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.text.DateFormat;
33 import java.text.SimpleDateFormat;
34 import java.util.Collections;
35 import java.util.Date;
36 import java.util.Enumeration;
37 import java.util.Locale;
38 import java.util.Properties;
39 import java.util.StringTokenizer;
40 import java.util.TreeSet;
41 import java.util.regex.Pattern;
43 import javax.swing.LookAndFeel;
44 import javax.swing.UIManager;
46 import org.apache.log4j.ConsoleAppender;
47 import org.apache.log4j.Level;
48 import org.apache.log4j.Logger;
49 import org.apache.log4j.SimpleLayout;
51 import jalview.datamodel.PDBEntry;
52 import jalview.gui.UserDefinedColours;
53 import jalview.schemes.ColourSchemeLoader;
54 import jalview.schemes.ColourSchemes;
55 import jalview.schemes.UserColourScheme;
56 import jalview.structure.StructureImportSettings;
57 import jalview.urls.IdOrgSettings;
58 import jalview.util.ColorUtils;
59 import jalview.ws.sifts.SiftsSettings;
62 * Stores and retrieves Jalview Application Properties Lists and fields within
63 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
64 * are alternative values for a tag. <br>
66 * Current properties include:
69 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
70 * logging level for axis (used for web services) <br>
72 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
73 * the logging level for castor (used for serialization) <br>
75 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
77 * <li>SCREEN_WIDTH</li>
78 * <li>SCREEN_HEIGHT</li>
79 * <li>SCREEN_Y=285</li>
80 * <li>SCREEN_X=371</li>
81 * <li>SHOW_FULLSCREEN boolean</li>
82 * <li>FONT_NAME java font name for alignment text display</li>
83 * <li>FONT_SIZE size of displayed alignment text</li>
84 * <li>FONT_STYLE style of font displayed (sequence labels are always
86 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
87 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
88 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
89 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
90 * <li>SHOW_IDENTITY show percentage identity annotation</li>
91 * <li>SHOW_QUALITY show alignment quality annotation</li>
92 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
93 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
94 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
95 * LABEL_AND_SEQUENCE</li>
96 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
97 * sequence annotations</li>
98 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
100 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
101 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
102 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
103 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
104 * <li>VERSION the version of the jalview build</li>
105 * <li>BUILD_DATE date of this build</li>
106 * <li>LATEST_VERSION the latest jalview version advertised on the
107 * www.jalview.org</li>
108 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
110 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
111 * suffix to file</li>
112 * <li>RECENT_URL list of recently retrieved URLs</li>
113 * <li>RECENT_FILE list of recently opened files</li>
114 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
115 * <li>PROXY_SERVER the proxy</li>
116 * <li>PROXY_PORT</li>
117 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
119 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
121 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
122 * collecting usage statistics</li>
123 * <li>SHOW_OVERVIEW boolean for overview window display</li>
124 * <li>ANTI_ALIAS boolean for smooth fonts</li>
125 * <li>RIGHT_ALIGN_IDS boolean</li>
126 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
127 * <li>PAD_GAPS boolean</li>
128 * <li>ID_ITALICS boolean</li>
129 * <li>SHOW_JV_SUFFIX</li>
130 * <li>WRAP_ALIGNMENT</li>
131 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
133 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
134 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
136 * <li>STORED_LINKS list of name|url pairs which user has entered but are not
138 * <li>DEFAULT_LINK name of single url to be used when user double clicks a
139 * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
140 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
141 * jalview.utils.GroupURLLink for more info</li>
142 * <li>DEFAULT_BROWSER for unix</li>
143 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
145 * <li>VERSION_CHECK (true) check for the latest release version from
146 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
147 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
149 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
151 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
152 * displayed as '.'</li>
153 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
154 * order of a newly displayed tree</li>
155 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
156 * sequence ID strings before attempting retrieval from any datasource</li>
157 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
159 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
160 * in the alignment.</li>
161 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
163 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
165 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
166 * logo normalised to row height rather than histogram height.</li>
167 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
168 * respond to selections made in other alignments containing the same sequences.
170 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
171 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
172 * warning dialog box is displayed.</li>
173 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
174 * when shading by annotation</li>
175 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
176 * when shading by annotation</li>
177 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
178 * requests to be redirected to a mirror of http://www.jalview.org</li>
179 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
180 * alignment figure to accommodate even the longest sequence ID or annotation
182 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
183 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
184 * will override this).</li>
185 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
187 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
188 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
190 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
192 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
194 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
195 * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
199 * Deprecated settings:
202 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
203 * startup (JWS1 services only)</li>
204 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
205 * (JWS1 services only)</li>
206 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
207 * services in the desktop GUI</li>
208 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
209 * panel in web service preferences</li>
213 * @version $Revision$
218 * property giving log4j level for CASTOR loggers
220 public static final String CASTORLOGLEVEL = "logs.Castor.level";
223 * property giving log4j level for AXIS loggers
225 public static final String AXISLOGLEVEL = "logs.Axis.level";
228 * property giving log4j level for Jalview Log
230 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
235 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
236 .getProperty("user.home") + File.separatorChar
237 + ".sifts_downloads" + File.separatorChar;
239 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
241 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
244 * Identifiers.org download settings
246 private static final String ID_ORG_FILE = System.getProperty("user.home")
247 + File.separatorChar + ".identifiers.org.ids.json";
250 * Allowed values are PDB or mmCIF
252 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
255 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
259 * a date formatter using a fixed (rather than the user's) locale;
260 * this ensures that date properties can be written and re-read successfully
261 * even if the user changes their locale setting
263 private static final DateFormat date_format = SimpleDateFormat
264 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
265 SimpleDateFormat.MEDIUM, Locale.UK);
268 * Initialises the Jalview Application Log
270 public static Logger log;
272 // save the proxy properties set at startup
273 public final static String[] startupProxyProperties = {
274 System.getProperty("http.proxyHost"),
275 System.getProperty("http.proxyPort"),
276 System.getProperty("https.proxyHost"),
277 System.getProperty("https.proxyPort") };
279 /** Jalview Properties */
280 public static Properties applicationProperties = new Properties()
282 // override results in properties output in alphabetical order
284 public synchronized Enumeration<Object> keys()
286 return Collections.enumeration(new TreeSet<>(super.keySet()));
290 /** Default file is ~/.jalview_properties */
291 static String propertiesFile;
293 private static boolean propsAreReadOnly = false;
295 public static void initLogger()
303 // TODO: redirect stdout and stderr here in order to grab the output of
306 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
308 ap.setName("JalviewLogger");
309 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
311 Logger laxis = Logger.getLogger("org.apache.axis");
312 Logger lcastor = Logger.getLogger("org.exolab.castor");
313 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
315 laxis.setLevel(Level.toLevel(
316 Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
317 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
318 Level.INFO.toString())));
319 lcastor = Logger.getLogger("org.exolab.castor.xml");
320 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
321 Level.INFO.toString())));
322 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
323 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
324 // Level.INFO.toString())));
325 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
326 .getDefault("logs.Jalview.level", Level.INFO.toString())));
327 // laxis.addAppender(ap);
328 // lcastor.addAppender(ap);
329 // jalview.bin.Cache.log.addAppender(ap);
330 // Tell the user that debug is enabled
331 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
332 } catch (Exception ex)
334 System.err.println("Problems initializing the log4j system\n");
335 ex.printStackTrace(System.err);
340 * Loads properties from the given properties file. Any existing properties
343 public static void loadProperties(String propsFile)
345 propertiesFile = propsFile;
346 if (propsFile == null)
348 propertiesFile = System.getProperty("user.home") + File.separatorChar
349 + ".jalview_properties";
353 // don't corrupt the file we've been given.
354 propsAreReadOnly = true;
362 fis = new java.net.URL(propertiesFile).openStream();
364 "Loading jalview properties from : " + propertiesFile);
366 "Disabling Jalview writing to user's local properties file.");
367 propsAreReadOnly = true;
369 } catch (Exception ex)
375 fis = new FileInputStream(propertiesFile);
377 applicationProperties.clear();
378 applicationProperties.load(fis);
380 // remove any old build properties
382 deleteBuildProperties();
384 } catch (Exception ex)
386 System.out.println("Error reading properties file: " + ex);
389 /* TO BE REPLACED WITH PROXY_TYPE SETTINGS
390 if (getDefault("USE_PROXY", false))
392 String proxyServer = getDefault("PROXY_SERVER", ""),
393 proxyPort = getDefault("PROXY_PORT", "8080");
397 // PROXY TYPE settings (now three options "none", "false", "true", but using
398 // backward compatible strings)
399 String proxyType = getDefault("USE_PROXY", "false");
400 // default to upgrading old settings
404 setProxyProperties(null, null, null, null);
406 case "false": // use system settings
407 resetProxyProperties();
409 case "true": // use specified proxy settings
410 String httpHost = getDefault("PROXY_SERVER", "");
411 String httpPort = getDefault("PROXY_PORT", "8080");
412 String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
413 String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
414 setProxyProperties(httpHost, httpPort, httpsHost, httpsPort);
417 String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
419 if (Cache.log == null)
421 System.out.println(message);
425 Cache.log.warn(message);
429 // LOAD THE AUTHORS FROM THE authors.props file
432 String authorDetails = "jar:"
433 .concat(Cache.class.getProtectionDomain().getCodeSource()
434 .getLocation().toString().concat("!/authors.props"));
436 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
438 InputStream in = localJarFileURL.openStream();
439 applicationProperties.load(in);
441 } catch (Exception ex)
443 System.out.println("Error reading author details: " + ex);
444 applicationProperties.remove("AUTHORS");
445 applicationProperties.remove("AUTHORFNAMES");
446 applicationProperties.remove("YEAR");
449 loadBuildProperties(false);
452 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
454 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
455 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
457 SiftsSettings.setFailSafePIDThreshold(
458 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
459 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
461 SiftsSettings.setCacheThresholdInDays(
462 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
463 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
465 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
466 "http://www.jalview.org/services/identifiers"));
467 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
469 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
470 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
471 StructureImportSettings
472 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
473 // StructureImportSettings
474 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
475 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
477 String jnlpVersion = System.getProperty("jalview.version");
479 // jnlpVersion will be null if a latest version check for the channel needs
481 // Dont do this check if running in headless mode
483 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
484 && (System.getProperty("java.awt.headless") == null || System
485 .getProperty("java.awt.headless").equals("false")))
488 class VersionChecker extends Thread
493 String orgtimeout = System
494 .getProperty("sun.net.client.defaultConnectTimeout");
495 if (orgtimeout == null)
498 System.out.println("# INFO: Setting default net timeout to "
499 + orgtimeout + " seconds.");
501 String remoteVersion = null;
504 System.setProperty("sun.net.client.defaultConnectTimeout",
506 java.net.URL url = new java.net.URL(Cache
507 .getDefault("www.jalview.org", "http://www.jalview.org")
508 + "/webstart/jalview.jnlp");
509 BufferedReader in = new BufferedReader(
510 new InputStreamReader(url.openStream()));
512 while ((line = in.readLine()) != null)
514 if (line.indexOf("jalview.version") == -1)
519 line = line.substring(line.indexOf("value=") + 7);
520 line = line.substring(0, line.lastIndexOf("\""));
521 remoteVersion = line;
524 } catch (Exception ex)
527 "Non-fatal exception when checking version at www.jalview.org :");
528 System.out.println(ex);
529 remoteVersion = getProperty("VERSION");
531 System.setProperty("sun.net.client.defaultConnectTimeout",
534 setProperty("LATEST_VERSION", remoteVersion);
538 VersionChecker vc = new VersionChecker();
543 if (jnlpVersion != null)
545 setProperty("LATEST_VERSION", jnlpVersion);
549 applicationProperties.remove("LATEST_VERSION");
553 // LOAD USERDEFINED COLOURS
555 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
556 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
560 public static void loadBuildProperties(boolean reportVersion)
562 String codeInstallation = getProperty("INSTALLATION");
563 boolean printV = codeInstallation == null;
565 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
568 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
569 .getCodeSource().getLocation().toString()
570 .concat("!/.build_properties"));
572 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
574 InputStream in = localJarFileURL.openStream();
575 applicationProperties.load(in);
577 } catch (Exception ex)
579 System.out.println("Error reading build details: " + ex);
580 applicationProperties.remove("VERSION");
582 String codeVersion = getProperty("VERSION");
583 codeInstallation = getProperty("INSTALLATION");
585 if (codeVersion == null)
587 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
588 codeVersion = "Test";
589 codeInstallation = "";
593 codeInstallation = " (" + codeInstallation + ")";
595 setProperty("VERSION", codeVersion);
596 new BuildDetails(codeVersion, null, codeInstallation);
597 if (printV && reportVersion)
600 "Jalview Version: " + codeVersion + codeInstallation);
604 private static void deleteBuildProperties()
606 applicationProperties.remove("LATEST_VERSION");
607 applicationProperties.remove("VERSION");
608 applicationProperties.remove("AUTHORS");
609 applicationProperties.remove("AUTHORFNAMES");
610 applicationProperties.remove("YEAR");
611 applicationProperties.remove("BUILD_DATE");
612 applicationProperties.remove("INSTALLATION");
616 * Gets Jalview application property of given key. Returns null if key not
622 * @return Property value
624 public static String getProperty(String key)
626 return applicationProperties.getProperty(key);
630 * These methods are used when checking if the saved preference is different
631 * to the default setting
634 public static boolean getDefault(String property, boolean def)
636 String string = getProperty(property);
639 def = Boolean.valueOf(string).booleanValue();
645 public static int getDefault(String property, int def)
647 String string = getProperty(property);
652 def = Integer.parseInt(string);
653 } catch (NumberFormatException e)
655 System.out.println("Error parsing int property '" + property
656 + "' with value '" + string + "'");
664 * These methods are used when checking if the saved preference is different
665 * to the default setting
667 public static String getDefault(String property, String def)
669 String string = getProperty(property);
679 * Stores property in the file "HOME_DIR/.jalview_properties"
684 * String value of property
686 * @return previous value of property (or null)
688 public static Object setProperty(String key, String obj)
690 Object oldValue = null;
693 oldValue = applicationProperties.setProperty(key, obj);
694 if (propertiesFile != null && !propsAreReadOnly)
696 FileOutputStream out = new FileOutputStream(propertiesFile);
697 applicationProperties.store(out, "---JalviewX Properties File---");
700 } catch (Exception ex)
703 "Error setting property: " + key + " " + obj + "\n" + ex);
709 * remove the specified property from the jalview properties file
713 public static void removeProperty(String string)
715 applicationProperties.remove(string);
720 * save the properties to the jalview properties path
722 public static void saveProperties()
724 if (!propsAreReadOnly)
728 FileOutputStream out = new FileOutputStream(propertiesFile);
729 applicationProperties.store(out, "---JalviewX Properties File---");
731 } catch (Exception ex)
733 System.out.println("Error saving properties: " + ex);
739 * internal vamsas class discovery state
741 private static int vamsasJarsArePresent = -1;
744 * Searches for vamsas client classes on class path.
746 * @return true if vamsas client is present on classpath
748 public static boolean vamsasJarsPresent()
750 if (vamsasJarsArePresent == -1)
754 if (jalview.jbgui.GDesktop.class.getClassLoader()
755 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
757 jalview.bin.Cache.log.debug(
758 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
759 vamsasJarsArePresent = 1;
760 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
761 lvclient.setLevel(Level.toLevel(Cache
762 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
764 lvclient.addAppender(log.getAppender("JalviewLogger"));
765 // Tell the user that debug is enabled
766 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
768 } catch (Exception e)
770 vamsasJarsArePresent = 0;
771 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
774 return (vamsasJarsArePresent > 0);
778 * internal vamsas class discovery state
780 private static int groovyJarsArePresent = -1;
783 * Searches for vamsas client classes on class path.
785 * @return true if vamsas client is present on classpath
787 public static boolean groovyJarsPresent()
789 if (groovyJarsArePresent == -1)
793 if (Cache.class.getClassLoader()
794 .loadClass("groovy.lang.GroovyObject") != null)
796 jalview.bin.Cache.log.debug(
797 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
798 groovyJarsArePresent = 1;
799 Logger lgclient = Logger.getLogger("groovy");
800 lgclient.setLevel(Level.toLevel(Cache
801 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
803 lgclient.addAppender(log.getAppender("JalviewLogger"));
804 // Tell the user that debug is enabled
805 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
809 groovyJarsArePresent = 0;
810 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
811 } catch (Exception e)
813 groovyJarsArePresent = 0;
814 jalview.bin.Cache.log.debug("Groovy Classes are not present");
817 return (groovyJarsArePresent > 0);
821 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
824 protected static Object tracker = null;
826 protected static Class trackerfocus = null;
828 protected static Class jgoogleanalyticstracker = null;
831 * Initialise the google tracker if it is not done already.
833 public static void initGoogleTracker()
837 if (jgoogleanalyticstracker == null)
839 // try to get the tracker class
842 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
843 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
844 trackerfocus = Cache.class.getClassLoader()
845 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
846 } catch (Exception e)
849 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
851 jgoogleanalyticstracker = null;
856 // now initialise tracker
857 Exception re = null, ex = null;
859 String vrs = "No Version Accessible";
862 // Google analytics tracking code for Library Finder
863 tracker = jgoogleanalyticstracker
864 .getConstructor(new Class[]
865 { String.class, String.class, String.class })
866 .newInstance(new Object[]
868 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
869 + jalview.bin.Cache.getDefault("BUILD_DATE",
872 jgoogleanalyticstracker
873 .getMethod("trackAsynchronously", new Class[]
875 .invoke(tracker, new Object[]
876 { trackerfocus.getConstructor(new Class[] { String.class })
877 .newInstance(new Object[]
878 { "Application Started." }) });
879 } catch (RuntimeException e)
882 } catch (Exception e)
889 if (re != null || ex != null || err != null)
895 log.debug("Caught runtime exception in googletracker init:",
901 "Failed to initialise GoogleTracker for Jalview Desktop with version "
908 "Whilst initing GoogleTracker for Jalview Desktop version "
918 "Debug: Caught runtime exception in googletracker init:"
920 re.printStackTrace();
925 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
927 ex.printStackTrace();
933 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
935 err.printStackTrace();
941 log.debug("Successfully initialised tracker.");
947 * get the user's default colour if available
953 public static Color getDefaultColour(String property, Color defcolour)
955 String colprop = getProperty(property);
960 Color col = ColorUtils.parseColourString(colprop);
963 log.warn("Couldn't parse '" + colprop + "' as a colour for "
966 return (col == null) ? defcolour : col;
970 * store a colour as a Jalview user default property
975 public static void setColourProperty(String property, Color colour)
977 setProperty(property, jalview.util.Format.getHexString(colour));
981 * Stores a formatted date in a jalview property, using a fixed locale.
983 * @param propertyName
985 * @return the formatted date string
987 public static String setDateProperty(String propertyName, Date date)
989 String formatted = date_format.format(date);
990 setProperty(propertyName, formatted);
995 * Reads a date stored in a Jalview property, parses it (using a fixed locale
996 * format) and returns as a Date, or null if parsing fails
998 * @param propertyName
1002 public static Date getDateProperty(String propertyName)
1004 String val = getProperty(propertyName);
1009 return date_format.parse(val);
1010 } catch (Exception ex)
1012 System.err.println("Invalid or corrupt date in property '"
1013 + propertyName + "' : value was '" + val + "'");
1020 * get and parse a property as an integer. send any parsing problems to
1024 * @return null or Integer
1026 public static Integer getIntegerProperty(String property)
1028 String val = getProperty(property);
1029 if (val != null && (val = val.trim()).length() > 0)
1033 return Integer.valueOf(val);
1034 } catch (NumberFormatException x)
1036 System.err.println("Invalid integer in property '" + property
1037 + "' (value was '" + val + "')");
1044 * Set the specified value, or remove it if null or empty. Does not save the
1050 public static void setOrRemove(String propName, String value)
1052 if (propName == null)
1056 if (value == null || value.trim().length() < 1)
1058 Cache.applicationProperties.remove(propName);
1062 Cache.applicationProperties.setProperty(propName, value);
1067 * Loads in user colour schemes from files.
1070 * a '|'-delimited list of file paths
1072 public static void initUserColourSchemes(String files)
1074 if (files == null || files.length() == 0)
1079 // In case colours can't be loaded, we'll remove them
1080 // from the default list here.
1081 StringBuffer coloursFound = new StringBuffer();
1082 StringTokenizer st = new StringTokenizer(files, "|");
1083 while (st.hasMoreElements())
1085 String file = st.nextToken();
1088 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1091 if (coloursFound.length() > 0)
1093 coloursFound.append("|");
1095 coloursFound.append(file);
1096 ColourSchemes.getInstance().registerColourScheme(ucs);
1098 } catch (Exception ex)
1100 System.out.println("Error loading User ColourFile\n" + ex);
1103 if (!files.equals(coloursFound.toString()))
1105 if (coloursFound.toString().length() > 1)
1107 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1108 coloursFound.toString());
1112 applicationProperties
1113 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1119 * Initial logging information helper for various versions output
1123 * @param defaultValue
1125 private static void appendIfNotNull(StringBuilder sb, String prefix,
1126 String value, String suffix, String defaultValue)
1128 if (value == null && defaultValue == null)
1132 String line = prefix + (value != null ? value : defaultValue) + suffix;
1138 * @return Jalview version, build details and JVM platform version for console
1140 public static String getVersionDetailsForConsole()
1142 StringBuilder sb = new StringBuilder();
1143 sb.append("Jalview Version: ");
1144 sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
1146 sb.append("Jalview Installation: ");
1147 sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1149 sb.append("Build Date: ");
1150 sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1152 sb.append("Java version: ");
1153 sb.append(System.getProperty("java.version"));
1155 sb.append(System.getProperty("os.arch"));
1157 sb.append(System.getProperty("os.name"));
1159 sb.append(System.getProperty("os.version"));
1161 appendIfNotNull(sb, "Install4j version: ",
1162 System.getProperty("sys.install4jVersion"), "\n", null);
1163 appendIfNotNull(sb, "Install4j template version: ",
1164 System.getProperty("installer_template_version"), "\n", null);
1165 appendIfNotNull(sb, "Launcher version: ",
1166 System.getProperty("launcher_version"), "\n", null);
1167 LookAndFeel laf = UIManager.getLookAndFeel();
1168 String lafName = laf == null ? "Not obtained" : laf.getName();
1169 String lafClass = laf == null ? "unknown" : laf.getClass().getName();
1170 sb.append("LookAndFeel: ");
1173 sb.append(lafClass);
1175 // Not displayed in release version ( determined by possible version number
1176 // regex 9[9.]*9[.-_a9]* )
1177 if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
1178 jalview.bin.Cache.getDefault("VERSION", "TEST")))
1180 appendIfNotNull(sb, "Getdown appdir: ",
1181 System.getProperty("getdownappdir"), "\n", null);
1182 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1185 return sb.toString();
1190 * @return build details as reported in splashscreen
1192 public static String getBuildDetailsForSplash()
1194 // consider returning more human friendly info
1195 // eg 'built from Source' or update channel
1196 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
1199 public static String getStackTraceString(Throwable t)
1201 StringWriter sw = new StringWriter();
1202 PrintWriter pw = new PrintWriter(sw);
1203 t.printStackTrace(pw);
1204 return sw.toString();
1207 // proxy properties methods
1208 public static void resetProxyProperties()
1210 setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
1211 startupProxyProperties[2], startupProxyProperties[3]);
1212 StringBuilder sb = new StringBuilder();
1213 sb.append("Setting proxy properties to: http.proxyHost=")
1214 .append(startupProxyProperties[0]).append(", http.proxyPort=")
1215 .append(startupProxyProperties[1]).append(", https.proxyHost=")
1216 .append(startupProxyProperties[2]).append(", https.proxyPort=")
1217 .append(startupProxyProperties[3]);
1218 if (Cache.log == null)
1220 System.err.println(sb.toString());
1224 Cache.log.debug(sb.toString());
1228 public static void setProxyProperties(String host, String port)
1230 setProxyProperties(host, port, host, port);
1233 public static void setProxyProperties(String httpHost, String httpPort,
1234 String httpsHost, String httpsPort)
1236 // cannot set property to null -- use clearProperty instead
1239 if (httpHost == null)
1241 System.clearProperty("http.proxyHost");
1245 System.setProperty("http.proxyHost", httpHost);
1249 if (httpPort == null)
1251 System.clearProperty("http.proxyPort");
1255 System.setProperty("http.proxyPort", httpPort);
1259 if (httpsHost == null)
1261 System.clearProperty("https.proxyHost");
1265 System.setProperty("https.proxyHost", httpsHost);
1269 if (httpsPort == null)
1271 System.clearProperty("https.proxyPort");
1275 System.setProperty("https.proxyPort", httpsPort);