/*
 * 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 jalview.datamodel.PDBEntry;
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.ColorUtils;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;

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.Locale;
import java.util.Properties;
import java.util.StringTokenizer;
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>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[|&lt;separator&gt;] 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>
 * <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";

  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";

  /**
   * 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;

  /** 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()));
    }
  };

  /** Default file is ~/.jalview_properties */
  static String propertiesFile;

  private static boolean propsAreReadOnly = Platform.isJS();

  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);
    }
  }

  /**
   * 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) {
	    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.clear();
	      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
    String authorDetails = (Platform.isJS() ? null :
            "jar:"
            .concat(Cache.class.getProtectionDomain().getCodeSource()
                    .getLocation().toString().concat("!/authors.props")));

    try
    {
      if (authorDetails != null) {
    	  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);
    	authorDetails = null;
    }
    if (authorDetails == null) 
    {
        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
    String buildDetails = (Platform.isJS() ? null :
            "jar:".concat(Cache.class.getProtectionDomain()
            .getCodeSource().getLocation().toString()
            .concat("!/.build_properties")));
    if (buildDetails != null) 
    {
	    try
	    {
	      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);
	      buildDetails = null;
	    }
    }
    if (buildDetails == null) 
    {
	      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);

    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);

    System.out
            .println("Jalview Version: " + codeVersion + codeInstallation);

    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));
    // 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
      {
        @Override
        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 remoteVersion = 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("\""));
              remoteVersion = line;
              break;
            }
          } catch (Exception ex)
          {
            System.out.println(
                    "Non-fatal exception when checking version at www.jalview.org :");
            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");
      }
    }

    setProperty("VERSION", codeVersion);

    // LOAD USERDEFINED COLOURS
    jalview.bin.Cache
            .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;
  }

  /**
   * 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 (!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("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 = 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);
      }
    }
  }

	/**
	 * Add a known domain that implements access-control-allow-origin:* bh 2018
	 * 
	 * @param defaultUniprotDomain
	 */
	public static void addJ2SDirectDatabaseCall(String domain) 
	{

		/**
		 * @j2sNative
		 * 
		 * 			J2S.addDirectDatabaseCall(domain);
		 */
	}
}