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 jalview.ws.dbsources.das.api.DasSourceRegistryI;
24 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
25 import jalview.ws.sifts.SiftsSettings;
27 import java.awt.Color;
28 import java.io.BufferedReader;
30 import java.io.FileInputStream;
31 import java.io.FileOutputStream;
32 import java.io.InputStream;
33 import java.io.InputStreamReader;
34 import java.text.DateFormat;
35 import java.text.SimpleDateFormat;
36 import java.util.Collections;
37 import java.util.Date;
38 import java.util.Enumeration;
39 import java.util.Properties;
40 import java.util.TreeSet;
42 import org.apache.log4j.ConsoleAppender;
43 import org.apache.log4j.Level;
44 import org.apache.log4j.Logger;
45 import org.apache.log4j.SimpleLayout;
48 * Stores and retrieves Jalview Application Properties Lists and fields within
49 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
50 * are alternative values for a tag. <br>
52 * Current properties include:
55 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
56 * logging level for axis (used for web services) <br>
58 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
59 * the logging level for castor (used for serialization) <br>
61 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
63 * <li>SCREEN_WIDTH</li>
64 * <li>SCREEN_HEIGHT</li>
65 * <li>SCREEN_Y=285</li>
66 * <li>SCREEN_X=371</li>
67 * <li>SHOW_FULLSCREEN boolean</li>
68 * <li>FONT_NAME java font name for alignment text display</li>
69 * <li>FONT_SIZE size of displayed alignment text</li>
70 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
71 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
72 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
73 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
74 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
75 * <li>SHOW_IDENTITY show percentage identity annotation</li>
76 * <li>SHOW_QUALITY show alignment quality annotation</li>
77 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
78 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
79 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
80 * LABEL_AND_SEQUENCE</li>
81 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
82 * sequence annotations</li>
83 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
85 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
86 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
87 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
88 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
89 * <li>VERSION the version of the jalview build</li>
90 * <li>BUILD_DATE date of this build</li>
91 * <li>LATEST_VERSION the latest jalview version advertised on the
92 * www.jalview.org</li>
93 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
95 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
97 * <li>RECENT_URL list of recently retrieved URLs</li>
98 * <li>RECENT_FILE list of recently opened files</li>
99 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
100 * <li>PROXY_SERVER the proxy</li>
101 * <li>PROXY_PORT</li>
102 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
104 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
106 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
107 * collecting usage statistics</li>
108 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
109 * <li>SHOW_OVERVIEW boolean for overview window display</li>
110 * <li>ANTI_ALIAS boolean for smooth fonts</li>
111 * <li>RIGHT_ALIGN_IDS boolean</li>
112 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
113 * <li>PAD_GAPS boolean</li>
114 * <li>ID_ITALICS boolean</li>
115 * <li>SHOW_JV_SUFFIX</li>
116 * <li>WRAP_ALIGNMENT</li>
117 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
119 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
120 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
122 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
123 * jalview.utils.GroupURLLink for more info</li>
124 * <li>DAS_REGISTRY_URL the registry to query</li>
125 * <li>DEFAULT_BROWSER for unix</li>
126 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
127 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
129 * <li>VERSION_CHECK (true) check for the latest release version from
130 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
131 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
133 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
135 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
136 * displayed as '.'</li>
137 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
138 * order of a newly displayed tree</li>
139 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
140 * sequence ID strings before attempting retrieval from any datasource</li>
141 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
143 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
144 * in the alignment.</li>
145 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
147 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
149 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
150 * logo normalised to row height rather than histogram height.</li>
151 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
152 * respond to selections made in other alignments containing the same sequences.
154 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
155 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
156 * warning dialog box is displayed.</li>
157 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
158 * when shading by annotation</li>
159 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
160 * when shading by annotation</li>
161 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
162 * requests to be redirected to a mirror of http://www.jalview.org</li>
163 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
164 * alignment figure to accommodate even the longest sequence ID or annotation
166 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
167 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
168 * will override this).</li>
169 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
171 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
172 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
174 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
176 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
178 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
181 * Deprecated settings:
184 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
185 * startup (JWS1 services only)</li>
186 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
187 * (JWS1 services only)</li>
188 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
189 * services in the desktop GUI</li>
190 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
191 * panel in web service preferences</li>
195 * @version $Revision$
200 * property giving log4j level for CASTOR loggers
202 public static final String CASTORLOGLEVEL = "logs.Castor.level";
205 * property giving log4j level for AXIS loggers
207 public static final String AXISLOGLEVEL = "logs.Axis.level";
210 * property giving log4j level for Jalview Log
212 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
214 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
216 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
218 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
220 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
221 .getProperty("user.home")
223 + ".sifts_downloads" + File.separatorChar;
225 * Initialises the Jalview Application Log
227 public static Logger log;
229 /** Jalview Properties */
230 public static Properties applicationProperties = new Properties()
232 // override results in properties output in alphabetical order
234 public synchronized Enumeration<Object> keys()
236 return Collections.enumeration(new TreeSet<Object>(super.keySet()));
240 /** Default file is ~/.jalview_properties */
241 static String propertiesFile;
243 private static boolean propsAreReadOnly = false;
245 public static void initLogger()
253 // TODO: redirect stdout and stderr here in order to grab the output of
256 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
258 ap.setName("JalviewLogger");
259 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
261 Logger laxis = Logger.getLogger("org.apache.axis");
262 Logger lcastor = Logger.getLogger("org.exolab.castor");
263 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
265 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
266 Level.INFO.toString())));
267 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
268 Level.INFO.toString())));
269 lcastor = Logger.getLogger("org.exolab.castor.xml");
270 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
271 Level.INFO.toString())));
272 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
273 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
274 // Level.INFO.toString())));
275 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
276 "logs.Jalview.level", Level.INFO.toString())));
277 // laxis.addAppender(ap);
278 // lcastor.addAppender(ap);
279 // jalview.bin.Cache.log.addAppender(ap);
280 // Tell the user that debug is enabled
281 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
282 } catch (Exception ex)
284 System.err.println("Problems initializing the log4j system\n");
285 ex.printStackTrace(System.err);
289 /** Called when Jalview is started */
290 public static void loadProperties(String propsFile)
292 propertiesFile = propsFile;
293 if (propsFile == null)
295 propertiesFile = System.getProperty("user.home") + File.separatorChar
296 + ".jalview_properties";
300 // don't corrupt the file we've been given.
301 propsAreReadOnly = true;
309 fis = new java.net.URL(propertiesFile).openStream();
310 System.out.println("Loading jalview properties from : "
313 .println("Disabling Jalview writing to user's local properties file.");
314 propsAreReadOnly = true;
316 } catch (Exception ex)
322 fis = new FileInputStream(propertiesFile);
324 applicationProperties.load(fis);
326 // remove any old build properties
328 deleteBuildProperties();
330 } catch (Exception ex)
332 System.out.println("Error reading properties file: " + ex);
335 if (getDefault("USE_PROXY", false))
337 String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
338 "PROXY_PORT", "8080");
340 System.out.println("Using proxyServer: " + proxyServer
341 + " proxyPort: " + proxyPort);
343 System.setProperty("http.proxyHost", proxyServer);
344 System.setProperty("http.proxyPort", proxyPort);
347 // LOAD THE AUTHORS FROM THE authors.props file
350 String authorDetails = "jar:".concat(Cache.class
351 .getProtectionDomain().getCodeSource().getLocation()
352 .toString().concat("!/authors.props"));
354 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
356 InputStream in = localJarFileURL.openStream();
357 applicationProperties.load(in);
359 } catch (Exception ex)
361 System.out.println("Error reading author details: " + ex);
362 applicationProperties.remove("AUTHORS");
363 applicationProperties.remove("AUTHORFNAMES");
364 applicationProperties.remove("YEAR");
367 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
368 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
369 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
372 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
373 .getCodeSource().getLocation().toString()
374 .concat("!/.build_properties"));
376 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
378 InputStream in = localJarFileURL.openStream();
379 applicationProperties.load(in);
381 } catch (Exception ex)
383 System.out.println("Error reading build details: " + ex);
384 applicationProperties.remove("VERSION");
387 String jnlpVersion = System.getProperty("jalview.version");
388 String codeVersion = getProperty("VERSION");
389 String codeInstallation = getProperty("INSTALLATION");
390 if (codeVersion == null)
392 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
393 codeVersion = "Test";
394 jnlpVersion = "Test";
395 codeInstallation = "";
399 codeInstallation = " (" + codeInstallation + ")";
401 new BuildDetails(codeVersion, null, codeInstallation);
404 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
406 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
407 "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
410 .println("Jalview Version: " + codeVersion + codeInstallation);
412 // jnlpVersion will be null if we're using InstallAnywhere
413 // Dont do this check if running in headless mode
414 if (jnlpVersion == null
415 && getDefault("VERSION_CHECK", true)
416 && (System.getProperty("java.awt.headless") == null || System
417 .getProperty("java.awt.headless").equals("false")))
420 class VersionChecker extends Thread
425 String orgtimeout = System
426 .getProperty("sun.net.client.defaultConnectTimeout");
427 if (orgtimeout == null)
430 System.out.println("# INFO: Setting default net timeout to "
431 + orgtimeout + " seconds.");
433 String remoteVersion = null;
436 System.setProperty("sun.net.client.defaultConnectTimeout",
438 java.net.URL url = new java.net.URL(Cache.getDefault(
439 "www.jalview.org", "http://www.jalview.org")
440 + "/webstart/jalview.jnlp");
441 BufferedReader in = new BufferedReader(new InputStreamReader(
444 while ((line = in.readLine()) != null)
446 if (line.indexOf("jalview.version") == -1)
451 line = line.substring(line.indexOf("value=") + 7);
452 line = line.substring(0, line.lastIndexOf("\""));
453 remoteVersion = line;
456 } catch (Exception ex)
459 .println("Non-fatal exception when checking version at www.jalview.org :");
460 System.out.println(ex);
461 remoteVersion = getProperty("VERSION");
463 System.setProperty("sun.net.client.defaultConnectTimeout",
466 setProperty("LATEST_VERSION", remoteVersion);
470 VersionChecker vc = new VersionChecker();
475 if (jnlpVersion != null)
477 setProperty("LATEST_VERSION", jnlpVersion);
481 applicationProperties.remove("LATEST_VERSION");
485 setProperty("VERSION", codeVersion);
487 // LOAD USERDEFINED COLOURS
488 jalview.gui.UserDefinedColours
489 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
490 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
494 private static void deleteBuildProperties()
496 applicationProperties.remove("LATEST_VERSION");
497 applicationProperties.remove("VERSION");
498 applicationProperties.remove("AUTHORS");
499 applicationProperties.remove("AUTHORFNAMES");
500 applicationProperties.remove("YEAR");
501 applicationProperties.remove("BUILD_DATE");
502 applicationProperties.remove("INSTALLATION");
506 * Gets Jalview application property of given key. Returns null if key not
512 * @return Property value
514 public static String getProperty(String key)
516 return applicationProperties.getProperty(key);
520 * These methods are used when checking if the saved preference is different
521 * to the default setting
524 public static boolean getDefault(String property, boolean def)
526 String string = getProperty(property);
529 def = Boolean.valueOf(string).booleanValue();
536 * These methods are used when checking if the saved preference is different
537 * to the default setting
539 public static String getDefault(String property, String def)
541 String string = getProperty(property);
551 * Stores property in the file "HOME_DIR/.jalview_properties"
556 * String value of property
558 * @return String value of property
560 public static String setProperty(String key, String obj)
565 applicationProperties.setProperty(key, obj);
566 if (!propsAreReadOnly)
568 FileOutputStream out = new FileOutputStream(propertiesFile);
569 applicationProperties.store(out, "---JalviewX Properties File---");
572 } catch (Exception ex)
574 System.out.println("Error setting property: " + key + " " + obj
581 * remove the specified property from the jalview properties file
585 public static void removeProperty(String string)
587 applicationProperties.remove(string);
592 * save the properties to the jalview properties path
594 public static void saveProperties()
596 if (!propsAreReadOnly)
600 FileOutputStream out = new FileOutputStream(propertiesFile);
601 applicationProperties.store(out, "---JalviewX Properties File---");
603 } catch (Exception ex)
605 System.out.println("Error saving properties: " + ex);
611 * internal vamsas class discovery state
613 private static int vamsasJarsArePresent = -1;
616 * Searches for vamsas client classes on class path.
618 * @return true if vamsas client is present on classpath
620 public static boolean vamsasJarsPresent()
622 if (vamsasJarsArePresent == -1)
626 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
627 "uk.ac.vamsas.client.VorbaId") != null)
629 jalview.bin.Cache.log
630 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
631 vamsasJarsArePresent = 1;
632 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
633 lvclient.setLevel(Level.toLevel(Cache.getDefault(
634 "logs.Vamsas.Level", Level.INFO.toString())));
636 lvclient.addAppender(log.getAppender("JalviewLogger"));
637 // Tell the user that debug is enabled
638 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
640 } catch (Exception e)
642 vamsasJarsArePresent = 0;
643 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
646 return (vamsasJarsArePresent > 0);
650 * internal vamsas class discovery state
652 private static int groovyJarsArePresent = -1;
655 * Searches for vamsas client classes on class path.
657 * @return true if vamsas client is present on classpath
659 public static boolean groovyJarsPresent()
661 if (groovyJarsArePresent == -1)
665 if (Cache.class.getClassLoader().loadClass(
666 "groovy.lang.GroovyObject") != null)
668 jalview.bin.Cache.log
669 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
670 groovyJarsArePresent = 1;
671 Logger lgclient = Logger.getLogger("groovy");
672 lgclient.setLevel(Level.toLevel(Cache.getDefault(
673 "logs.Groovy.Level", Level.INFO.toString())));
675 lgclient.addAppender(log.getAppender("JalviewLogger"));
676 // Tell the user that debug is enabled
677 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
681 groovyJarsArePresent = 0;
682 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
683 } catch (Exception e)
685 groovyJarsArePresent = 0;
686 jalview.bin.Cache.log.debug("Groovy Classes are not present");
689 return (groovyJarsArePresent > 0);
693 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
696 protected static Object tracker = null;
698 protected static Class trackerfocus = null;
700 protected static Class jgoogleanalyticstracker = null;
703 * Initialise the google tracker if it is not done already.
705 public static void initGoogleTracker()
709 if (jgoogleanalyticstracker == null)
711 // try to get the tracker class
714 jgoogleanalyticstracker = Cache.class
717 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
718 trackerfocus = Cache.class.getClassLoader().loadClass(
719 "com.boxysystems.jgoogleanalytics.FocusPoint");
720 } catch (Exception e)
722 log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
724 jgoogleanalyticstracker = null;
729 // now initialise tracker
730 Exception re = null, ex = null;
732 String vrs = "No Version Accessible";
735 // Google analytics tracking code for Library Finder
736 tracker = jgoogleanalyticstracker.getConstructor(
737 new Class[] { String.class, String.class, String.class })
741 (vrs = jalview.bin.Cache.getProperty("VERSION")
743 + jalview.bin.Cache.getDefault(
744 "BUILD_DATE", "unknown")),
746 jgoogleanalyticstracker.getMethod("trackAsynchronously",
747 new Class[] { trackerfocus }).invoke(
749 new Object[] { trackerfocus.getConstructor(
750 new Class[] { String.class }).newInstance(
751 new Object[] { "Application Started." }) });
752 } catch (RuntimeException e)
755 } catch (Exception e)
762 if (re != null || ex != null || err != null)
768 log.debug("Caught runtime exception in googletracker init:", re);
773 "Failed to initialise GoogleTracker for Jalview Desktop with version "
779 "Whilst initing GoogleTracker for Jalview Desktop version "
788 .println("Debug: Caught runtime exception in googletracker init:"
790 re.printStackTrace();
795 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
797 ex.printStackTrace();
803 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
805 err.printStackTrace();
811 log.debug("Successfully initialised tracker.");
817 * get the user's default colour if available
823 public static Color getDefaultColour(String property, Color defcolour)
825 String colprop = getProperty(property);
830 Color col = jalview.schemes.ColourSchemeProperty
831 .getAWTColorFromName(colprop);
836 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
837 } catch (Exception ex)
839 log.warn("Couldn't parse '" + colprop + "' as a colour for "
844 return (col == null) ? defcolour : col;
848 * store a colour as a Jalview user default property
853 public static void setColourProperty(String property, Color colour)
855 setProperty(property, jalview.util.Format.getHexString(colour));
858 public static final DateFormat date_format = SimpleDateFormat
859 .getDateTimeInstance();
862 * store a date in a jalview property
867 public static void setDateProperty(String property, Date time)
869 setProperty(property, date_format.format(time));
873 * read a date stored in a jalview property
876 * @return valid date as stored by setDateProperty, or null
879 public static Date getDateProperty(String property)
881 String val = getProperty(property);
886 return date_format.parse(val);
887 } catch (Exception ex)
889 System.err.println("Invalid or corrupt date in property '"
890 + property + "' : value was '" + val + "'");
897 * get and parse a property as an integer. send any parsing problems to
901 * @return null or Integer
903 public static Integer getIntegerProperty(String property)
905 String val = getProperty(property);
906 if (val != null && (val = val.trim()).length() > 0)
910 return Integer.valueOf(val);
911 } catch (NumberFormatException x)
913 System.err.println("Invalid integer in property '" + property
914 + "' (value was '" + val + "')");
920 private static DasSourceRegistryI sourceRegistry = null;
925 * @return instance of the das source registry
927 public static DasSourceRegistryI getDasSourceRegistry()
929 if (sourceRegistry == null)
931 sourceRegistry = new DasSourceRegistry();
933 return sourceRegistry;
937 * Set the specified value, or remove it if null or empty. Does not save the
943 public static void setOrRemove(String propName, String value)
945 if (propName == null)
949 if (value == null || value.trim().length() < 1)
951 Cache.applicationProperties.remove(propName);
955 Cache.applicationProperties.setProperty(propName, value);