2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 import org.apache.log4j.*;
27 * Stores and retrieves Jalview Application Properties
28 * Lists and fields within list entries are separated by '|' symbols unless otherwise stated
29 * (|) clauses are alternative values for a tag.
30 * <br><br>Current properties include:
32 * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
34 * </li><li>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
36 * </li><li>logs.Jalview.Level - Cache.log stringified level.
38 * </li><li>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
39 * </li><li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
40 * </li><li>SCREEN_WIDTH
41 * </li><li>SCREEN_HEIGHT
42 * </li><li>SCREEN_Y=285
43 * </li><li>SCREEN_X=371
44 * </li><li>SHOW_FULLSCREEN boolean
45 * </li><li>FONT_NAME java font name for alignment text display
46 * </li><li>FONT_SIZE size of displayed alignment text
47 * </li><li>FONT_STYLE style of font displayed (sequence labels are always italic)
48 * </li><li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
49 * </li><li>LAST_DIRECTORY last directory for browsing alignment
50 * </li><li>USER_DEFINED_COLOURS list of user defined colour scheme files
51 * </li><li>SHOW_FULL_ID show id with '/start-end' numbers appended
52 * </li><li>SHOW_IDENTITY show percentage identity annotation
53 * </li><li>SHOW_QUALITY show alignment quality annotation
54 * </li><li>SHOW_ANNOTATIONS show alignment annotation rows
55 * </li><li>SHOW_CONSERVATION show alignment conservation annotation
56 * </li><li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed annotation row
57 * </li><li>DEFAULT_COLOUR default colour scheme to apply for a new alignment
58 * </li><li>DEFAULT_FILE_FORMAT file format used to save
59 * </li><li>STARTUP_FILE file loaded on startup (may be a fully qualified url)
60 * </li><li>SHOW_STARTUP_FILE flag to control loading of startup file
61 * </li><li>VERSION the version of the jalview build
62 * </li><li>BUILD_DATE date of this build
63 * </li><li>LATEST_VERSION the latest jalview version advertised on the www.jalview.org
64 * </li><li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER descriptions
65 * </li><li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv suffix to file
66 * </li><li>RECENT_URL list of recently retrieved URLs
67 * </li><li>RECENT_FILE list of recently opened files
68 * </li><li>USE_PROXY flag for whether a http proxy is to be used
69 * </li><li>PROXY_SERVER the proxy
71 * </li><li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire service
72 * </li><li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire service
73 * </li><li>DAS_LOCAL_SOURCE list of local das sources
74 * </li><li>SHOW_OVERVIEW boolean for overview window display
75 * </li><li>ANTI_ALIAS boolean for smooth fonts
76 * </li><li>RIGHT_ALIGN_IDS boolean
77 * </li><li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
78 * </li><li>PAD_GAPS boolean
79 * </li><li>ID_ITALICS boolean
80 * </li><li>SHOW_JV_SUFFIX
81 * </li><li>WRAP_ALIGNMENT
82 * </li><li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering style check
83 * </li><li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
84 * </li><li>SEQUENCE_LINKS list of name|URL pairs for opening a url with $SEQUENCE_ID$
85 * </li><li>DAS_REGISTRY_URL the registry to query
86 * </li><li>DEFAULT_BROWSER for unix
87 * </li><li>DAS_ACTIVE_SOURCE list of active sources
88 * </li><li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop (false)
100 * property giving log4j level for CASTOR loggers
102 public static final String CASTORLOGLEVEL = "logs.Castor.level";
104 * property giving log4j level for AXIS loggers
106 public static final String AXISLOGLEVEL = "logs.Axis.level";
108 * property giving log4j level for Jalview Log
110 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
111 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
114 * Initialises the Jalview Application Log
116 public static Logger log;
118 /** Jalview Properties */
119 public static Properties applicationProperties = new Properties();
121 /** Default file is ~/.jalview_properties */
122 static String propertiesFile;
124 public static void initLogger()
128 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
130 ap.setName("JalviewLogger");
131 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for log output
132 Logger laxis = Logger.getLogger("org.apache.axis");
133 Logger lcastor = Logger.getLogger("org.exolab.castor");
134 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
136 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
137 Level.INFO.toString())));
138 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
139 Level.INFO.toString())));
140 lcastor = Logger.getLogger("org.exolab.castor.xml");
141 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
142 Level.INFO.toString())));
143 //lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
144 //lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
145 // Level.INFO.toString())));
146 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
147 "logs.Jalview.level",
148 Level.INFO.toString())));
149 //laxis.addAppender(ap);
150 //lcastor.addAppender(ap);
151 //jalview.bin.Cache.log.addAppender(ap);
152 // Tell the user that debug is enabled
153 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
157 System.err.println("Problems initializing the log4j system\n");
158 ex.printStackTrace(System.err);
162 /** Called when Jalview is started */
163 public static void loadProperties(String propsFile)
165 propertiesFile = propsFile;
166 if (propsFile == null)
168 propertiesFile = System.getProperty("user.home") + File.separatorChar +
169 ".jalview_properties";
174 FileInputStream fis = new FileInputStream(propertiesFile);
175 applicationProperties.load(fis);
176 applicationProperties.remove("LATEST_VERSION");
177 applicationProperties.remove("VERSION");
182 System.out.println("Error reading properties file: " + ex);
185 if (getDefault("USE_PROXY", false))
187 System.out.println("Using proxyServer: " + getDefault("PROXY_SERVER", null) +
188 " proxyPort: " + getDefault("PROXY_PORT", null));
189 System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
190 System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
193 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
194 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
195 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
198 String buildDetails = "jar:"
200 Cache.class.getProtectionDomain().getCodeSource().getLocation().
202 .concat("!/.build_properties")
205 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
207 InputStream in = localJarFileURL.openStream();
208 applicationProperties.load(in);
213 System.out.println("Error reading build details: " + ex);
214 applicationProperties.remove("VERSION");
217 String jnlpVersion = System.getProperty("jalview.version");
218 String codeVersion = getProperty("VERSION");
220 if (codeVersion == null)
222 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
223 codeVersion = "Test";
224 jnlpVersion = "Test";
227 System.out.println("Jalview Version: " + codeVersion);
229 // jnlpVersion will be null if we're using InstallAnywhere
230 // Dont do this check if running in headless mode
231 if (jnlpVersion == null && (
232 System.getProperty("java.awt.headless") == null
233 || System.getProperty("java.awt.headless").equals("false")))
241 String orgtimeout = System.getProperty("sun.net.client.defaultConnectTimeout");
242 if (orgtimeout==null)
245 System.out.println("# INFO: Setting default net timeout to "+orgtimeout+" seconds.");
247 String jnlpVersion = null;
250 System.setProperty("sun.net.client.defaultConnectTimeout", "5000");
251 java.net.URL url = new java.net.URL(
252 "http://www.jalview.org/webstart/jalview.jnlp");
253 BufferedReader in = new BufferedReader(new InputStreamReader(url.
256 while ( (line = in.readLine()) != null)
258 if (line.indexOf("jalview.version") == -1)
263 line = line.substring(line.indexOf("value=") + 7);
264 line = line.substring(0, line.lastIndexOf("\""));
271 System.out.println("Non-fatal exceptions when checking version at www.jalview.org :");
272 System.out.println(ex);
273 jnlpVersion = getProperty("VERSION");
275 System.setProperty("sun.net.client.defaultConnectTimeout", orgtimeout);
277 setProperty("LATEST_VERSION", jnlpVersion);
281 VersionChecker vc = new VersionChecker();
286 if (jnlpVersion != null)
288 setProperty("LATEST_VERSION", jnlpVersion);
292 applicationProperties.remove("LATEST_VERSION");
296 setProperty("VERSION", codeVersion);
298 //LOAD USERDEFINED COLOURS
299 jalview.gui.UserDefinedColours.initUserColourSchemes(getProperty(
300 "USER_DEFINED_COLOURS"));
301 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
305 * Gets Jalview application property of given key. Returns null
308 * @param key Name of property
310 * @return Property value
312 public static String getProperty(String key)
314 return applicationProperties.getProperty(key);
317 /** These methods are used when checking if the saved preference
318 * is different to the default setting
321 public static boolean getDefault(String property, boolean def)
323 String string = getProperty(property);
326 def = Boolean.valueOf(string).booleanValue();
332 /** These methods are used when checking if the saved preference
333 * is different to the default setting
335 public static String getDefault(String property, String def)
337 String string = getProperty(property);
347 * Stores property in the file "HOME_DIR/.jalview_properties"
349 * @param key Name of object
350 * @param obj String value of property
352 * @return String value of property
354 public static String setProperty(String key, String obj)
358 FileOutputStream out = new FileOutputStream(propertiesFile);
359 applicationProperties.setProperty(key, obj);
360 applicationProperties.store(out, "---JalviewX Properties File---");
365 System.out.println("Error setting property: " + key + " " + obj + "\n" +
371 public static void saveProperties()
375 FileOutputStream out = new FileOutputStream(propertiesFile);
376 applicationProperties.store(out, "---JalviewX Properties File---");
381 System.out.println("Error saving properties: " + ex);
386 * internal vamsas class discovery state
388 private static int vamsasJarsArePresent = -1;
390 * Searches for vamsas client classes on class path.
391 * @return true if vamsas client is present on classpath
393 public static boolean vamsasJarsPresent()
395 if (vamsasJarsArePresent == -1)
399 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
400 "uk.ac.vamsas.client.VorbaId") != null)
402 jalview.bin.Cache.log.debug(
403 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
404 vamsasJarsArePresent = 1;
405 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
406 lvclient.setLevel(Level.toLevel(Cache.getDefault("logs.Vamsas.Level",
407 Level.INFO.toString())));
409 lvclient.addAppender(log.getAppender("JalviewLogger"));
410 // Tell the user that debug is enabled
411 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
416 vamsasJarsArePresent = 0;
417 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
420 return (vamsasJarsArePresent > 0);
423 * internal vamsas class discovery state
425 private static int groovyJarsArePresent = -1;
427 * Searches for vamsas client classes on class path.
428 * @return true if vamsas client is present on classpath
430 public static boolean groovyJarsPresent()
432 if (groovyJarsArePresent == -1)
436 if (Cache.class.getClassLoader().loadClass(
437 "groovy.lang.GroovyObject") != null)
439 jalview.bin.Cache.log.debug(
440 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
441 groovyJarsArePresent = 1;
442 Logger lgclient = Logger.getLogger("groovy");
443 lgclient.setLevel(Level.toLevel(Cache.getDefault("logs.Groovy.Level",
444 Level.INFO.toString())));
446 lgclient.addAppender(log.getAppender("JalviewLogger"));
447 // Tell the user that debug is enabled
448 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
453 groovyJarsArePresent = 0;
454 jalview.bin.Cache.log.debug("Groovy Classes are not present");
457 return (groovyJarsArePresent > 0);