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Sourcecode: jalview version File versions

Jalview.java

/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
 * 
 * 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/>.
 */
package jalview.bin;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.lang.reflect.Constructor;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
import java.net.URLDecoder;
import java.security.AllPermission;
import java.security.CodeSource;
import java.security.PermissionCollection;
import java.security.Permissions;
import java.security.Policy;
import java.util.*;

import javax.swing.*;

import jalview.gui.*;
import jalview.util.Platform;

/**
 * Main class for Jalview Application <br>
 * <br>
 * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
 * 
 * @author $author$
 * @version $Revision$
 */
00051 public class Jalview
{
  static
  {
    // grab all the rights we can the JVM
    Policy.setPolicy(new Policy()
    {
      public PermissionCollection getPermissions(CodeSource codesource)
      {
        Permissions perms = new Permissions();
        perms.add(new AllPermission());
        return (perms);
      }

      public void refresh()
      {
      }
    });
  }

  /**
   * main class for Jalview application
   * 
   * @param args
   *          open <em>filename</em>
   */
00077   public static void main(String[] args)
  {
    System.out.println("Java version: "
            + System.getProperty("java.version"));
    System.out.println(System.getProperty("os.arch") + " "
            + System.getProperty("os.name") + " "
            + System.getProperty("os.version"));
    if (new Platform().isAMac())
    {
      System.setProperty("com.apple.mrj.application.apple.menu.about.name",
              "Jalview");
      System.setProperty("apple.laf.useScreenMenuBar", "true");
    }

    ArgsParser aparser = new ArgsParser(args);
    boolean headless = false;

    if (aparser.contains("help") || aparser.contains("h"))
    {
      System.out
              .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
                      + "-nodisplay\tRun Jalview without User Interface.\n"
                      + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
                      + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
                      + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
                      + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
                      + "-features FILE\tUse the given file to mark features on the alignment.\n"
                      + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
                      + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
                      + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
                      + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
                      + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
                      + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
                      + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
                      + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
                      + "-png FILE\tCreate PNG image FILE from alignment.\n"
                      + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
                      + "-eps FILE\tCreate EPS file FILE from alignment.\n"
                      + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
                      + "-noquestionnaire\tTurn off questionnaire check.\n"
                      + "-nousagestats\tTurn off google analytics tracking for this session.\n"
                      + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
                      // +
                      // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
                      + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
                      + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
                      + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
                      + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                      // +
                      // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
                      // + "-vses vamsas-session\tJoin session with given URN\n"
                      + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
                      + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
      System.exit(0);
    }
    Cache.loadProperties(aparser.getValue("props")); // must do this before
    // anything else!
    String defs = aparser.getValue("setprop");
    while (defs != null)
    {
      int p = defs.indexOf('=');
      if (p == -1)
      {
        System.err.println("Ignoring invalid setprop argument : " + defs);
      }
      else
      {
        System.out.println("Executing setprop argument: " + defs);
        // DISABLED FOR SECURITY REASONS
        // TODO: add a property to allow properties to be overriden by cli args
        // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
      }
      defs = aparser.getValue("setprop");
    }
    if (aparser.contains("nodisplay"))
    {
      System.setProperty("java.awt.headless", "true");
    }
    if (System.getProperty("java.awt.headless") != null
            && System.getProperty("java.awt.headless").equals("true"))
    {
      headless = true;
    }

    try
    {
      Cache.initLogger();
    } catch (java.lang.NoClassDefFoundError error)
    {
      error.printStackTrace();
      System.out
              .println("\nEssential logging libraries not found."
                      + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
      System.exit(0);
    }

    Desktop desktop = null;

    try
    {
      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
    } catch (Exception ex)
    {
    }

    if (!headless)
    {
      desktop = new Desktop();
      desktop.setInBatchMode(true); // indicate we are starting up
      desktop.setVisible(true);
      desktop.startServiceDiscovery();
      if (!aparser.contains("nousagestats"))
      {
        startUsageStats(desktop);
      }
      if (!aparser.contains("noquestionnaire"))
      {
        String url = aparser.getValue("questionnaire");
        if (url != null)
        {
          // Start the desktop questionnaire prompter with the specified
          // questionnaire
          Cache.log.debug("Starting questionnaire url at " + url);
          desktop.checkForQuestionnaire(url);
        }
        else
        {
          if (Cache.getProperty("NOQUESTIONNAIRES") == null)
          {
            // Start the desktop questionnaire prompter with the specified
            // questionnaire
            // String defurl =
            // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
            // //
            String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
            Cache.log.debug("Starting questionnaire with default url: "
                    + defurl);
            desktop.checkForQuestionnaire(defurl);

          }
        }
      }
    }

    String file = null, protocol = null, format = null, data = null;
    jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
    Vector getFeatures = null; // vector of das source nicknames to fetch
    // features from
    // loading is done.
    String groovyscript = null; // script to execute after all loading is
    // completed one way or another
    // extract groovy argument and execute if necessary
    groovyscript = aparser.getValue("groovy", true);
    file = aparser.getValue("open", true);

    if (file == null && desktop == null)
    {
      System.out.println("No files to open!");
      System.exit(1);
    }
    String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser
            .getValue("vsess");
    if (vamsasImport != null || vamsasSession != null)
    {
      if (desktop == null || headless)
      {
        System.out
                .println("Headless vamsas sessions not yet supported. Sorry.");
        System.exit(1);
      }
      // if we have a file, start a new session and import it.
      boolean inSession = false;
      if (vamsasImport != null)
      {
        try
        {
          String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport);
          if (viprotocol == jalview.io.FormatAdapter.FILE)
          {
            inSession = desktop.vamsasImport(new File(vamsasImport));
          }
          else if (viprotocol == jalview.io.FormatAdapter.URL)
          {
            inSession = desktop.vamsasImport(new URL(vamsasImport));
          }

        } catch (Exception e)
        {
          System.err.println("Exeption when importing " + vamsasImport
                  + " as a vamsas document.");
          e.printStackTrace();
        }
        if (!inSession)
        {
          System.err.println("Failed to import " + vamsasImport
                  + " as a vamsas document.");
        }
        else
        {
          System.out.println("Imported Successfully into new session "
                  + desktop.getVamsasApplication().getCurrentSession());
        }
      }
      if (vamsasSession != null)
      {
        if (vamsasImport != null)
        {
          // close the newly imported session and import the Jalview specific
          // remnants into the new session later on.
          desktop.vamsasStop_actionPerformed(null);
        }
        // now join the new session
        try
        {
          if (desktop.joinVamsasSession(vamsasSession))
          {
            System.out.println("Successfully joined vamsas session "
                    + vamsasSession);
          }
          else
          {
            System.err.println("WARNING: Failed to join vamsas session "
                    + vamsasSession);
          }
        } catch (Exception e)
        {
          System.err.println("ERROR: Failed to join vamsas session "
                  + vamsasSession);
          e.printStackTrace();
        }
        if (vamsasImport != null)
        {
          // the Jalview specific remnants can now be imported into the new
          // session at the user's leisure.
          Cache.log
                  .info("Skipping Push for import of data into existing vamsas session."); // TODO:
          // enable
          // this
          // when
          // debugged
          // desktop.getVamsasApplication().push_update();
        }
      }
    }
    long progress=-1;
    // Finally, deal with the remaining input data.
    if (file != null)
    {
      if (!headless)
      {
        desktop.setProgressBar("Processing commandline arguments...", progress=System.currentTimeMillis());
      }
      System.out.println("Opening file: " + file);

      if (!file.startsWith("http://"))
      {
        if (!(new java.io.File(file)).exists())
        {
          System.out.println("Can't find " + file);
          if (headless)
          {
            System.exit(1);
          }
        }
      }

      protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);

      format = new jalview.io.IdentifyFile().Identify(file, protocol);

      AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
              format);
      if (af == null)
      {
        System.out.println("error");
        return;
      }

      data = aparser.getValue("colour", true);
      if (data != null)
      {
        data.replaceAll("%20", " ");

        jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
                .getColour(af.getViewport().getAlignment(), data);

        if (cs == null)
        {
          jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
                  "white");
          ucs.parseAppletParameter(data);
          cs = ucs;
        }

        System.out.println("colour is " + data);
        af.changeColour(cs);
      }

      // Must maintain ability to use the groups flag
      data = aparser.getValue("groups", true);
      if (data != null)
      {
        af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
        System.out.println("Added " + data);
      }
      data = aparser.getValue("features", true);
      if (data != null)
      {
        af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
        System.out.println("Added " + data);
      }

      data = aparser.getValue("annotations", true);
      if (data != null)
      {
        af.loadJalviewDataFile(data, null, null, null);
        System.out.println("Added " + data);
      }
      // set or clear the sortbytree flag.
      if (aparser.contains("sortbytree"))
      {
        af.getViewport().setSortByTree(true);
      }
      if (aparser.contains("nosortbytree"))
      {
        af.getViewport().setSortByTree(false);
      }
      data = aparser.getValue("tree", true);
      if (data != null)
      {
        jalview.io.NewickFile fin = null;
        try
        {
          fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
          if (fin != null)
          {
            af.getViewport().setCurrentTree(
                    af.ShowNewickTree(fin, data).getTree());
            System.out.println("Added tree " + data);
          }
        } catch (IOException ex)
        {
          System.err.println("Couldn't add tree " + data);
          ex.printStackTrace(System.err);
        }
      }
      // TODO - load PDB structure(s) to alignment JAL-629
      // (associate with identical sequence in alignment, or a specified
      // sequence)

      getFeatures = checkDasArguments(aparser);
      if (af != null && getFeatures != null)
      {
        FeatureFetcher ff = startFeatureFetching(getFeatures);
        if (ff != null)
          while (!ff.allFinished() || af.operationInProgress())
          {
            // wait around until fetching is finished.
            try
            {
              Thread.sleep(100);
            } catch (Exception e)
            {

            }
          }
        getFeatures = null; // have retrieved features - forget them now.
      }
      if (groovyscript != null)
      {
        // Execute the groovy script after we've done all the rendering stuff
        // and before any images or figures are generated.
        if (jalview.bin.Cache.groovyJarsPresent())
        {
          System.out.println("Executing script " + groovyscript);
          executeGroovyScript(groovyscript, new Object[] {desktop,af});
        }
        else
        {
          System.err
                  .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
                          + groovyscript);
        }
        groovyscript = null;
      }
      String imageName = "unnamed.png";
      while (aparser.getSize() > 1)
      {
        format = aparser.nextValue();
        file = aparser.nextValue();

        if (format.equalsIgnoreCase("png"))
        {
          af.createPNG(new java.io.File(file));
          imageName = (new java.io.File(file)).getName();
          System.out.println("Creating PNG image: " + file);
          continue;
        }
        else if (format.equalsIgnoreCase("imgMap"))
        {
          af.createImageMap(new java.io.File(file), imageName);
          System.out.println("Creating image map: " + file);
          continue;
        }
        else if (format.equalsIgnoreCase("eps"))
        {
          System.out.println("Creating EPS file: " + file);
          af.createEPS(new java.io.File(file));
          continue;
        }

        if (af.saveAlignment(file, format))
        {
          System.out.println("Written alignment in " + format
                  + " format to " + file);
        }
        else
        {
          System.out.println("Error writing file " + file + " in " + format
                  + " format!!");
        }

      }

      while (aparser.getSize() > 0)
      {
        System.out.println("Unknown arg: " + aparser.nextValue());
      }
    }
    AlignFrame startUpAlframe = null;
    // We'll only open the default file if the desktop is visible.
    // And the user
    // ////////////////////
    if (!headless && file == null && vamsasImport == null
            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
    {
      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
              jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/examples/exampleFile_2_7.jar");
      if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
      {
        // hardwire upgrade of the startup file
        file.replace("_2_3.jar","_2_7.jar");
        // and remove the stale setting 
        jalview.bin.Cache.removeProperty("STARTUP_FILE");
      }
      
      protocol = "File";

      if (file.indexOf("http:") > -1)
      {
        protocol = "URL";
      }

      if (file.endsWith(".jar"))
      {
        format = "Jalview";
      }
      else
      {
        format = new jalview.io.IdentifyFile().Identify(file, protocol);
      }

      startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
              format);
      getFeatures = checkDasArguments(aparser);
      // extract groovy arguments before anything else.
    }
    // If the user has specified features to be retrieved,
    // or a groovy script to be executed, do them if they
    // haven't been done already
    // fetch features for the default alignment
    if (getFeatures != null)
    {
      if (startUpAlframe != null)
      {
        startFeatureFetching(getFeatures);
      }
    }
    // Once all other stuff is done, execute any groovy scripts (in order)
    if (groovyscript != null)
    {
      if (jalview.bin.Cache.groovyJarsPresent())
      {
        System.out.println("Executing script " + groovyscript);
        executeGroovyScript(groovyscript, new Object[] { desktop, startUpAlframe});
      }
      else
      {
        System.err
                .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
                        + groovyscript);
      }
    }
    // and finally, turn off batch mode indicator - if the desktop still exists
    if (desktop != null)
    {
      if (progress!=-1) {
        desktop.setProgressBar(null, progress);
      }
      desktop.setInBatchMode(false);
    }
  }

00580   private static void startUsageStats(final Desktop desktop)
  {
    /**
     * start a User Config prompt asking if we can log usage statistics.
     */
    jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
            desktop.desktop,
            "USAGESTATS",
            "Jalview Usage Statistics",
            "Do you want to help make Jalview better by enabling "
                    + "the collection of usage statistics with Google Analytics ?"
                    + "\n\n(you can enable or disable usage tracking in the preferences)",
            new Runnable()
            {
              public void run()
              {
                Cache.log
                        .info("Initialising googletracker for usage stats.");
                Cache.initGoogleTracker();
                Cache.log.debug("Tracking enabled.");
              }
            }, new Runnable()
            {
              public void run()
              {
                Cache.log.info("Not enabling Google Tracking.");
              }
            }, null, true);
    SwingUtilities.invokeLater(prompter);
  }

  /**
   * Locate the given string as a file and pass it to the groovy interpreter.
   * 
   * @param groovyscript
   *          the script to execute
   * @param jalviewContext
   *          the Jalview Desktop object passed in to the groovy binding as the
   *          'Jalview' object.
   */
00620   private static void executeGroovyScript(String groovyscript,
          Object[] jalviewContext)
  {
    if (jalviewContext == null)
    {
      System.err
              .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
    }
    /**
     * for scripts contained in files
     */
    File tfile = null;
    /**
     * script's URI
     */
    URL sfile = null;
    if (groovyscript.trim().equals("STDIN"))
    {
      // read from stdin into a tempfile and execute it
      try
      {
        tfile = File.createTempFile("jalview", "groovy");
        PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
                new FileOutputStream(tfile)));
        BufferedReader br = new BufferedReader(
                new java.io.InputStreamReader(System.in));
        String line = null;
        while ((line = br.readLine()) != null)
        {
          outfile.write(line + "\n");
        }
        br.close();
        outfile.flush();
        outfile.close();

      } catch (Exception ex)
      {
        System.err.println("Failed to read from STDIN into tempfile "
                + ((tfile == null) ? "(tempfile wasn't created)" : tfile
                        .toString()));
        ex.printStackTrace();
        return;
      }
      try {
        sfile = tfile.toURI().toURL();
      } catch (Exception x)
      {
        System.err.println("Unexpected Malformed URL Exception for temporary file created from STDIN: "+tfile.toURI());
        x.printStackTrace();
        return;
      }
    }
    else
    {
      try
      {
        sfile = new URI(groovyscript).toURL();
      } catch (Exception x)
      {
        tfile = new File(groovyscript);
        if (!tfile.exists())
        {
          System.err.println("File '" + groovyscript + "' does not exist.");
          return;
        }
        if (!tfile.canRead())
        {
          System.err.println("File '" + groovyscript + "' cannot be read.");
          return;
        }
        if (tfile.length() < 1)
        {
          System.err.println("File '" + groovyscript + "' is empty.");
          return;
        }
        try {
        sfile = tfile.getAbsoluteFile().toURI().toURL();
        } catch (Exception ex)
        {
          System.err.println("Failed to create a file URL for "+tfile.getAbsoluteFile());
          return;
        }
      }
    }
    boolean success = false;
    try
    {
      /*
       * The following code performs the GroovyScriptEngine invocation using
       * reflection, and is equivalent to this fragment from the embedding
       * groovy documentation on the groovy site: <code> import
       * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
       * 
       * String[] roots = new String[] { "/my/groovy/script/path" };
       * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding
       * = new Binding(); binding.setVariable("input", "world");
       * gse.run("hello.groovy", binding); </code>
       */
      Class[] bspec;
      Object[] binding;
      int blen = ((jalviewContext[0] == null) ? 0 : 1)
              + ((jalviewContext[1] == null) ? 0 : 1);
      String cnames[] = new String[]
      { "Jalview", "currentAlFrame" };
      bspec = new Class[blen * 2];
      binding = new Object[blen * 2];
      blen = 0;
      ClassLoader cl = null;
      Map vbinding = new Hashtable();
      for (int jc = 0; jc < jalviewContext.length; jc++)
      {
        if (jalviewContext[jc] != null)
        {
          if (cl == null)
          {
            cl = jalviewContext[jc].getClass().getClassLoader();
          }
          bspec[blen * 2] = String.class;
          bspec[blen * 2 + 1] = Object.class;
          binding[blen * 2] = cnames[jc];
          binding[blen * 2 + 1] = jalviewContext[jc];
          vbinding.put(cnames[jc], jalviewContext[jc]);
          blen++;
        }
      }
      Class gbindingc = cl.loadClass("groovy.lang.Binding");
      Constructor gbcons;
      Object gbinding;
      try
      {
        gbcons = gbindingc.getConstructor(Map.class);
        gbinding = gbcons.newInstance(vbinding);
      } catch (NoSuchMethodException x)
      {
        // old style binding config - using series of string/object values to
        // setVariable.
        gbcons = gbindingc.getConstructor(null);
        gbinding = gbcons.newInstance(null);
        java.lang.reflect.Method setvar = gbindingc.getMethod(
                "setVariable", bspec);
        setvar.invoke(gbinding, binding);
      }
      ;
      Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
      Constructor gseccons = gsec.getConstructor(new Class[]
      { URL[].class }); // String[].class });
      Object gse = gseccons.newInstance(new Object[]
      { new URL[]
      { sfile } }); // .toString() } });
      java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
      { String.class, gbindingc });
      run.invoke(gse, new Object[]
      { sfile.toString(), gbinding });
      success = true;
    } catch (Exception e)
    {
      System.err.println("Exception Whilst trying to execute file " + sfile
              + " as a groovy script.");
      e.printStackTrace(System.err);

    }
    if (success && groovyscript.equals("STDIN"))
    {
      // delete temp file that we made - but only if it was successfully
      // executed
      tfile.delete();
    }
  }

  /**
   * Check commandline for any das server definitions or any fetchfrom switches
   * 
   * @return vector of DAS source nicknames to retrieve from
   */
00794   private static Vector checkDasArguments(ArgsParser aparser)
  {
    Vector source = null;
    String data;
    String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
    while ((data = aparser.getValue("dasserver", true)) != null)
    {
      String nickname = null;
      String url = null;
      boolean seq = false, feat = true;
      int pos = data.indexOf('=');
      // determine capabilities
      if (pos > 0)
      {
        nickname = data.substring(0, pos);
      }
      url = data.substring(pos + 1);
      if (url != null
              && (url.startsWith("http:") || url
                      .startsWith("sequence:http:")))
      {
        if (nickname == null)
        {
          nickname = url;
        }
        if (locsources == null)
        {
          locsources = "";
        }
        else
        {
          locsources += "\t";
        }
        locsources = locsources + nickname + "|" + url;
        System.err
                .println("NOTE! dasserver parameter not yet really supported (got args of "
                        + nickname + "|" + url);
        if (source == null)
        {
          source = new Vector();
        }
        source.addElement(nickname);
      }
    } // loop until no more server entries are found.
    if (locsources != null && locsources.indexOf('|') > -1)
    {
      Cache.log.debug("Setting local source list in properties file to:\n"
              + locsources);
      Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
    }
    while ((data = aparser.getValue("fetchfrom", true)) != null)
    {
      System.out.println("adding source '" + data + "'");
      if (source == null)
      {
        source = new Vector();
      }
      source.addElement(data);
    }
    return source;
  }

  /**
   * start a feature fetcher for every alignment frame
   * 
   * @param dasSources
   */
00861   private static FeatureFetcher startFeatureFetching(final Vector dasSources)
  {
    FeatureFetcher ff = new FeatureFetcher();
    AlignFrame afs[] = Desktop.getAlignframes();
    if (afs == null || afs.length == 0)
    {
      return null;
    }
    for (int i = 0; i < afs.length; i++)
    {
      ff.addFetcher(afs[i], dasSources);
    }
    return ff;
  }
}

/**
 * Notes: this argParser does not distinguish between parameter switches,
 * parameter values and argument text. If an argument happens to be identical to
 * a parameter, it will be taken as such (even though it didn't have a '-'
 * prefixing it).
 * 
 * @author Andrew Waterhouse and JBP documented.
 * 
 */
00886 class ArgsParser
{
  Vector vargs = null;

  public ArgsParser(String[] args)
  {
    vargs = new Vector();
    for (int i = 0; i < args.length; i++)
    {
      String arg = args[i].trim();
      if (arg.charAt(0) == '-')
      {
        arg = arg.substring(1);
      }
      vargs.addElement(arg);
    }
  }

  /**
   * check for and remove first occurence of arg+parameter in arglist.
   * 
   * @param arg
   * @return return the argument following the given arg if arg was in list.
   */
00910   public String getValue(String arg)
  {
    return getValue(arg, false);
  }

  public String getValue(String arg, boolean utf8decode)
  {
    int index = vargs.indexOf(arg);
    String dc = null, ret = null;
    if (index != -1)
    {
      ret = vargs.elementAt(index + 1).toString();
      vargs.removeElementAt(index);
      vargs.removeElementAt(index);
      if (utf8decode && ret != null)
      {
        try
        {
          dc = URLDecoder.decode(ret, "UTF-8");
          ret = dc;
        } catch (Exception e)
        {
          // TODO: log failure to decode
        }
      }
    }
    return ret;
  }

  /**
   * check for and remove first occurence of arg in arglist.
   * 
   * @param arg
   * @return true if arg was present in argslist.
   */
00945   public boolean contains(String arg)
  {
    if (vargs.contains(arg))
    {
      vargs.removeElement(arg);
      return true;
    }
    else
    {
      return false;
    }
  }

  public String nextValue()
  {
    return vargs.remove(0).toString();
  }

  public int getSize()
  {
    return vargs.size();
  }

}

/**
 * keep track of feature fetching tasks.
 * 
 * @author JimP
 * 
 */
00976 class FeatureFetcher
{
  /*
   * TODO: generalise to track all jalview events to orchestrate batch
   * processing events.
   */

  private int queued = 0;

  private int running = 0;

  public FeatureFetcher()
  {

  }

  public void addFetcher(final AlignFrame af, final Vector dasSources)
  {
    final long id = System.currentTimeMillis();
    queued++;
    final FeatureFetcher us = this;
    new Thread(new Runnable()
    {

      public void run()
      {
        synchronized (us)
        {
          queued--;
          running++;
        }

        af.setProgressBar("DAS features being retrieved...", id);
        af.featureSettings_actionPerformed(null);
        af.featureSettings.fetchDasFeatures(dasSources, true);
        af.setProgressBar(null, id);
        synchronized (us)
        {
          running--;
        }
      }
    }).start();
  }

  public synchronized boolean allFinished()
  {
    return queued == 0 && running == 0;
  }
};

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