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;
26 import java.awt.Color;
27 import java.io.BufferedReader;
29 import java.io.FileInputStream;
30 import java.io.FileOutputStream;
31 import java.io.InputStream;
32 import java.io.InputStreamReader;
33 import java.text.DateFormat;
34 import java.text.SimpleDateFormat;
35 import java.util.Collections;
36 import java.util.Date;
37 import java.util.Enumeration;
38 import java.util.Properties;
39 import java.util.TreeSet;
41 import org.apache.log4j.ConsoleAppender;
42 import org.apache.log4j.Level;
43 import org.apache.log4j.Logger;
44 import org.apache.log4j.SimpleLayout;
47 * Stores and retrieves Jalview Application Properties Lists and fields within
48 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
49 * are alternative values for a tag. <br>
51 * Current properties include:
54 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
55 * logging level for axis (used for web services) <br>
57 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
58 * the logging level for castor (used for serialization) <br>
60 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
62 * <li>SCREEN_WIDTH</li>
63 * <li>SCREEN_HEIGHT</li>
64 * <li>SCREEN_Y=285</li>
65 * <li>SCREEN_X=371</li>
66 * <li>SHOW_FULLSCREEN boolean</li>
67 * <li>FONT_NAME java font name for alignment text display</li>
68 * <li>FONT_SIZE size of displayed alignment text</li>
69 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
70 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
71 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
72 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
73 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
74 * <li>SHOW_IDENTITY show percentage identity annotation</li>
75 * <li>SHOW_QUALITY show alignment quality annotation</li>
76 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
77 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
78 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
79 * LABEL_AND_SEQUENCE</li>
80 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
81 * sequence annotations</li>
82 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
84 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
85 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
86 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
87 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
88 * <li>VERSION the version of the jalview build</li>
89 * <li>BUILD_DATE date of this build</li>
90 * <li>LATEST_VERSION the latest jalview version advertised on the
91 * www.jalview.org</li>
92 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
94 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
96 * <li>RECENT_URL list of recently retrieved URLs</li>
97 * <li>RECENT_FILE list of recently opened files</li>
98 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
99 * <li>PROXY_SERVER the proxy</li>
100 * <li>PROXY_PORT</li>
101 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
103 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
105 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
106 * collecting usage statistics</li>
107 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
108 * <li>SHOW_OVERVIEW boolean for overview window display</li>
109 * <li>ANTI_ALIAS boolean for smooth fonts</li>
110 * <li>RIGHT_ALIGN_IDS boolean</li>
111 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
112 * <li>PAD_GAPS boolean</li>
113 * <li>ID_ITALICS boolean</li>
114 * <li>SHOW_JV_SUFFIX</li>
115 * <li>WRAP_ALIGNMENT</li>
116 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
118 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
119 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
121 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
122 * jalview.utils.GroupURLLink for more info</li>
123 * <li>DAS_REGISTRY_URL the registry to query</li>
124 * <li>DEFAULT_BROWSER for unix</li>
125 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
126 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
128 * <li>VERSION_CHECK (true) check for the latest release version from
129 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
130 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
132 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
134 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
135 * displayed as '.'</li>
136 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
137 * order of a newly displayed tree</li>
138 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
139 * sequence ID strings before attempting retrieval from any datasource</li>
140 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
142 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
143 * in the alignment.</li>
144 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
146 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
148 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
149 * logo normalised to row height rather than histogram height.</li>
150 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
151 * respond to selections made in other alignments containing the same sequences.
153 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
154 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
155 * warning dialog box is displayed.</li>
156 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
157 * when shading by annotation</li>
158 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
159 * when shading by annotation</li>
160 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
161 * requests to be redirected to a mirror of http://www.jalview.org</li>
162 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
163 * alignment figure to accommodate even the longest sequence ID or annotation
165 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
166 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
167 * will override this).</li>
168 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
170 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
171 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
173 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
175 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
177 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
180 * Deprecated settings:
183 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
184 * startup (JWS1 services only)</li>
185 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
186 * (JWS1 services only)</li>
187 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
188 * services in the desktop GUI</li>
189 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
190 * panel in web service preferences</li>
194 * @version $Revision$
199 * property giving log4j level for CASTOR loggers
201 public static final String CASTORLOGLEVEL = "logs.Castor.level";
204 * property giving log4j level for AXIS loggers
206 public static final String AXISLOGLEVEL = "logs.Axis.level";
209 * property giving log4j level for Jalview Log
211 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
213 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
215 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
217 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
220 * Initialises the Jalview Application Log
222 public static Logger log;
224 /** Jalview Properties */
225 public static Properties applicationProperties = new Properties()
227 // override results in properties output in alphabetical order
229 public synchronized Enumeration<Object> keys()
231 return Collections.enumeration(new TreeSet<Object>(super.keySet()));
235 /** Default file is ~/.jalview_properties */
236 static String propertiesFile;
238 private static boolean propsAreReadOnly = false;
240 public static void initLogger()
248 // TODO: redirect stdout and stderr here in order to grab the output of
251 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
253 ap.setName("JalviewLogger");
254 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
256 Logger laxis = Logger.getLogger("org.apache.axis");
257 Logger lcastor = Logger.getLogger("org.exolab.castor");
258 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
260 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
261 Level.INFO.toString())));
262 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
263 Level.INFO.toString())));
264 lcastor = Logger.getLogger("org.exolab.castor.xml");
265 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
266 Level.INFO.toString())));
267 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
268 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
269 // Level.INFO.toString())));
270 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
271 "logs.Jalview.level", Level.INFO.toString())));
272 // laxis.addAppender(ap);
273 // lcastor.addAppender(ap);
274 // jalview.bin.Cache.log.addAppender(ap);
275 // Tell the user that debug is enabled
276 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
277 } catch (Exception ex)
279 System.err.println("Problems initializing the log4j system\n");
280 ex.printStackTrace(System.err);
284 /** Called when Jalview is started */
285 public static void loadProperties(String propsFile)
287 propertiesFile = propsFile;
288 if (propsFile == null)
290 propertiesFile = System.getProperty("user.home") + File.separatorChar
291 + ".jalview_properties";
295 // don't corrupt the file we've been given.
296 propsAreReadOnly = true;
304 fis = new java.net.URL(propertiesFile).openStream();
305 System.out.println("Loading jalview properties from : "
308 .println("Disabling Jalview writing to user's local properties file.");
309 propsAreReadOnly = true;
311 } catch (Exception ex)
317 fis = new FileInputStream(propertiesFile);
319 applicationProperties.load(fis);
321 // remove any old build properties
323 deleteBuildProperties();
325 } catch (Exception ex)
327 System.out.println("Error reading properties file: " + ex);
330 if (getDefault("USE_PROXY", false))
332 String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
333 "PROXY_PORT", "8080");
335 System.out.println("Using proxyServer: " + proxyServer
336 + " proxyPort: " + proxyPort);
338 System.setProperty("http.proxyHost", proxyServer);
339 System.setProperty("http.proxyPort", proxyPort);
342 // LOAD THE AUTHORS FROM THE authors.props file
345 String authorDetails = "jar:".concat(Cache.class
346 .getProtectionDomain().getCodeSource().getLocation()
347 .toString().concat("!/authors.props"));
349 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
351 InputStream in = localJarFileURL.openStream();
352 applicationProperties.load(in);
354 } catch (Exception ex)
356 System.out.println("Error reading author details: " + ex);
357 applicationProperties.remove("AUTHORS");
358 applicationProperties.remove("AUTHORFNAMES");
359 applicationProperties.remove("YEAR");
362 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
363 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
364 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
367 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
368 .getCodeSource().getLocation().toString()
369 .concat("!/.build_properties"));
371 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
373 InputStream in = localJarFileURL.openStream();
374 applicationProperties.load(in);
376 } catch (Exception ex)
378 System.out.println("Error reading build details: " + ex);
379 applicationProperties.remove("VERSION");
382 String jnlpVersion = System.getProperty("jalview.version");
383 String codeVersion = getProperty("VERSION");
384 String codeInstallation = getProperty("INSTALLATION");
385 if (codeVersion == null)
387 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
388 codeVersion = "Test";
389 jnlpVersion = "Test";
390 codeInstallation = "";
394 codeInstallation = " (" + codeInstallation + ")";
396 new BuildDetails(codeVersion, null, codeInstallation);
398 .println("Jalview Version: " + codeVersion + codeInstallation);
400 // jnlpVersion will be null if we're using InstallAnywhere
401 // Dont do this check if running in headless mode
402 if (jnlpVersion == null
403 && getDefault("VERSION_CHECK", true)
404 && (System.getProperty("java.awt.headless") == null || System
405 .getProperty("java.awt.headless").equals("false")))
408 class VersionChecker extends Thread
412 String orgtimeout = System
413 .getProperty("sun.net.client.defaultConnectTimeout");
414 if (orgtimeout == null)
417 System.out.println("# INFO: Setting default net timeout to "
418 + orgtimeout + " seconds.");
420 String remoteVersion = null;
423 System.setProperty("sun.net.client.defaultConnectTimeout",
425 java.net.URL url = new java.net.URL(Cache.getDefault(
426 "www.jalview.org", "http://www.jalview.org")
427 + "/webstart/jalview.jnlp");
428 BufferedReader in = new BufferedReader(new InputStreamReader(
431 while ((line = in.readLine()) != null)
433 if (line.indexOf("jalview.version") == -1)
438 line = line.substring(line.indexOf("value=") + 7);
439 line = line.substring(0, line.lastIndexOf("\""));
440 remoteVersion = line;
443 } catch (Exception ex)
446 .println("Non-fatal exception when checking version at www.jalview.org :");
447 System.out.println(ex);
448 remoteVersion = getProperty("VERSION");
450 System.setProperty("sun.net.client.defaultConnectTimeout",
453 setProperty("LATEST_VERSION", remoteVersion);
457 VersionChecker vc = new VersionChecker();
462 if (jnlpVersion != null)
464 setProperty("LATEST_VERSION", jnlpVersion);
468 applicationProperties.remove("LATEST_VERSION");
472 setProperty("VERSION", codeVersion);
474 // LOAD USERDEFINED COLOURS
475 jalview.gui.UserDefinedColours
476 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
477 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
481 private static void deleteBuildProperties()
483 applicationProperties.remove("LATEST_VERSION");
484 applicationProperties.remove("VERSION");
485 applicationProperties.remove("AUTHORS");
486 applicationProperties.remove("AUTHORFNAMES");
487 applicationProperties.remove("YEAR");
488 applicationProperties.remove("BUILD_DATE");
489 applicationProperties.remove("INSTALLATION");
493 * Gets Jalview application property of given key. Returns null if key not
499 * @return Property value
501 public static String getProperty(String key)
503 return applicationProperties.getProperty(key);
507 * These methods are used when checking if the saved preference is different
508 * to the default setting
511 public static boolean getDefault(String property, boolean def)
513 String string = getProperty(property);
516 def = Boolean.valueOf(string).booleanValue();
523 * These methods are used when checking if the saved preference is different
524 * to the default setting
526 public static String getDefault(String property, String def)
528 String string = getProperty(property);
538 * Stores property in the file "HOME_DIR/.jalview_properties"
543 * String value of property
545 * @return String value of property
547 public static String setProperty(String key, String obj)
552 applicationProperties.setProperty(key, obj);
553 if (!propsAreReadOnly)
555 FileOutputStream out = new FileOutputStream(propertiesFile);
556 applicationProperties.store(out, "---JalviewX Properties File---");
559 } catch (Exception ex)
561 System.out.println("Error setting property: " + key + " " + obj
568 * remove the specified property from the jalview properties file
572 public static void removeProperty(String string)
574 applicationProperties.remove(string);
579 * save the properties to the jalview properties path
581 public static void saveProperties()
583 if (!propsAreReadOnly)
587 FileOutputStream out = new FileOutputStream(propertiesFile);
588 applicationProperties.store(out, "---JalviewX Properties File---");
590 } catch (Exception ex)
592 System.out.println("Error saving properties: " + ex);
598 * internal vamsas class discovery state
600 private static int vamsasJarsArePresent = -1;
603 * Searches for vamsas client classes on class path.
605 * @return true if vamsas client is present on classpath
607 public static boolean vamsasJarsPresent()
609 if (vamsasJarsArePresent == -1)
613 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
614 "uk.ac.vamsas.client.VorbaId") != null)
616 jalview.bin.Cache.log
617 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
618 vamsasJarsArePresent = 1;
619 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
620 lvclient.setLevel(Level.toLevel(Cache.getDefault(
621 "logs.Vamsas.Level", Level.INFO.toString())));
623 lvclient.addAppender(log.getAppender("JalviewLogger"));
624 // Tell the user that debug is enabled
625 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
627 } catch (Exception e)
629 vamsasJarsArePresent = 0;
630 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
633 return (vamsasJarsArePresent > 0);
637 * internal vamsas class discovery state
639 private static int groovyJarsArePresent = -1;
642 * Searches for vamsas client classes on class path.
644 * @return true if vamsas client is present on classpath
646 public static boolean groovyJarsPresent()
648 if (groovyJarsArePresent == -1)
652 if (Cache.class.getClassLoader().loadClass(
653 "groovy.lang.GroovyObject") != null)
655 jalview.bin.Cache.log
656 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
657 groovyJarsArePresent = 1;
658 Logger lgclient = Logger.getLogger("groovy");
659 lgclient.setLevel(Level.toLevel(Cache.getDefault(
660 "logs.Groovy.Level", Level.INFO.toString())));
662 lgclient.addAppender(log.getAppender("JalviewLogger"));
663 // Tell the user that debug is enabled
664 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
668 groovyJarsArePresent = 0;
669 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
670 } catch (Exception e)
672 groovyJarsArePresent = 0;
673 jalview.bin.Cache.log.debug("Groovy Classes are not present");
676 return (groovyJarsArePresent > 0);
680 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
683 protected static Object tracker = null;
685 protected static Class trackerfocus = null;
687 protected static Class jgoogleanalyticstracker = null;
690 * Initialise the google tracker if it is not done already.
692 public static void initGoogleTracker()
696 if (jgoogleanalyticstracker == null)
698 // try to get the tracker class
701 jgoogleanalyticstracker = Cache.class
704 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
705 trackerfocus = Cache.class.getClassLoader().loadClass(
706 "com.boxysystems.jgoogleanalytics.FocusPoint");
707 } catch (Exception e)
709 log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
711 jgoogleanalyticstracker = null;
716 // now initialise tracker
717 Exception re = null, ex = null;
719 String vrs = "No Version Accessible";
722 // Google analytics tracking code for Library Finder
723 tracker = jgoogleanalyticstracker.getConstructor(
724 new Class[] { String.class, String.class, String.class })
728 (vrs = jalview.bin.Cache.getProperty("VERSION")
730 + jalview.bin.Cache.getDefault(
731 "BUILD_DATE", "unknown")),
733 jgoogleanalyticstracker.getMethod("trackAsynchronously",
734 new Class[] { trackerfocus }).invoke(
736 new Object[] { trackerfocus.getConstructor(
737 new Class[] { String.class }).newInstance(
738 new Object[] { "Application Started." }) });
739 } catch (RuntimeException e)
742 } catch (Exception e)
749 if (re != null || ex != null || err != null)
755 log.debug("Caught runtime exception in googletracker init:", re);
760 "Failed to initialise GoogleTracker for Jalview Desktop with version "
766 "Whilst initing GoogleTracker for Jalview Desktop version "
775 .println("Debug: Caught runtime exception in googletracker init:"
777 re.printStackTrace();
782 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
784 ex.printStackTrace();
790 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
792 err.printStackTrace();
798 log.debug("Successfully initialised tracker.");
804 * get the user's default colour if available
810 public static Color getDefaultColour(String property, Color defcolour)
812 String colprop = getProperty(property);
817 Color col = jalview.schemes.ColourSchemeProperty
818 .getAWTColorFromName(colprop);
823 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
824 } catch (Exception ex)
826 log.warn("Couldn't parse '" + colprop + "' as a colour for "
831 return (col == null) ? defcolour : col;
835 * store a colour as a Jalview user default property
840 public static void setColourProperty(String property, Color colour)
842 setProperty(property, jalview.util.Format.getHexString(colour));
845 public static final DateFormat date_format = SimpleDateFormat
846 .getDateTimeInstance();
849 * store a date in a jalview property
854 public static void setDateProperty(String property, Date time)
856 setProperty(property, date_format.format(time));
860 * read a date stored in a jalview property
863 * @return valid date as stored by setDateProperty, or null
866 public static Date getDateProperty(String property)
868 String val = getProperty(property);
873 return date_format.parse(val);
874 } catch (Exception ex)
876 System.err.println("Invalid or corrupt date in property '"
877 + property + "' : value was '" + val + "'");
884 * get and parse a property as an integer. send any parsing problems to
888 * @return null or Integer
890 public static Integer getIntegerProperty(String property)
892 String val = getProperty(property);
893 if (val != null && (val = val.trim()).length() > 0)
897 return Integer.valueOf(val);
898 } catch (NumberFormatException x)
900 System.err.println("Invalid integer in property '" + property
901 + "' (value was '" + val + "')");
907 private static DasSourceRegistryI sourceRegistry = null;
912 * @return instance of the das source registry
914 public static DasSourceRegistryI getDasSourceRegistry()
916 if (sourceRegistry == null)
918 sourceRegistry = new DasSourceRegistry();
920 return sourceRegistry;
924 * Set the specified value, or remove it if null or empty. Does not save the
930 public static void setOrRemove(String propName, String value)
932 if (propName == null)
936 if (value == null || value.trim().length() < 1)
938 Cache.applicationProperties.remove(propName);
942 Cache.applicationProperties.setProperty(propName, value);