2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.bin;
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25 import org.apache.log4j.Logger;
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26 import org.apache.log4j.SimpleLayout;
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27 import org.apache.log4j.Level;
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28 import org.apache.log4j.ConsoleAppender;
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32 * Stores and retrieves Jalview Application Properties
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33 * <br><br>Current properties include:
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34 * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
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35 * <br>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
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36 * <br>logs.Jalview.Level - Cache.log stringified level.
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37 * <br>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
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38 * <br>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
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39 * <br>SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN
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40 * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
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41 * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
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42 * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE
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45 * @version $Revision$
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50 * Initialises the Apache Axis logger
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52 public static Logger log;
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54 /** Jalview Properties */
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55 public static Properties applicationProperties = new Properties();
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57 /** Default file is ~/.jalview_properties */
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58 static String propertiesFile;
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60 public static void initLogger()
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64 Logger laxis = Logger.getLogger("org.apache.axis");
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65 Logger lcastor = Logger.getLogger("org.exolab.castor");
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66 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
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68 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
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69 Level.INFO.toString())));
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70 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
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71 Level.INFO.toString())));
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72 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
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73 "logs.Jalview.level",
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74 Level.INFO.toString())));
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75 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
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77 ap.setName("JalviewLogger");
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79 laxis.addAppender(ap);
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80 lcastor.addAppender(ap);
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81 jalview.bin.Cache.log.addAppender(ap);
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82 // Tell the user that debug is enabled
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83 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
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85 catch (Exception ex)
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87 System.err.println("Problems initializing the log4j system\n");
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92 /** Called when Jalview is started */
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93 public static void loadProperties(String propsFile)
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95 propertiesFile = propsFile;
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96 if (propsFile == null)
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98 propertiesFile = System.getProperty("user.home") + "/.jalview_properties";
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103 FileInputStream fis = new FileInputStream(propertiesFile);
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104 applicationProperties.load(fis);
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105 applicationProperties.remove("LATEST_VERSION");
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106 applicationProperties.remove("VERSION");
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109 catch (Exception ex)
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111 System.out.println("Error reading properties file: "+ex);
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114 if(getDefault("USE_PROXY", false))
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116 System.out.println("Using proxyServer: "+getDefault("PROXY_SERVER", null)+
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117 " proxyPort: "+getDefault("PROXY_PORT", null));
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118 System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
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119 System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
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122 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
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123 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
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124 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
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127 String buildDetails = "jar:"
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129 Cache.class.getProtectionDomain().getCodeSource().getLocation().toString()
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130 .concat("!/.build_properties")
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133 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
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135 InputStream in = localJarFileURL.openStream();
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136 applicationProperties.load(in);
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139 catch (Exception ex)
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141 System.out.println("Error reading build details: "+ex);
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142 applicationProperties.remove("VERSION");
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145 String jnlpVersion = System.getProperty("jalview.version");
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146 String codeVersion = getProperty("VERSION");
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149 if(codeVersion==null)
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151 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
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152 codeVersion = "Test";
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153 jnlpVersion = "Test";
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157 System.out.println("Jalview Version: "+codeVersion);
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160 // jnlpVersion will be null if we're using InstallAnywhere
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161 // Dont do this check if running in headless mode
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162 if(jnlpVersion==null && (
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163 System.getProperty("java.awt.headless")==null
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164 || System.getProperty("java.awt.headless").equals("false")))
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167 class VersionChecker
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172 String jnlpVersion = null;
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175 java.net.URL url = new java.net.URL(
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176 "http://www.jalview.org/webstart/jalview.jnlp");
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177 BufferedReader in = new BufferedReader(new InputStreamReader(url.
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179 String line = null;
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180 while ( (line = in.readLine()) != null)
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182 if (line.indexOf("jalview.version") == -1)
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185 line = line.substring(line.indexOf("value=") + 7);
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186 line = line.substring(0, line.lastIndexOf("\""));
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187 jnlpVersion = line;
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191 catch (Exception ex)
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193 System.out.println(ex);
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194 jnlpVersion = getProperty("VERSION");
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197 setProperty("LATEST_VERSION", jnlpVersion);
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201 VersionChecker vc = new VersionChecker();
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206 if(jnlpVersion!=null)
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207 setProperty("LATEST_VERSION", jnlpVersion);
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209 applicationProperties.remove("LATEST_VERSION");
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212 setProperty("VERSION", codeVersion);
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214 //LOAD USERDEFINED COLOURS
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215 jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
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221 * Gets Jalview application property of given key. Returns null
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224 * @param key Name of property
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226 * @return Property value
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228 public static String getProperty(String key)
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230 return applicationProperties.getProperty(key);
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234 /** These methods are used when checking if the saved preference
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235 * is different to the default setting
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238 public static boolean getDefault(String property, boolean def)
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240 String string = getProperty(property);
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241 if (string != null)
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243 def = Boolean.valueOf(string).booleanValue();
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249 /** These methods are used when checking if the saved preference
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250 * is different to the default setting
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252 public static String getDefault(String property, String def)
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254 String string = getProperty(property);
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255 if (string != null)
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265 * Stores property in the file "HOME_DIR/.jalview_properties"
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267 * @param key Name of object
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268 * @param obj String value of property
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270 * @return String value of property
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272 public static String setProperty(String key, String obj)
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276 FileOutputStream out = new FileOutputStream(propertiesFile);
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277 applicationProperties.setProperty(key, obj);
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278 applicationProperties.store(out, "---JalviewX Properties File---");
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281 catch (Exception ex)
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282 { System.out.println("Error setting property: "+key+" "+obj+"\n"+ex); }
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286 public static void saveProperties()
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290 FileOutputStream out = new FileOutputStream(propertiesFile);
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291 applicationProperties.store(out, "---JalviewX Properties File---");
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294 catch (Exception ex)
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295 { System.out.println("Error saving properties: "+ex); }
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