.printStackTrace(pw);
1297 return sw.toString();
1300 // proxy properties methods
1301 public static void clearProxyProperties()
1303 setProxyProperties(null, null, null, null, null, null, null, null,
1307 public static void resetProxyProperties()
1309 setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
1310 startupProxyProperties[2], startupProxyProperties[3],
1311 startupProxyProperties[4],
1312 startupProxyProperties[5] == null ? null
1313 : startupProxyProperties[5].toCharArray(),
1314 startupProxyProperties[6],
1315 startupProxyProperties[7] == null ? null
1316 : startupProxyProperties[7].toCharArray(),
1317 startupProxyProperties[8]);
1318 StringBuilder sb = new StringBuilder();
1319 sb.append("Setting proxy properties to: http.proxyHost=")
1320 .append(startupProxyProperties[0]).append(", http.proxyPort=")
1321 .append(startupProxyProperties[1])
1322 .append(startupProxyProperties[4] != null
1323 && !startupProxyProperties[4].isEmpty()
1324 ? " [" + startupProxyProperties[4] + "]"
1326 .append(", https.proxyHost=").append(startupProxyProperties[2])
1327 .append(", https.proxyPort=").append(startupProxyProperties[3])
1328 .append(startupProxyProperties[6] != null
1329 && !startupProxyProperties[6].isEmpty()
1330 ? " [" + startupProxyProperties[6] + "]"
1333 Console.debug(sb.toString());
1336 public static void setProxyPropertiesFromPreferences()
1338 setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
1341 public static void setProxyPropertiesFromPreferences(
1342 String previousProxyType)
1344 String proxyType = Cache.getDefault("USE_PROXY",
1345 Cache.PROXYTYPE_SYSTEM);
1346 if (previousProxyType != null
1347 && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
1349 && proxyType.equals(previousProxyType))
1356 case Cache.PROXYTYPE_NONE:
1357 if (!previousProxyType.equals(proxyType))
1359 Console.info("Setting no proxy settings");
1360 Cache.setProxyProperties(null, null, null, null, null, null, null,
1364 case Cache.PROXYTYPE_CUSTOM:
1365 // always re-set a custom proxy -- it might have changed, particularly
1367 Console.info("Setting custom proxy settings");
1368 boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
1369 Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
1370 Cache.getDefault("PROXY_PORT", null),
1371 Cache.getDefault("PROXY_SERVER_HTTPS", null),
1372 Cache.getDefault("PROXY_PORT_HTTPS", null),
1373 proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
1375 proxyAuthSet ? Cache.proxyAuthPassword : null,
1376 proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
1378 proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
1380 default: // system proxy settings by default
1381 Console.info("Setting system proxy settings");
1382 Cache.resetProxyProperties();
1386 public static void setProxyProperties(String httpHost, String httpPort,
1387 String httpsHost, String httpsPort, String httpUser,
1388 char[] httpPassword, String httpsUser, char[] httpsPassword,
1389 String nonProxyHosts)
1391 setOrClearSystemProperty("http.proxyHost", httpHost);
1392 setOrClearSystemProperty("http.proxyPort", httpPort);
1393 setOrClearSystemProperty("https.proxyHost", httpsHost);
1394 setOrClearSystemProperty("https.proxyPort", httpsPort);
1395 setOrClearSystemProperty("http.proxyUser", httpUser);
1396 setOrClearSystemProperty("https.proxyUser", httpsUser);
1397 // note: passwords for http.proxyPassword and https.proxyPassword are sent
1398 // via the Authenticator, properties do not need to be set
1400 // are we using a custom proxy (password prompt might be required)?
1401 boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
1402 .equals(PROXYTYPE_CUSTOM);
1405 * A bug in Java means the AuthCache does not get reset, so once it has working credentials,
1406 * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
1407 * is not re-called).
1408 * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
1410 * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
1412 * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
1417 sun.net.www.protocol.http.AuthCacheValue
1418 .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
1419 } catch (Throwable t)
1421 Cache.error(t.getMessage());
1422 Cache.debug(getStackTraceString(t));
1426 if (httpUser != null || httpsUser != null)
1430 char[] displayHttpPw = new char[httpPassword == null ? 0
1431 : httpPassword.length];
1432 Arrays.fill(displayHttpPw, '*');
1434 "CACHE Proxy: setting new Authenticator with httpUser='"
1435 + httpUser + "' httpPassword='" + displayHttpPw
1437 if (!Platform.isJS())
1439 * java.net.Authenticator not implemented in SwingJS yet
1445 Authenticator.setDefault(new Authenticator()
1448 protected PasswordAuthentication getPasswordAuthentication()
1450 if (getRequestorType() == RequestorType.PROXY)
1452 String protocol = getRequestingProtocol();
1453 boolean needProxyPasswordSet = false;
1454 if (customProxySet &&
1455 // we have a username but no password for the scheme being
1457 (protocol.equalsIgnoreCase("http")
1458 && (httpUser != null
1459 && httpUser.length() > 0
1460 && (httpPassword == null
1461 || httpPassword.length == 0)))
1462 || (protocol.equalsIgnoreCase("https")
1463 && (httpsUser != null
1464 && httpsUser.length() > 0
1465 && (httpsPassword == null
1466 || httpsPassword.length == 0))))
1468 // open Preferences -> Connections
1469 String message = MessageManager
1470 .getString("label.proxy_password_required");
1471 Preferences.openPreferences(
1472 Preferences.TabRef.CONNECTIONS_TAB, message);
1473 Preferences.getInstance()
1474 .proxyAuthPasswordCheckHighlight(true, true);
1480 if (protocol.equalsIgnoreCase("http")
1481 && getRequestingHost()
1482 .equalsIgnoreCase(httpHost)
1483 && getRequestingPort() == Integer
1487 "AUTHENTICATOR returning PasswordAuthentication(\""
1488 + httpUser + "\", '"
1489 + new String(displayHttpPw) + "')");
1490 return new PasswordAuthentication(httpUser,
1493 if (protocol.equalsIgnoreCase("https")
1494 && getRequestingHost()
1495 .equalsIgnoreCase(httpsHost)
1496 && getRequestingPort() == Integer
1497 .valueOf(httpsPort))
1499 char[] displayHttpsPw = new char[httpPassword.length];
1500 Arrays.fill(displayHttpsPw, '*');
1502 "AUTHENTICATOR returning PasswordAuthentication(\""
1503 + httpsUser + "\", '" + displayHttpsPw
1505 return new PasswordAuthentication(httpsUser,
1508 } catch (NumberFormatException e)
1510 Console.error("Problem with proxy port values [http:"
1511 + httpPort + ", https:" + httpsPort + "]");
1514 "AUTHENTICATOR after trying to get PasswordAuthentication");
1517 // non proxy request
1518 Console.debug("AUTHENTICATOR returning null");
1522 } // end of j2sIgnore for java.net.Authenticator
1524 // required to re-enable basic authentication (should be okay for a
1527 "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
1528 System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
1529 } catch (SecurityException e)
1531 Console.error("Could not set default Authenticator");
1532 Console.debug(getStackTraceString(e));
1537 // reset the Authenticator to protect http.proxyUser and
1538 // http.proxyPassword Just In Case
1539 /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
1540 * has working credentials. No workaround for Java 11.
1542 if (!Platform.isJS())
1544 * java.net.Authenticator not implemented in SwingJS yet
1551 "AUTHENTICATOR setting default Authenticator to null");
1552 Authenticator.setDefault(null);
1556 // nonProxyHosts not currently configurable in Preferences
1558 "AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
1559 + nonProxyHosts + "\"");
1560 setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
1563 public static void setOrClearSystemProperty(String key, char[] value)
1565 setOrClearSystemProperty(key,
1566 (value == null) ? null : new String(value));
1569 public static void setOrClearSystemProperty(String key, String value)
1577 System.clearProperty(key);
1581 System.setProperty(key, value);
1586 * Getdown appbase methods
1589 private static final String releaseAppbase;
1591 private static String getdownAppbase;
1593 private static String getdownDistDir;
1597 if (!Platform.isJS())
1599 Float specversion = Float
1600 .parseFloat(System.getProperty("java.specification.version"));
1601 releaseAppbase = (specversion < 9)
1602 ? "https://www.jalview.org/getdown/release/1.8"
1603 : "https://www.jalview.org/getdown/release/11";
1607 // this value currenly made up, can be changed to URL that will be
1608 // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
1609 releaseAppbase = "https://www.jalview.org/jalview-js";
1610 getdownAppbase = releaseAppbase;
1611 getdownDistDir = "/swingjs/j2s";
1615 // look for properties (passed in by getdown) otherwise default to release
1616 private static void setGetdownAppbase()
1618 if (getdownAppbase != null)
1622 String appbase = System.getProperty("getdownappbase");
1623 String distDir = System.getProperty("getdowndistdir");
1624 if (appbase == null)
1626 appbase = buildProperties.getProperty("GETDOWNAPPBASE");
1627 distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
1629 if (appbase == null)
1631 appbase = releaseAppbase;
1632 distDir = "release";
1634 if (appbase.endsWith("/"))
1636 appbase = appbase.substring(0, appbase.length() - 1);
1638 if (distDir == null)
1640 distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
1642 getdownAppbase = appbase;
1643 getdownDistDir = distDir;
1646 public static String getGetdownAppbase()
1648 setGetdownAppbase();
1649 return getdownAppbase;
1652 public static String getAppbaseBuildProperties()
1654 String appbase = getGetdownAppbase();
1655 return appbase + "/" + getdownDistDir + "/build_properties";
1658 private static final Collection<String> bootstrapProperties = new ArrayList<>(
1659 Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST));
1661 public static Properties bootstrapProperties(String filename)
1663 Properties bootstrapProps = new Properties();
1665 if (filename != null)
1667 file = new File(filename);
1669 if (file == null || !file.exists())
1674 .errPrintln("Could not load bootstrap preferences file '"
1675 + file.getPath() + "'");
1677 String channelPrefsFilename = ChannelProperties
1678 .getProperty("preferences.filename");
1679 String propertiesFilename = System.getProperty("user.home")
1680 + File.separatorChar + channelPrefsFilename;
1681 jalview.bin.Console.errPrintln(
1682 "Using default properties file '" + propertiesFilename + "'");
1683 file = new File(propertiesFilename);
1685 if (file == null || !file.exists())
1688 String releasePrefsFilename = fallbackPropertiesFile;
1689 String releasePropertiesFilename = System.getProperty("user.home")
1690 + File.separatorChar + releasePrefsFilename;
1691 jalview.bin.Console.errPrintln("Falling back to properties file '"
1692 + releasePropertiesFilename + "'");
1693 file = new File(releasePropertiesFilename);
1699 .errPrintln("Could not load bootstrap preferences file '"
1700 + file.getPath() + "'");
1706 FileInputStream in = new FileInputStream(file.getAbsoluteFile());
1707 Properties props = new Properties();
1709 for (String prop : bootstrapProperties)
1711 if (props.containsKey(prop))
1712 bootstrapProps.put(prop, props.getProperty(prop));
1714 } catch (FileNotFoundException e)
1717 .errPrintln("Could not find bootstrap preferences file '"
1718 + file.getAbsolutePath() + "'");
1719 } catch (IOException e)
1721 jalview.bin.Console.errPrintln(
1722 "IOException when loading bootstrap preferences file '"
1723 + file.getAbsolutePath() + "'");
1725 return bootstrapProps;
1728 public static void setSessionProperty(String key, String val)
1732 sessionProperties.put(key, val);
1736 public static String getSessionProperty(String key)
1738 return key == null ? null : sessionProperties.get(key);
1741 public static boolean getArgCacheDefault(Arg a, String pref, boolean def)
1743 ArgParser ap = Jalview.getInstance().getArgParser();
1744 return ap.isSet(a) ? ap.getBoolean(a) : getDefault(pref, def);