-/*\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
-\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>jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.\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
- /** Jalview Properties */\r
- public static Properties applicationProperties;\r
-\r
- /** Default file is ~/.jalview_properties */\r
- static String propertiesFile;\r
-\r
- /** Called when Jalview is started */\r
- public static void loadProperties(String propsFile)\r
- {\r
- applicationProperties = new Properties();\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
- // 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
- // jnlpVersion will be null if we're using InstallAnywhere\r
- if(jnlpVersion==null)\r
- {\r
- try{\r
- java.net.URL url = new java.net.URL("http://www.jalview.org/webstart/jalview.jnlp");\r
- BufferedReader in = new BufferedReader(new InputStreamReader(url.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
- }catch(Exception ex)\r
- { jnlpVersion = codeVersion; }\r
- }\r
-\r
- System.out.println("Version: "+codeVersion);\r
- System.out.println("Latest : "+jnlpVersion);\r
-\r
- setProperty("LATEST_VERSION", jnlpVersion);\r
- setProperty("VERSION", codeVersion);\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
- * 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
-\r
- applicationProperties.setProperty(key, obj);\r
-\r
- applicationProperties.store(out, "---JalviewX Properties File---");\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- return obj;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 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.io.PrintWriter;
+import java.io.StringWriter;
+import java.net.Authenticator;
+import java.net.PasswordAuthentication;
+import java.net.URL;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.Locale;
+import java.util.Properties;
+import java.util.StringTokenizer;
+import java.util.TreeSet;
+import java.util.regex.Pattern;
+
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+
+import jalview.datamodel.PDBEntry;
+import jalview.gui.Preferences;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ChannelProperties;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
+
+/**
+ * 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>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>STORED_LINKS list of name|url pairs which user has entered but are not
+ * currently used
+ * <li>DEFAULT_LINK name of single url to be used when user double clicks a
+ * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
+ * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
+ * jalview.utils.GroupURLLink for more info</li>
+ * <li>DEFAULT_BROWSER for unix</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>
+ * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
+ * </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";
+
+ /**
+ * Sifts settings
+ */
+ public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
+ .getProperty("user.home") + File.separatorChar
+ + ".sifts_downloads" + File.separatorChar;
+
+ private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
+
+ private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
+
+ /**
+ * Identifiers.org download settings
+ */
+ private static final String ID_ORG_FILE = System.getProperty("user.home")
+ + File.separatorChar + ".identifiers.org.ids.json";
+
+ /**
+ * Allowed values are PDB or mmCIF
+ */
+ private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
+ .toString();
+
+ private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString();
+
+ /*
+ * a date formatter using a fixed (rather than the user's) locale;
+ * this ensures that date properties can be written and re-read successfully
+ * even if the user changes their locale setting
+ */
+ private static final DateFormat date_format = SimpleDateFormat
+ .getDateTimeInstance(SimpleDateFormat.MEDIUM,
+ SimpleDateFormat.MEDIUM, Locale.UK);
+
+ /**
+ * Initialises the Jalview Application Log
+ */
+ public static Logger log;
+
+ // save the proxy properties set at startup
+ public final static String[] startupProxyProperties = {
+ System.getProperty("http.proxyHost"),
+ System.getProperty("http.proxyPort"),
+ System.getProperty("https.proxyHost"),
+ System.getProperty("https.proxyPort"),
+ System.getProperty("http.proxyUser"),
+ System.getProperty("http.proxyPassword"),
+ System.getProperty("https.proxyUser"),
+ System.getProperty("https.proxyPassword"),
+ System.getProperty("http.nonProxyHosts") };
+
+ public final static String PROXYTYPE_NONE = "none";
+
+ // "false" and "true" for backward compatibility
+ public final static String PROXYTYPE_SYSTEM = "false";
+
+ public final static String PROXYTYPE_CUSTOM = "true";
+
+ // in-memory only storage of proxy password, safer to use char array
+ public static char[] proxyAuthPassword = null;
+
+ /** 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<>(super.keySet()));
+ }
+ };
+
+ /* build Properties (not all saved to .jalview_properties) */
+ public static Properties buildProperties = new Properties();
+
+ /** Default file is ~/.jalview_properties */
+ static String propertiesFile;
+
+ private static boolean propsAreReadOnly = Platform.isJS();
+
+ private final static String JS_PROPERTY_PREFIX = "jalview_";
+
+ 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())));
+ // we shouldn't need to do this
+ org.apache.log4j.Logger.getRootLogger()
+ .setLevel(org.apache.log4j.Level.INFO);
+
+ 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(ChannelProperties.getProperty("app_name")
+ + " Debugging Output Follows.");
+ } catch (Exception ex)
+ {
+ System.err.println("Problems initializing the log4j system\n");
+ ex.printStackTrace(System.err);
+ }
+ }
+
+ /**
+ * Loads properties from the given properties file. Any existing properties
+ * are first cleared.
+ */
+ public static void loadProperties(String propsFile)
+ {
+ propertiesFile = propsFile;
+ if (propsFile == null && !propsAreReadOnly)
+ {
+ propertiesFile = System.getProperty("user.home") + File.separatorChar
+ + ".jalview_properties";
+ }
+ else
+ {
+ // don't corrupt the file we've been given.
+ propsAreReadOnly = true;
+ }
+
+ if (propertiesFile == null)
+ { // BH 2019
+ Platform.readInfoProperties(JS_PROPERTY_PREFIX,
+ applicationProperties);
+ }
+ else
+ {
+ try
+ {
+ InputStream fis;
+ try
+ {
+ fis = new 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.clear();
+ applicationProperties.load(fis);
+
+ // remove any old build properties
+
+ deleteBuildProperties();
+ fis.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading properties file: " + ex);
+ }
+ }
+
+ /* TO BE REPLACED WITH PROXY_TYPE SETTINGS
+ if (getDefault("USE_PROXY", false))
+ {
+ String proxyServer = getDefault("PROXY_SERVER", ""),
+ proxyPort = getDefault("PROXY_PORT", "8080");
+ }
+ */
+
+ // PROXY TYPE settings (now three options "none", "false", "true", but using
+ // backward compatible strings)
+ String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM);
+ // default to upgrading old settings
+ switch (proxyType)
+ {
+ case PROXYTYPE_NONE:
+ clearProxyProperties();
+ break;
+ case PROXYTYPE_SYSTEM: // use system settings
+ resetProxyProperties();
+ break;
+ case PROXYTYPE_CUSTOM: // use specified proxy settings
+ String httpHost = getDefault("PROXY_SERVER", "");
+ String httpPort = getDefault("PROXY_PORT", "8080");
+ String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
+ String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
+ String httpUser = getDefault("PROXY_AUTH_USER", null);
+ // https.proxyUser and https.proxyPassword are not able to be
+ // independently set in Preferences yet (or http.nonProxyHosts)
+ String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
+ setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
+ proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
+ break;
+ default:
+ String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ + proxyType;
+ Cache.warn(message);
+ }
+
+ // LOAD THE AUTHORS FROM THE authors.props file
+ String authorDetails = resolveResourceURLFor("/authors.props");
+
+ try
+ {
+ if (authorDetails != null)
+ {
+ URL localJarFileURL = new URL(authorDetails);
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading author details: " + ex);
+ authorDetails = null;
+ }
+ if (authorDetails == null)
+ {
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
+ }
+
+ loadBuildProperties(false);
+
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
+ SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+
+ SiftsSettings.setFailSafePIDThreshold(
+ jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+ DEFAULT_FAIL_SAFE_PID_THRESHOLD));
+
+ SiftsSettings.setCacheThresholdInDays(
+ jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+ DEFAULT_CACHE_THRESHOLD_IN_DAYS));
+
+ IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
+ "http://www.jalview.org/services/identifiers"));
+ IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
+
+ StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
+ .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+ StructureImportSettings
+ .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+ // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
+
+ String jnlpVersion = System.getProperty("jalview.version");
+
+ // jnlpVersion will be null if a latest version check for the channel needs
+ // to be done
+ // 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
+ {
+
+ @Override
+ public void run()
+ {
+ String remoteBuildPropertiesUrl = Cache
+ .getAppbaseBuildProperties();
+
+ 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 remoteVersion = null;
+ try
+ {
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ "5000");
+ java.net.URL url = new java.net.URL(remoteBuildPropertiesUrl);
+
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(url.openStream()));
+
+ Properties remoteBuildProperties = new Properties();
+ remoteBuildProperties.load(in);
+ remoteVersion = remoteBuildProperties.getProperty("VERSION");
+ } catch (Exception ex)
+ {
+ System.out
+ .println("Non-fatal exception when checking version at "
+ + remoteBuildPropertiesUrl + ":");
+ System.out.println(ex);
+ remoteVersion = getProperty("VERSION");
+ }
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ orgtimeout);
+
+ setProperty("LATEST_VERSION", remoteVersion);
+ }
+ }
+
+ VersionChecker vc = new VersionChecker();
+ vc.start();
+ }
+ else
+ {
+ if (jnlpVersion != null)
+ {
+ setProperty("LATEST_VERSION", jnlpVersion);
+ }
+ else
+ {
+ applicationProperties.remove("LATEST_VERSION");
+ }
+ }
+
+ // LOAD USERDEFINED COLOURS
+ Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+ jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+ false);
+ }
+
+ /**
+ * construct a resource URL for the given absolute resource pathname
+ *
+ * @param resourcePath
+ * @return
+ */
+ private static String resolveResourceURLFor(String resourcePath)
+ {
+ String url = null;
+ if (Platform.isJS() || !Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString().endsWith(".jar"))
+ {
+ try
+ {
+ url = Cache.class.getResource(resourcePath).toString();
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to resolve resource " + resourcePath
+ + ": " + ex.getMessage());
+ }
+ }
+ else
+ {
+ url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
+ .getLocation().toString().concat("!" + resourcePath));
+ }
+ return url;
+ }
+
+ public static void loadBuildProperties(boolean reportVersion)
+ {
+ String codeInstallation = getProperty("INSTALLATION");
+ boolean printVersion = codeInstallation == null;
+
+ /*
+ * read build properties - from the Jalview jar for a Java distribution,
+ * or from codebase file in test or JalviewJS context
+ */
+ try
+ {
+ String buildDetails = resolveResourceURLFor("/.build_properties");
+ URL localJarFileURL = new URL(buildDetails);
+ InputStream in = localJarFileURL.openStream();
+ buildProperties.load(in);
+ in.close();
+ if (buildProperties.getProperty("BUILD_DATE", null) != null)
+ {
+ applicationProperties.put("BUILD_DATE",
+ buildProperties.getProperty("BUILD_DATE"));
+ }
+ if (buildProperties.getProperty("INSTALLATION", null) != null)
+ {
+ applicationProperties.put("INSTALLATION",
+ buildProperties.getProperty("INSTALLATION"));
+ }
+ if (buildProperties.getProperty("VERSION", null) != null)
+ {
+ applicationProperties.put("VERSION",
+ buildProperties.getProperty("VERSION"));
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading build details: " + ex);
+ applicationProperties.remove("VERSION");
+ }
+ String codeVersion = getProperty("VERSION");
+ codeInstallation = getProperty("INSTALLATION");
+
+ if (codeVersion == null)
+ {
+ // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+ codeVersion = "Test";
+ codeInstallation = "";
+ }
+ else
+ {
+ codeInstallation = " (" + codeInstallation + ")";
+ }
+ setProperty("VERSION", codeVersion);
+ new BuildDetails(codeVersion, null, codeInstallation);
+ if (printVersion && reportVersion)
+ {
+ System.out.println(ChannelProperties.getProperty("app_name")
+ + " Version: " + codeVersion + codeInstallation);
+ }
+ }
+
+ 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)
+ {
+ String prop = applicationProperties.getProperty(key);
+ if (prop == null && Platform.isJS())
+ {
+ prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+ + "_" + JS_PROPERTY_PREFIX + key);
+ }
+ return prop;
+ }
+
+ /**
+ * 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;
+ }
+
+ public static int getDefault(String property, int def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ try
+ {
+ def = Integer.parseInt(string);
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Error parsing int property '" + property
+ + "' with value '" + string + "'");
+ }
+ }
+
+ return def;
+ }
+
+ /**
+ * Answers the value of the given property, or the supplied default value if
+ * the property is not set
+ */
+ public static String getDefault(String property, String def)
+ {
+ String value = getProperty(property);
+ return value == null ? def : value;
+ }
+
+ /**
+ * Stores property in the file "HOME_DIR/.jalview_properties"
+ *
+ * @param key
+ * Name of object
+ * @param obj
+ * String value of property
+ *
+ * @return previous value of property (or null)
+ */
+ public static Object setProperty(String key, String obj)
+ {
+ Object oldValue = null;
+ try
+ {
+ oldValue = applicationProperties.setProperty(key, obj);
+ if (propertiesFile != null && !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 oldValue;
+ }
+
+ /**
+ * 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(ChannelProperties.getProperty("app_name")
+ + " 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(ChannelProperties.getProperty("app_name")
+ + " 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[]
+ { ChannelProperties.getProperty("app_name") + " 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 = ColorUtils.parseColourString(colprop);
+ if (col == null)
+ {
+ log.warn("Couldn't parse '" + colprop + "' as a colour for "
+ + property);
+ }
+ 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));
+ }
+
+ /**
+ * Stores a formatted date in a jalview property, using a fixed locale.
+ *
+ * @param propertyName
+ * @param date
+ * @return the formatted date string
+ */
+ public static String setDateProperty(String propertyName, Date date)
+ {
+ String formatted = date_format.format(date);
+ setProperty(propertyName, formatted);
+ return formatted;
+ }
+
+ /**
+ * Reads a date stored in a Jalview property, parses it (using a fixed locale
+ * format) and returns as a Date, or null if parsing fails
+ *
+ * @param propertyName
+ * @return
+ *
+ */
+ public static Date getDateProperty(String propertyName)
+ {
+ String val = getProperty(propertyName);
+ if (val != null)
+ {
+ try
+ {
+ return date_format.parse(val);
+ } catch (Exception ex)
+ {
+ System.err.println("Invalid or corrupt date in property '"
+ + propertyName + "' : 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;
+ }
+
+ /**
+ * 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);
+ }
+ }
+
+ /**
+ * Loads in user colour schemes from files.
+ *
+ * @param files
+ * a '|'-delimited list of file paths
+ */
+ public static void initUserColourSchemes(String files)
+ {
+ if (files == null || files.length() == 0)
+ {
+ return;
+ }
+
+ // In case colours can't be loaded, we'll remove them
+ // from the default list here.
+ StringBuffer coloursFound = new StringBuffer();
+ StringTokenizer st = new StringTokenizer(files, "|");
+ while (st.hasMoreElements())
+ {
+ String file = st.nextToken();
+ try
+ {
+ UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
+ if (ucs != null)
+ {
+ if (coloursFound.length() > 0)
+ {
+ coloursFound.append("|");
+ }
+ coloursFound.append(file);
+ ColourSchemes.getInstance().registerColourScheme(ucs);
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error loading User ColourFile\n" + ex);
+ }
+ }
+ if (!files.equals(coloursFound.toString()))
+ {
+ if (coloursFound.toString().length() > 1)
+ {
+ setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
+ coloursFound.toString());
+ }
+ else
+ {
+ applicationProperties
+ .remove(UserDefinedColours.USER_DEFINED_COLOURS);
+ }
+ }
+ }
+
+ /**
+ * Initial logging information helper for various versions output
+ *
+ * @param prefix
+ * @param value
+ * @param defaultValue
+ */
+ private static void appendIfNotNull(StringBuilder sb, String prefix,
+ String value, String suffix, String defaultValue)
+ {
+ if (value == null && defaultValue == null)
+ {
+ return;
+ }
+ String line = prefix + (value != null ? value : defaultValue) + suffix;
+ sb.append(line);
+ }
+
+ /**
+ *
+ * @return Jalview version, build details and JVM platform version for console
+ */
+ public static String getVersionDetailsForConsole()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append(ChannelProperties.getProperty("app_name"))
+ .append(" Version: ");
+ sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append("\n");
+ sb.append(ChannelProperties.getProperty("app_name"))
+ .append(" Installation: ");
+ sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append("\n");
+ sb.append("Build Date: ");
+ sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append("\n");
+ sb.append("Java version: ");
+ sb.append(System.getProperty("java.version"));
+ sb.append("\n");
+ sb.append(System.getProperty("os.arch"));
+ sb.append(" ");
+ sb.append(System.getProperty("os.name"));
+ sb.append(" ");
+ sb.append(System.getProperty("os.version"));
+ sb.append("\n");
+ appendIfNotNull(sb, "Install4j version: ",
+ System.getProperty("sys.install4jVersion"), "\n", null);
+ appendIfNotNull(sb, "Install4j template version: ",
+ System.getProperty("installer_template_version"), "\n", null);
+ appendIfNotNull(sb, "Launcher version: ",
+ System.getProperty("launcher_version"), "\n", null);
+ LookAndFeel laf = UIManager.getLookAndFeel();
+ String lafName = laf == null ? "Not obtained" : laf.getName();
+ String lafClass = laf == null ? "unknown" : laf.getClass().getName();
+ sb.append("LookAndFeel: ");
+ sb.append(lafName);
+ sb.append(" (");
+ sb.append(lafClass);
+ sb.append(")\n");
+ // Not displayed in release version ( determined by possible version number
+ // regex 9[9.]*9[.-_a9]* )
+ if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
+ jalview.bin.Cache.getDefault("VERSION", "TEST")))
+ {
+ appendIfNotNull(sb, "Getdown appdir: ",
+ System.getProperty("getdownappdir"), "\n", null);
+ appendIfNotNull(sb, "Getdown appbase: ",
+ System.getProperty("getdownappbase"), "\n", null);
+ appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
+ "\n", "unknown");
+ }
+ return sb.toString();
+ }
+
+ /**
+ *
+ * @return build details as reported in splashscreen
+ */
+ public static String getBuildDetailsForSplash()
+ {
+ // consider returning more human friendly info
+ // eg 'built from Source' or update channel
+ return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ }
+
+ public static String getStackTraceString(Throwable t)
+ {
+ StringWriter sw = new StringWriter();
+ PrintWriter pw = new PrintWriter(sw);
+ t.printStackTrace(pw);
+ return sw.toString();
+ }
+
+ // proxy properties methods
+ public static void clearProxyProperties()
+ {
+ setProxyProperties(null, null, null, null, null, null, null, null,
+ null);
+ }
+
+ public static void resetProxyProperties()
+ {
+ setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
+ startupProxyProperties[2], startupProxyProperties[3],
+ startupProxyProperties[4],
+ startupProxyProperties[5] == null ? null
+ : startupProxyProperties[5].toCharArray(),
+ startupProxyProperties[6],
+ startupProxyProperties[7] == null ? null
+ : startupProxyProperties[7].toCharArray(),
+ startupProxyProperties[8]);
+ StringBuilder sb = new StringBuilder();
+ sb.append("Setting proxy properties to: http.proxyHost=")
+ .append(startupProxyProperties[0]).append(", http.proxyPort=")
+ .append(startupProxyProperties[1])
+ .append(startupProxyProperties[4] != null
+ && !startupProxyProperties[4].isEmpty()
+ ? " [" + startupProxyProperties[4] + "]"
+ : "")
+ .append(", https.proxyHost=").append(startupProxyProperties[2])
+ .append(", https.proxyPort=").append(startupProxyProperties[3])
+ .append(startupProxyProperties[6] != null
+ && !startupProxyProperties[6].isEmpty()
+ ? " [" + startupProxyProperties[6] + "]"
+ : "");
+
+ Cache.debug(sb.toString());
+ }
+
+ public static void setProxyPropertiesFromPreferences()
+ {
+ setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
+ }
+
+ public static void setProxyPropertiesFromPreferences(
+ String previousProxyType)
+ {
+ String proxyType = Cache.getDefault("USE_PROXY",
+ Cache.PROXYTYPE_SYSTEM);
+ if (previousProxyType != null
+ && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
+ // customProxy
+ && proxyType.equals(previousProxyType))
+ {
+ // no change
+ return;
+ }
+ switch (proxyType)
+ {
+ case Cache.PROXYTYPE_NONE:
+ if (!previousProxyType.equals(proxyType))
+ {
+ Cache.log.info("Setting no proxy settings");
+ Cache.setProxyProperties(null, null, null, null, null, null, null,
+ null, null);
+ }
+ break;
+ case Cache.PROXYTYPE_CUSTOM:
+ // always re-set a custom proxy -- it might have changed, particularly
+ // password
+ Cache.log.info("Setting custom proxy settings");
+ boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
+ Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
+ Cache.getDefault("PROXY_PORT", null),
+ Cache.getDefault("PROXY_SERVER_HTTPS", null),
+ Cache.getDefault("PROXY_PORT_HTTPS", null),
+ proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+ : null,
+ proxyAuthSet ? Cache.proxyAuthPassword : null,
+ proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+ : null,
+ proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
+ break;
+ default: // system proxy settings by default
+ Cache.log.info("Setting system proxy settings");
+ Cache.resetProxyProperties();
+ }
+ }
+
+ public static void setProxyProperties(String httpHost, String httpPort,
+ String httpsHost, String httpsPort, String httpUser,
+ char[] httpPassword, String httpsUser, char[] httpsPassword,
+ String nonProxyHosts)
+ {
+ setOrClearSystemProperty("http.proxyHost", httpHost);
+ setOrClearSystemProperty("http.proxyPort", httpPort);
+ setOrClearSystemProperty("https.proxyHost", httpsHost);
+ setOrClearSystemProperty("https.proxyPort", httpsPort);
+ setOrClearSystemProperty("http.proxyUser", httpUser);
+ setOrClearSystemProperty("https.proxyUser", httpsUser);
+ // note: passwords for http.proxyPassword and https.proxyPassword are sent
+ // via the Authenticator, properties do not need to be set
+
+ // are we using a custom proxy (password prompt might be required)?
+ boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
+ .equals(PROXYTYPE_CUSTOM);
+
+ /*
+ * A bug in Java means the AuthCache does not get reset, so once it has working credentials,
+ * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
+ * is not re-called).
+ * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
+ * the AuthCache.
+ * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
+ * ...
+ * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
+ */
+ /*
+ try
+ {
+ sun.net.www.protocol.http.AuthCacheValue
+ .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
+ } catch (Throwable t)
+ {
+ Cache.error(t.getMessage());
+ Cache.debug(getStackTraceString(t));
+ }
+ */
+
+ if (httpUser != null || httpsUser != null)
+ {
+ try
+ {
+ char[] displayHttpPw = new char[httpPassword == null ? 0
+ : httpPassword.length];
+ Arrays.fill(displayHttpPw, '*');
+ Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='"
+ + httpUser + "' httpPassword='" + displayHttpPw + "'");
+ if (!Platform.isJS())
+ /* *
+ * java.net.Authenticator not implemented in SwingJS yet
+ *
+ * @j2sIgnore
+ *
+ */
+ {
+ Authenticator.setDefault(new Authenticator()
+ {
+ @Override
+ protected PasswordAuthentication getPasswordAuthentication()
+ {
+ if (getRequestorType() == RequestorType.PROXY)
+ {
+ String protocol = getRequestingProtocol();
+ boolean needProxyPasswordSet = false;
+ if (customProxySet &&
+ // we have a username but no password for the scheme being
+ // requested
+ (protocol.equalsIgnoreCase("http")
+ && (httpUser != null && httpUser.length() > 0
+ && (httpPassword == null
+ || httpPassword.length == 0)))
+ || (protocol.equalsIgnoreCase("https")
+ && (httpsUser != null
+ && httpsUser.length() > 0
+ && (httpsPassword == null
+ || httpsPassword.length == 0))))
+ {
+ // open Preferences -> Connections
+ String message = MessageManager
+ .getString("label.proxy_password_required");
+ Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
+ message);
+ Preferences.getInstance()
+ .proxyAuthPasswordCheckHighlight(true, true);
+ }
+ else
+ {
+ try
+ {
+ if (protocol.equalsIgnoreCase("http")
+ && getRequestingHost()
+ .equalsIgnoreCase(httpHost)
+ && getRequestingPort() == Integer
+ .valueOf(httpPort))
+ {
+ Cache.debug(
+ "AUTHENTICATOR returning PasswordAuthentication(\""
+ + httpUser + "\", '"
+ + new String(displayHttpPw) + "')");
+ return new PasswordAuthentication(httpUser,
+ httpPassword);
+ }
+ if (protocol.equalsIgnoreCase("https")
+ && getRequestingHost()
+ .equalsIgnoreCase(httpsHost)
+ && getRequestingPort() == Integer
+ .valueOf(httpsPort))
+ {
+ char[] displayHttpsPw = new char[httpPassword.length];
+ Arrays.fill(displayHttpsPw, '*');
+ Cache.debug(
+ "AUTHENTICATOR returning PasswordAuthentication(\""
+ + httpsUser + "\", '" + displayHttpsPw
+ + "'");
+ return new PasswordAuthentication(httpsUser,
+ httpsPassword);
+ }
+ } catch (NumberFormatException e)
+ {
+ Cache.error("Problem with proxy port values [http:"
+ + httpPort + ", https:" + httpsPort + "]");
+ }
+ Cache.debug(
+ "AUTHENTICATOR after trying to get PasswordAuthentication");
+ }
+ }
+ // non proxy request
+ Cache.debug("AUTHENTICATOR returning null");
+ return null;
+ }
+ });
+ } // end of j2sIgnore for java.net.Authenticator
+
+ // required to re-enable basic authentication (should be okay for a
+ // local proxy)
+ Cache.debug(
+ "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
+ System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
+ } catch (SecurityException e)
+ {
+ Cache.error("Could not set default Authenticator");
+ Cache.debug(getStackTraceString(e));
+ }
+ }
+ else
+ {
+ // reset the Authenticator to protect http.proxyUser and
+ // http.proxyPassword Just In Case
+ /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
+ * has working credentials. No workaround for Java 11.
+ */
+ if (!Platform.isJS())
+ /* *
+ * java.net.Authenticator not implemented in SwingJS yet
+ *
+ * @j2sIgnore
+ *
+ */
+ {
+ Cache.debug("AUTHENTICATOR setting default Authenticator to null");
+ Authenticator.setDefault(null);
+ }
+ }
+
+ // nonProxyHosts not currently configurable in Preferences
+ Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ + nonProxyHosts + "\"");
+ setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
+ }
+
+ public static void setOrClearSystemProperty(String key, char[] value)
+ {
+ setOrClearSystemProperty(key,
+ (value == null) ? null : new String(value));
+ }
+
+ public static void setOrClearSystemProperty(String key, String value)
+ {
+ if (key == null)
+ {
+ return;
+ }
+ if (value == null)
+ {
+ System.clearProperty(key);
+ }
+ else
+ {
+ System.setProperty(key, value);
+ }
+ }
+
+ public final static int TRACE = 10;
+
+ public final static int DEBUG = 20;
+
+ public final static int INFO = 30;
+
+ public final static int WARN = 40;
+
+ public final static int ERROR = 50;
+
+ public static boolean println(int level, String message)
+ {
+ if (Cache.log == null)
+ {
+ if (level >= WARN)
+ System.err.println(message);
+ else if (level >= INFO)
+ System.out.println(message);
+ // not printing debug or trace messages
+ return false;
+ }
+ if (level >= ERROR)
+ {
+ Cache.log.error(message);
+ }
+ else if (level >= WARN)
+ {
+ Cache.log.warn(message);
+ }
+ else if (level >= INFO)
+ {
+ Cache.log.info(message);
+ }
+ else if (level >= DEBUG)
+ {
+ Cache.log.debug(message);
+ }
+ else
+ {
+ Cache.log.trace(message);
+ }
+ return true;
+ }
+
+ public static void trace(String message)
+ {
+ println(TRACE, message);
+ }
+
+ public static void debug(String message)
+ {
+ println(DEBUG, message);
+ }
+
+ public static void info(String message)
+ {
+ println(INFO, message);
+ }
+
+ public static void warn(String message)
+ {
+ println(WARN, message);
+ }
+
+ public static void error(String message)
+ {
+ println(ERROR, message);
+ }
+
+ /**
+ * Getdown appbase methods
+ */
+
+ private static final String releaseAppbase;
+
+ private static String getdownAppbase;
+
+ private static String getdownDistDir;
+
+ static
+ {
+ if (!Platform.isJS())
+ {
+ Float specversion = Float
+ .parseFloat(System.getProperty("java.specification.version"));
+ releaseAppbase = (specversion < 9)
+ ? "https://www.jalview.org/getdown/release/1.8"
+ : "https://www.jalview.org/getdown/release/11";
+ }
+ else
+ {
+ // this value currenly made up, can be changed to URL that will be
+ // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
+ releaseAppbase = "https://www.jalview.org/jalview-js";
+ getdownAppbase = releaseAppbase;
+ getdownDistDir = "/swingjs/j2s";
+ }
+ }
+
+ // look for properties (passed in by getdown) otherwise default to release
+ private static void setGetdownAppbase()
+ {
+ if (getdownAppbase != null)
+ {
+ return;
+ }
+ String appbase = System.getProperty("getdownappbase");
+ String distDir = System.getProperty("getdowndistdir");
+ if (appbase == null)
+ {
+ appbase = buildProperties.getProperty("GETDOWNAPPBASE");
+ distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
+ }
+ if (appbase == null)
+ {
+ appbase = releaseAppbase;
+ distDir = "release";
+ }
+ if (appbase.endsWith("/"))
+ {
+ appbase = appbase.substring(0, appbase.length() - 1);
+ }
+ if (distDir == null)
+ {
+ distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
+ }
+ getdownAppbase = appbase;
+ getdownDistDir = distDir;
+ }
+
+ public static String getGetdownAppbase()
+ {
+ setGetdownAppbase();
+ return getdownAppbase;
+ }
+
+ public static String getAppbaseBuildProperties()
+ {
+ String appbase = getGetdownAppbase();
+ return appbase + "/" + getdownDistDir + "/build_properties";
+ }
+}
git://source.jalview.org / jalview.git / blobdiff