-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.bin;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-import java.net.*;\r
-import org.apache.log4j.Logger;\r
-import org.apache.log4j.SimpleLayout;\r
-import org.apache.log4j.Level;\r
-import org.apache.log4j.ConsoleAppender;\r
-\r
-\r
-/**\r
- * Stores and retrieves Jalview Application Properties\r
- * <br><br>Current properties include:\r
- * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)\r
- * <br>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)\r
- * <br>logs.Jalview.Level - Cache.log stringified level.\r
- * <br>DISCOVERY_START - Boolean - controls if discovery services are queried on startup\r
- * <br>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.\r
- * <br>SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN\r
- * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR\r
- * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,\r
- * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE\r
-\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Cache\r
-{\r
- /**\r
- * Initialises the Apache Axis logger\r
- */\r
- public static Logger log;\r
-\r
- /** Jalview Properties */\r
- public static Properties applicationProperties = new Properties();\r
-\r
- /** Default file is ~/.jalview_properties */\r
- static String propertiesFile;\r
-\r
- public static void initLogger()\r
- {\r
- try\r
- {\r
- Logger laxis = Logger.getLogger("org.apache.axis");\r
- Logger lcastor = Logger.getLogger("org.exolab.castor");\r
- jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");\r
-\r
- laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",\r
- Level.INFO.toString())));\r
- lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",\r
- Level.INFO.toString())));\r
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(\r
- "logs.Jalview.level",\r
- Level.INFO.toString())));\r
-\r
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),\r
- "System.err");\r
- ap.setName("JalviewLogger");\r
-\r
- laxis.addAppender(ap);\r
- lcastor.addAppender(ap);\r
- jalview.bin.Cache.log.addAppender(ap);\r
- }\r
- catch (Exception ex)\r
- {\r
- System.err.println("Problems initializing the log4j system\n");\r
- }\r
- }\r
-\r
-\r
- /** Called when Jalview is started */\r
- public static void loadProperties(String propsFile)\r
- {\r
- propertiesFile = propsFile;\r
- if (propsFile == null)\r
- {\r
- propertiesFile = System.getProperty("user.home") + "/.jalview_properties";\r
- }\r
-\r
- try\r
- {\r
- FileInputStream fis = new FileInputStream(propertiesFile);\r
- applicationProperties.load(fis);\r
- applicationProperties.remove("LATEST_VERSION");\r
- applicationProperties.remove("VERSION");\r
- fis.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error reading properties file: "+ex);\r
- }\r
-\r
- if(getDefault("USE_PROXY", false))\r
- {\r
- System.out.println("Using proxyServer: "+getDefault("PROXY_SERVER", null)+\r
- " proxyPort: "+getDefault("PROXY_PORT", null));\r
- System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));\r
- System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));\r
- }\r
-\r
- // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar\r
- // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE\r
- // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW\r
- try\r
- {\r
- String buildDetails = "jar:"\r
- .concat(\r
- Cache.class.getProtectionDomain().getCodeSource().getLocation().toString()\r
- .concat("!/.build_properties")\r
- );\r
-\r
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);\r
-\r
- InputStream in = localJarFileURL.openStream();\r
- applicationProperties.load(in);\r
- in.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error reading build details: "+ex);\r
- applicationProperties.remove("VERSION");\r
- }\r
-\r
- String jnlpVersion = System.getProperty("jalview.version");\r
- String codeVersion = getProperty("VERSION");\r
-\r
-\r
- if(codeVersion==null)\r
- {\r
- // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!\r
- codeVersion = "Test";\r
- jnlpVersion = "Test";\r
- }\r
-\r
-\r
- System.out.println("Jalview Version: "+codeVersion);\r
-\r
-\r
- // jnlpVersion will be null if we're using InstallAnywhere\r
- // Dont do this check if running in headless mode\r
- if(jnlpVersion==null && (\r
- System.getProperty("java.awt.headless")==null\r
- || System.getProperty("java.awt.headless").equals("false")))\r
- {\r
-\r
- class VersionChecker\r
- extends Thread\r
- {\r
- public void run()\r
- {\r
- String jnlpVersion = null;\r
- try\r
- {\r
- java.net.URL url = new java.net.URL(\r
- "http://www.jalview.org/webstart/jalview.jnlp");\r
- BufferedReader in = new BufferedReader(new InputStreamReader(url.\r
- openStream()));\r
- String line = null;\r
- while ( (line = in.readLine()) != null)\r
- {\r
- if (line.indexOf("jalview.version") == -1)\r
- continue;\r
-\r
- line = line.substring(line.indexOf("value=") + 7);\r
- line = line.substring(0, line.lastIndexOf("\""));\r
- jnlpVersion = line;\r
- break;\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println(ex);\r
- jnlpVersion = getProperty("VERSION");\r
- }\r
-\r
- setProperty("LATEST_VERSION", jnlpVersion);\r
- }\r
- }\r
-\r
- VersionChecker vc = new VersionChecker();\r
- vc.start();\r
- }\r
- else\r
- {\r
- applicationProperties.remove("LATEST_VERSION");\r
- }\r
-\r
- setProperty("VERSION", codeVersion);\r
-\r
- //LOAD USERDEFINED COLOURS\r
- jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));\r
- }\r
-\r
-\r
-\r
- /**\r
- * Gets Jalview application property of given key. Returns null\r
- * if key not found\r
- *\r
- * @param key Name of property\r
- *\r
- * @return Property value\r
- */\r
- public static String getProperty(String key)\r
- {\r
- return applicationProperties.getProperty(key);\r
- }\r
-\r
-\r
- /** These methods are used when checking if the saved preference\r
- * is different to the default setting\r
- */\r
-\r
- public static boolean getDefault(String property, boolean def)\r
- {\r
- String string = getProperty(property);\r
- if (string != null)\r
- {\r
- def = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- return def;\r
- }\r
-\r
- /** These methods are used when checking if the saved preference\r
- * is different to the default setting\r
- */\r
- public static String getDefault(String property, String def)\r
- {\r
- String string = getProperty(property);\r
- if (string != null)\r
- {\r
- return string;\r
- }\r
-\r
- return def;\r
- }\r
-\r
-\r
- /**\r
- * Stores property in the file "HOME_DIR/.jalview_properties"\r
- *\r
- * @param key Name of object\r
- * @param obj String value of property\r
- *\r
- * @return String value of property\r
- */\r
- public static String setProperty(String key, String obj)\r
- {\r
- try\r
- {\r
- FileOutputStream out = new FileOutputStream(propertiesFile);\r
- applicationProperties.setProperty(key, obj);\r
- applicationProperties.store(out, "---JalviewX Properties File---");\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- { System.out.println("Error setting property: "+key+" "+obj+"\n"+ex); }\r
- return obj;\r
- }\r
-\r
- public static void saveProperties()\r
- {\r
- try\r
- {\r
- FileOutputStream out = new FileOutputStream(propertiesFile);\r
- applicationProperties.store(out, "---JalviewX Properties File---");\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- { System.out.println("Error saving properties: "+ex); }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.bin;
+
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.Properties;
+import java.util.TreeSet;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+
+/**
+ * Stores and retrieves Jalview Application Properties Lists and fields within
+ * list entries are separated by '|' symbols unless otherwise stated (|) clauses
+ * are alternative values for a tag. <br>
+ * <br>
+ * Current properties include:
+ * <ul>
+ * <br>
+ * logs.Axis.Level - one of the stringified Levels for log4j controlling the
+ * logging level for axis (used for web services) <br>
+ * </li>
+ * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
+ * the logging level for castor (used for serialization) <br>
+ * </li>
+ * <li>logs.Jalview.Level - Cache.log stringified level. <br>
+ * </li>
+ * <li>SCREEN_WIDTH</li>
+ * <li>SCREEN_HEIGHT</li>
+ * <li>SCREEN_Y=285</li>
+ * <li>SCREEN_X=371</li>
+ * <li>SHOW_FULLSCREEN boolean</li>
+ * <li>FONT_NAME java font name for alignment text display</li>
+ * <li>FONT_SIZE size of displayed alignment text</li>
+ * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
+ * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
+ * <li>LAST_DIRECTORY last directory for browsing alignment</li>
+ * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
+ * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
+ * <li>SHOW_IDENTITY show percentage identity annotation</li>
+ * <li>SHOW_QUALITY show alignment quality annotation</li>
+ * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
+ * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
+ * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
+ * LABEL_AND_SEQUENCE</li>
+ * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
+ * sequence annotations</li>
+ * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
+ * annotation row</li>
+ * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
+ * <li>DEFAULT_FILE_FORMAT file format used to save</li>
+ * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
+ * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
+ * <li>VERSION the version of the jalview build</li>
+ * <li>BUILD_DATE date of this build</li>
+ * <li>LATEST_VERSION the latest jalview version advertised on the
+ * www.jalview.org</li>
+ * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
+ * descriptions</li>
+ * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
+ * suffix to file</li>
+ * <li>RECENT_URL list of recently retrieved URLs</li>
+ * <li>RECENT_FILE list of recently opened files</li>
+ * <li>USE_PROXY flag for whether a http proxy is to be used</li>
+ * <li>PROXY_SERVER the proxy</li>
+ * <li>PROXY_PORT</li>
+ * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
+ * service</li>
+ * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
+ * service</li>
+ * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * collecting usage statistics</li>
+ * <li>DAS_LOCAL_SOURCE list of local das sources</li>
+ * <li>SHOW_OVERVIEW boolean for overview window display</li>
+ * <li>ANTI_ALIAS boolean for smooth fonts</li>
+ * <li>RIGHT_ALIGN_IDS boolean</li>
+ * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
+ * <li>PAD_GAPS boolean</li>
+ * <li>ID_ITALICS boolean</li>
+ * <li>SHOW_JV_SUFFIX</li>
+ * <li>WRAP_ALIGNMENT</li>
+ * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
+ * style check</li>
+ * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
+ * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
+ * $SEQUENCE_ID$</li>
+ * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
+ * jalview.utils.GroupURLLink for more info</li>
+ * <li>DAS_REGISTRY_URL the registry to query</li>
+ * <li>DEFAULT_BROWSER for unix</li>
+ * <li>DAS_ACTIVE_SOURCE list of active sources</li>
+ * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
+ * (false)</li>
+ * <li>VERSION_CHECK (true) check for the latest release version from
+ * www.jalview.org (or the alias given by the www.jalview.org property)</li>
+ * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
+ * ID tooltip</li>
+ * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
+ * ID tooltip</li>
+ * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
+ * displayed as '.'</li>
+ * <li>SORT_BY_TREE (false) sort the current alignment view according to the
+ * order of a newly displayed tree</li>
+ * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
+ * sequence ID strings before attempting retrieval from any datasource</li>
+ * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
+ * alignment.</li>
+ * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
+ * in the alignment.</li>
+ * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
+ * histogram.</li>
+ * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo.</li>
+ * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.</li>
+ * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
+ * respond to selections made in other alignments containing the same sequences.
+ * </li>
+ * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
+ * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
+ * warning dialog box is displayed.</li>
+ * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
+ * when shading by annotation</li>
+ * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
+ * when shading by annotation</li>
+ * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
+ * alignment figure to accommodate even the longest sequence ID or annotation
+ * label.</li>
+ * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
+ * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
+ * will override this).</li>
+ * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
+ * record</li>
+ * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
+ * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
+ * display</li>
+ * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
+ * display</li>
+ * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
+ * display</li>
+ * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
+ *
+ * </ul>
+ * Deprecated settings:
+ * <ul>
+ * *
+ * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
+ * startup (JWS1 services only)</li>
+ * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
+ * (JWS1 services only)</li>
+ * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
+ * services in the desktop GUI</li>
+ * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
+ * panel in web service preferences</li>
+ * </ul>
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Cache
+{
+ /**
+ * property giving log4j level for CASTOR loggers
+ */
+ public static final String CASTORLOGLEVEL = "logs.Castor.level";
+
+ /**
+ * property giving log4j level for AXIS loggers
+ */
+ public static final String AXISLOGLEVEL = "logs.Axis.level";
+
+ /**
+ * property giving log4j level for Jalview Log
+ */
+ public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+
+ public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
+
+ public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
+
+ public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+
+ /**
+ * Initialises the Jalview Application Log
+ */
+ public static Logger log;
+
+ /** Jalview Properties */
+ public static Properties applicationProperties = new Properties()
+ {
+ // override results in properties output in alphabetical order
+ @Override
+ public synchronized Enumeration<Object> keys()
+ {
+ return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+ }
+ };
+
+ /** Default file is ~/.jalview_properties */
+ static String propertiesFile;
+
+ private static boolean propsAreReadOnly = false;
+
+ public static void initLogger()
+ {
+ if (log != null)
+ {
+ return;
+ }
+ try
+ {
+ // TODO: redirect stdout and stderr here in order to grab the output of
+ // the log
+
+ ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+ "System.err");
+ ap.setName("JalviewLogger");
+ org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
+ // log output
+ Logger laxis = Logger.getLogger("org.apache.axis");
+ Logger lcastor = Logger.getLogger("org.exolab.castor");
+ jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
+
+ laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
+ Level.INFO.toString())));
+ lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ Level.INFO.toString())));
+ lcastor = Logger.getLogger("org.exolab.castor.xml");
+ lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ Level.INFO.toString())));
+ // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
+ // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ // Level.INFO.toString())));
+ jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
+ "logs.Jalview.level", Level.INFO.toString())));
+ // laxis.addAppender(ap);
+ // lcastor.addAppender(ap);
+ // jalview.bin.Cache.log.addAppender(ap);
+ // Tell the user that debug is enabled
+ jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
+ } catch (Exception ex)
+ {
+ System.err.println("Problems initializing the log4j system\n");
+ ex.printStackTrace(System.err);
+ }
+ }
+
+ /** Called when Jalview is started */
+ public static void loadProperties(String propsFile)
+ {
+ propertiesFile = propsFile;
+ if (propsFile == null)
+ {
+ propertiesFile = System.getProperty("user.home") + File.separatorChar
+ + ".jalview_properties";
+ }
+ else
+ {
+ // don't corrupt the file we've been given.
+ propsAreReadOnly = true;
+ }
+
+ try
+ {
+ InputStream fis;
+ try
+ {
+ fis = new java.net.URL(propertiesFile).openStream();
+ System.out.println("Loading jalview properties from : "
+ + propertiesFile);
+ System.out
+ .println("Disabling Jalview writing to user's local properties file.");
+ propsAreReadOnly = true;
+
+ } catch (Exception ex)
+ {
+ fis = null;
+ }
+ if (fis == null)
+ {
+ fis = new FileInputStream(propertiesFile);
+ }
+ applicationProperties.load(fis);
+
+ // remove any old build properties
+
+ deleteBuildProperties();
+ fis.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading properties file: " + ex);
+ }
+
+ if (getDefault("USE_PROXY", false))
+ {
+ String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
+ "PROXY_PORT", "8080");
+
+ System.out.println("Using proxyServer: " + proxyServer
+ + " proxyPort: " + proxyPort);
+
+ System.setProperty("http.proxyHost", proxyServer);
+ System.setProperty("http.proxyPort", proxyPort);
+ }
+
+ // LOAD THE AUTHORS FROM THE authors.props file
+ try
+ {
+ String authorDetails = "jar:".concat(Cache.class
+ .getProtectionDomain().getCodeSource().getLocation()
+ .toString().concat("!/authors.props"));
+
+ java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading author details: " + ex);
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
+ }
+
+ // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+ // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
+ // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
+ try
+ {
+ String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/.build_properties"));
+
+ java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading build details: " + ex);
+ applicationProperties.remove("VERSION");
+ }
+
+ String jnlpVersion = System.getProperty("jalview.version");
+ String codeVersion = getProperty("VERSION");
+ String codeInstallation = getProperty("INSTALLATION");
+ if (codeVersion == null)
+ {
+ // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+ codeVersion = "Test";
+ jnlpVersion = "Test";
+ codeInstallation = "";
+ }
+ else
+ {
+ codeInstallation = " (" + codeInstallation + ")";
+ }
+ new BuildDetails(codeVersion, null, codeInstallation);
+ System.out
+ .println("Jalview Version: " + codeVersion + codeInstallation);
+
+ // jnlpVersion will be null if we're using InstallAnywhere
+ // Dont do this check if running in headless mode
+ if (jnlpVersion == null
+ && getDefault("VERSION_CHECK", true)
+ && (System.getProperty("java.awt.headless") == null || System
+ .getProperty("java.awt.headless").equals("false")))
+ {
+
+ class VersionChecker extends Thread
+ {
+ public void run()
+ {
+ String orgtimeout = System
+ .getProperty("sun.net.client.defaultConnectTimeout");
+ if (orgtimeout == null)
+ {
+ orgtimeout = "30";
+ System.out.println("# INFO: Setting default net timeout to "
+ + orgtimeout + " seconds.");
+ }
+ String jnlpVersion = null;
+ try
+ {
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ "5000");
+ java.net.URL url = new java.net.URL(Cache.getDefault(
+ "www.jalview.org", "http://www.jalview.org")
+ + "/webstart/jalview.jnlp");
+ BufferedReader in = new BufferedReader(new InputStreamReader(
+ url.openStream()));
+ String line = null;
+ while ((line = in.readLine()) != null)
+ {
+ if (line.indexOf("jalview.version") == -1)
+ {
+ continue;
+ }
+
+ line = line.substring(line.indexOf("value=") + 7);
+ line = line.substring(0, line.lastIndexOf("\""));
+ jnlpVersion = line;
+ break;
+ }
+ } catch (Exception ex)
+ {
+ System.out
+ .println("Non-fatal exceptions when checking version at www.jalview.org :");
+ System.out.println(ex);
+ jnlpVersion = getProperty("VERSION");
+ }
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ orgtimeout);
+
+ setProperty("LATEST_VERSION", jnlpVersion);
+ }
+ }
+
+ VersionChecker vc = new VersionChecker();
+ vc.start();
+ }
+ else
+ {
+ if (jnlpVersion != null)
+ {
+ setProperty("LATEST_VERSION", jnlpVersion);
+ }
+ else
+ {
+ applicationProperties.remove("LATEST_VERSION");
+ }
+ }
+
+ setProperty("VERSION", codeVersion);
+
+ // LOAD USERDEFINED COLOURS
+ jalview.gui.UserDefinedColours
+ .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+ jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+ false);
+ }
+
+ private static void deleteBuildProperties()
+ {
+ applicationProperties.remove("LATEST_VERSION");
+ applicationProperties.remove("VERSION");
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
+ applicationProperties.remove("BUILD_DATE");
+ applicationProperties.remove("INSTALLATION");
+ }
+
+ /**
+ * Gets Jalview application property of given key. Returns null if key not
+ * found
+ *
+ * @param key
+ * Name of property
+ *
+ * @return Property value
+ */
+ public static String getProperty(String key)
+ {
+ return applicationProperties.getProperty(key);
+ }
+
+ /**
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
+ */
+
+ public static boolean getDefault(String property, boolean def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ def = Boolean.valueOf(string).booleanValue();
+ }
+
+ return def;
+ }
+
+ /**
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
+ */
+ public static String getDefault(String property, String def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ return string;
+ }
+
+ return def;
+ }
+
+ /**
+ * Stores property in the file "HOME_DIR/.jalview_properties"
+ *
+ * @param key
+ * Name of object
+ * @param obj
+ * String value of property
+ *
+ * @return String value of property
+ */
+ public static String setProperty(String key, String obj)
+ {
+
+ try
+ {
+ applicationProperties.setProperty(key, obj);
+ if (!propsAreReadOnly)
+ {
+ FileOutputStream out = new FileOutputStream(propertiesFile);
+ applicationProperties.store(out, "---JalviewX Properties File---");
+ out.close();
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error setting property: " + key + " " + obj
+ + "\n" + ex);
+ }
+ return obj;
+ }
+
+ /**
+ * remove the specified property from the jalview properties file
+ *
+ * @param string
+ */
+ public static void removeProperty(String string)
+ {
+ applicationProperties.remove(string);
+ saveProperties();
+ }
+
+ /**
+ * save the properties to the jalview properties path
+ */
+ public static void saveProperties()
+ {
+ if (!propsAreReadOnly)
+ {
+ try
+ {
+ FileOutputStream out = new FileOutputStream(propertiesFile);
+ applicationProperties.store(out, "---JalviewX Properties File---");
+ out.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error saving properties: " + ex);
+ }
+ }
+ }
+
+ /**
+ * internal vamsas class discovery state
+ */
+ private static int vamsasJarsArePresent = -1;
+
+ /**
+ * Searches for vamsas client classes on class path.
+ *
+ * @return true if vamsas client is present on classpath
+ */
+ public static boolean vamsasJarsPresent()
+ {
+ if (vamsasJarsArePresent == -1)
+ {
+ try
+ {
+ if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
+ "uk.ac.vamsas.client.VorbaId") != null)
+ {
+ jalview.bin.Cache.log
+ .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ vamsasJarsArePresent = 1;
+ Logger lvclient = Logger.getLogger("uk.ac.vamsas");
+ lvclient.setLevel(Level.toLevel(Cache.getDefault(
+ "logs.Vamsas.Level", Level.INFO.toString())));
+
+ lvclient.addAppender(log.getAppender("JalviewLogger"));
+ // Tell the user that debug is enabled
+ lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
+ }
+ } catch (Exception e)
+ {
+ vamsasJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+ }
+ }
+ return (vamsasJarsArePresent > 0);
+ }
+
+ /**
+ * internal vamsas class discovery state
+ */
+ private static int groovyJarsArePresent = -1;
+
+ /**
+ * Searches for vamsas client classes on class path.
+ *
+ * @return true if vamsas client is present on classpath
+ */
+ public static boolean groovyJarsPresent()
+ {
+ if (groovyJarsArePresent == -1)
+ {
+ try
+ {
+ if (Cache.class.getClassLoader().loadClass(
+ "groovy.lang.GroovyObject") != null)
+ {
+ jalview.bin.Cache.log
+ .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ groovyJarsArePresent = 1;
+ Logger lgclient = Logger.getLogger("groovy");
+ lgclient.setLevel(Level.toLevel(Cache.getDefault(
+ "logs.Groovy.Level", Level.INFO.toString())));
+
+ lgclient.addAppender(log.getAppender("JalviewLogger"));
+ // Tell the user that debug is enabled
+ lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
+ }
+ } catch (Error e)
+ {
+ groovyJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+ } catch (Exception e)
+ {
+ groovyJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Groovy Classes are not present");
+ }
+ }
+ return (groovyJarsArePresent > 0);
+ }
+
+ /**
+ * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
+ * enabled.
+ */
+ protected static Object tracker = null;
+
+ protected static Class trackerfocus = null;
+
+ protected static Class jgoogleanalyticstracker = null;
+
+ /**
+ * Initialise the google tracker if it is not done already.
+ */
+ public static void initGoogleTracker()
+ {
+ if (tracker == null)
+ {
+ if (jgoogleanalyticstracker == null)
+ {
+ // try to get the tracker class
+ try
+ {
+ jgoogleanalyticstracker = Cache.class
+ .getClassLoader()
+ .loadClass(
+ "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+ trackerfocus = Cache.class.getClassLoader().loadClass(
+ "com.boxysystems.jgoogleanalytics.FocusPoint");
+ } catch (Exception e)
+ {
+ log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ tracker = null;
+ jgoogleanalyticstracker = null;
+ trackerfocus = null;
+ return;
+ }
+ }
+ // now initialise tracker
+ Exception re = null, ex = null;
+ Error err = null;
+ String vrs = "No Version Accessible";
+ try
+ {
+ // Google analytics tracking code for Library Finder
+ tracker = jgoogleanalyticstracker.getConstructor(
+ new Class[] { String.class, String.class, String.class })
+ .newInstance(
+ new Object[] {
+ "Jalview Desktop",
+ (vrs = jalview.bin.Cache.getProperty("VERSION")
+ + "_"
+ + jalview.bin.Cache.getDefault(
+ "BUILD_DATE", "unknown")),
+ "UA-9060947-1" });
+ jgoogleanalyticstracker.getMethod("trackAsynchronously",
+ new Class[] { trackerfocus }).invoke(
+ tracker,
+ new Object[] { trackerfocus.getConstructor(
+ new Class[] { String.class }).newInstance(
+ new Object[] { "Application Started." }) });
+ } catch (RuntimeException e)
+ {
+ re = e;
+ } catch (Exception e)
+ {
+ ex = e;
+ } catch (Error e)
+ {
+ err = e;
+ }
+ if (re != null || ex != null || err != null)
+ {
+ if (log != null)
+ {
+ if (re != null)
+ {
+ log.debug("Caught runtime exception in googletracker init:", re);
+ }
+ if (ex != null)
+ {
+ log.warn(
+ "Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs, ex);
+ }
+ if (err != null)
+ {
+ log.error(
+ "Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs, err);
+ }
+ }
+ else
+ {
+ if (re != null)
+ {
+ System.err
+ .println("Debug: Caught runtime exception in googletracker init:"
+ + vrs);
+ re.printStackTrace();
+ }
+ if (ex != null)
+ {
+ System.err
+ .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs);
+ ex.printStackTrace();
+ }
+
+ if (err != null)
+ {
+ System.err
+ .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs);
+ err.printStackTrace();
+ }
+ }
+ }
+ else
+ {
+ log.debug("Successfully initialised tracker.");
+ }
+ }
+ }
+
+ /**
+ * get the user's default colour if available
+ *
+ * @param property
+ * @param defcolour
+ * @return
+ */
+ public static Color getDefaultColour(String property, Color defcolour)
+ {
+ String colprop = getProperty(property);
+ if (colprop == null)
+ {
+ return defcolour;
+ }
+ Color col = jalview.schemes.ColourSchemeProperty
+ .getAWTColorFromName(colprop);
+ if (col == null)
+ {
+ try
+ {
+ col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+ } catch (Exception ex)
+ {
+ log.warn("Couldn't parse '" + colprop + "' as a colour for "
+ + property);
+ col = null;
+ }
+ }
+ return (col == null) ? defcolour : col;
+ }
+
+ /**
+ * store a colour as a Jalview user default property
+ *
+ * @param property
+ * @param colour
+ */
+ public static void setColourProperty(String property, Color colour)
+ {
+ setProperty(property, jalview.util.Format.getHexString(colour));
+ }
+
+ public static final DateFormat date_format = SimpleDateFormat
+ .getDateTimeInstance();
+
+ /**
+ * store a date in a jalview property
+ *
+ * @param string
+ * @param time
+ */
+ public static void setDateProperty(String property, Date time)
+ {
+ setProperty(property, date_format.format(time));
+ }
+
+ /**
+ * read a date stored in a jalview property
+ *
+ * @param property
+ * @return valid date as stored by setDateProperty, or null
+ *
+ */
+ public static Date getDateProperty(String property)
+ {
+ String val = getProperty(property);
+ if (val != null)
+ {
+ try
+ {
+ return date_format.parse(val);
+ } catch (Exception ex)
+ {
+ System.err.println("Invalid or corrupt date in property '"
+ + property + "' : value was '" + val + "'");
+ }
+ }
+ return null;
+ }
+
+ /**
+ * get and parse a property as an integer. send any parsing problems to
+ * System.err
+ *
+ * @param property
+ * @return null or Integer
+ */
+ public static Integer getIntegerProperty(String property)
+ {
+ String val = getProperty(property);
+ if (val != null && (val = val.trim()).length() > 0)
+ {
+ try
+ {
+ return Integer.valueOf(val);
+ } catch (NumberFormatException x)
+ {
+ System.err.println("Invalid integer in property '" + property
+ + "' (value was '" + val + "')");
+ }
+ }
+ return null;
+ }
+
+ private static DasSourceRegistryI sourceRegistry = null;
+
+ /**
+ * initialise and ..
+ *
+ * @return instance of the das source registry
+ */
+ public static DasSourceRegistryI getDasSourceRegistry()
+ {
+ if (sourceRegistry == null)
+ {
+ sourceRegistry = new DasSourceRegistry();
+ }
+ return sourceRegistry;
+ }
+
+ /**
+ * Set the specified value, or remove it if null or empty. Does not save the
+ * properties file.
+ *
+ * @param propName
+ * @param value
+ */
+ public static void setOrRemove(String propName, String value)
+ {
+ if (propName == null)
+ {
+ return;
+ }
+ if (value == null || value.trim().length() < 1)
+ {
+ Cache.applicationProperties.remove(propName);
+ }
+ else
+ {
+ Cache.applicationProperties.setProperty(propName, value);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff