net.sf.jabref.JabRef.java Source code

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Here is the source code for net.sf.jabref.JabRef.java

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/*  Copyright (C) 2003-2014 JabRef contributors.
This program 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 2 of the License, or
(at your option) any later version.
    
This program 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 this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package net.sf.jabref;

import com.jgoodies.looks.plastic.Plastic3DLookAndFeel;
import com.jgoodies.looks.plastic.theme.SkyBluer;

import java.awt.Font;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Enumeration;
import java.util.Iterator;
import java.util.List;
import java.util.Vector;
import java.util.prefs.BackingStoreException;

import javax.swing.*;
import javax.swing.plaf.FontUIResource;

import net.sf.jabref.export.AutoSaveManager;
import net.sf.jabref.export.ExportFormats;
import net.sf.jabref.export.FileActions;
import net.sf.jabref.export.IExportFormat;
import net.sf.jabref.export.SaveException;
import net.sf.jabref.export.SaveSession;
import net.sf.jabref.imports.*;
import net.sf.jabref.plugin.PluginCore;
import net.sf.jabref.plugin.PluginInstaller;
import net.sf.jabref.plugin.SidePanePlugin;
import net.sf.jabref.plugin.core.JabRefPlugin;
import net.sf.jabref.plugin.core.generated._JabRefPlugin;
import net.sf.jabref.plugin.core.generated._JabRefPlugin.EntryFetcherExtension;
import net.sf.jabref.remote.RemotePreferences;
import net.sf.jabref.remote.client.RemoteListenerClient;
import net.sf.jabref.remote.JabRefMessageHandler;
import net.sf.jabref.splash.SplashScreenLifecycle;
import net.sf.jabref.util.FileBasedLock;
import net.sf.jabref.util.StringUtil;
import net.sf.jabref.util.Util;
import net.sf.jabref.wizard.auximport.AuxCommandLine;

import com.sun.jna.Native;
import com.sun.jna.NativeLong;
import com.sun.jna.Pointer;
import com.sun.jna.WString;
import com.sun.jna.ptr.PointerByReference;

/**
 * JabRef Main Class - The application gets started here.
 */
public class JabRef {

    public static JabRefFrame jrf;

    private static final int MAX_DIALOG_WARNINGS = 10;

    private boolean graphicFailure = false;
    private JabRefCLI cli;
    private SplashScreenLifecycle splashScreen = new SplashScreenLifecycle();

    public void start(String[] args) {
        JabRefPreferences prefs = JabRefPreferences.getInstance();

        // See if there are plugins scheduled for deletion:
        if (prefs.hasKey(JabRefPreferences.DELETE_PLUGINS)
                && (prefs.get(JabRefPreferences.DELETE_PLUGINS).length() > 0)) {
            String[] toDelete = prefs.getStringArray(JabRefPreferences.DELETE_PLUGINS);
            PluginInstaller.deletePluginsOnStartup(toDelete);
            prefs.put(JabRefPreferences.DELETE_PLUGINS, "");
        }

        if (prefs.getBoolean(JabRefPreferences.USE_PROXY)) {
            // NetworkTab.java ensures that proxyHostname and proxyPort are not null
            System.setProperty("http.proxyHost", prefs.get(JabRefPreferences.PROXY_HOSTNAME));
            System.setProperty("http.proxyPort", prefs.get(JabRefPreferences.PROXY_PORT));

            // currently, the following cannot be configured
            if (prefs.get("proxyUsername") != null) {
                System.setProperty("http.proxyUser", prefs.get("proxyUsername"));
                System.setProperty("http.proxyPassword", prefs.get("proxyPassword"));
            }
        } else {
            // The following two lines signal that the system proxy settings
            // should be used:
            System.setProperty("java.net.useSystemProxies", "true");
            System.setProperty("proxySet", "true");
        }

        Globals.startBackgroundTasks();
        Globals.setupLogging();
        Globals.prefs = prefs;
        setLanguage(prefs);
        Globals.prefs.setLanguageDependentDefaultValues();
        /*
         * The Plug-in System is started automatically on the first call to
         * PluginCore.getManager().
         * 
         * Plug-ins are activated on the first call to their getInstance method.
         */

        // Update which fields should be treated as numeric, based on preferences:
        BibtexFields.setNumericFieldsFromPrefs();

        /* Build list of Import and Export formats */
        Globals.importFormatReader.resetImportFormats();
        BibtexEntryType.loadCustomEntryTypes(prefs);
        ExportFormats.initAllExports();

        // Read list(s) of journal names and abbreviations:
        Globals.initializeJournalNames();

        // Check for running JabRef
        RemotePreferences remotePreferences = new RemotePreferences(Globals.prefs);
        if (remotePreferences.useRemoteServer()) {

            Globals.remoteListener.open(new JabRefMessageHandler(this), remotePreferences.getPort());

            if (Globals.remoteListener.isOpen()) {
                Globals.remoteListener.start(); // we are alone, we start the server
            } else {
                // we are not alone, there is already a server out there, try to contact already running JabRef:
                if (RemoteListenerClient.sendToActiveJabRefInstance(args, remotePreferences.getPort())) {
                    /*
                     * We have successfully sent our command line options
                     * through the socket to another JabRef instance. So we
                     * assume it's all taken care of, and quit.
                     */
                    System.out.println(
                            Globals.lang("Arguments passed on to running JabRef instance. Shutting down."));
                    JabRefExecutorService.INSTANCE.shutdownEverything();
                    return;
                }
            }
        }

        /*
         * See if the user has a personal journal list set up. If so, add these
         * journal names and abbreviations to the list:
         */
        String personalJournalList = prefs.get(JabRefPreferences.PERSONAL_JOURNAL_LIST);
        if ((personalJournalList != null) && !personalJournalList.isEmpty()) {
            try {
                Globals.journalAbbrev.readJournalListFromFile(new File(personalJournalList));
            } catch (FileNotFoundException e) {
                JOptionPane.showMessageDialog(null, Globals.lang("Journal file not found") + ": " + e.getMessage(),
                        Globals.lang("Error opening file"), JOptionPane.ERROR_MESSAGE);
                Globals.prefs.put(JabRefPreferences.PERSONAL_JOURNAL_LIST, "");
            }
        }

        // override used newline character with the one stored in the preferences
        // The preferences return the system newline character sequence as default
        Globals.NEWLINE = Globals.prefs.get(JabRefPreferences.NEWLINE);
        Globals.NEWLINE_LENGTH = Globals.NEWLINE.length();

        if (Globals.ON_WIN) {
            // Set application user model id so that pinning JabRef to the Win7/8 taskbar works
            // Based on http://stackoverflow.com/a/1928830
            JabRef.setCurrentProcessExplicitAppUserModelID("JabRef." + Globals.BUILD_INFO.getVersion());
            //System.out.println(getCurrentProcessExplicitAppUserModelID());
        }

        Vector<ParserResult> loaded = processArguments(args, true);

        if (loaded == null || graphicFailure || cli.isDisableGui() || cli.isShowVersion()) {
            JabRefExecutorService.INSTANCE.shutdownEverything();
            return;
        }

        openWindow(loaded);
    }

    private void setLanguage(JabRefPreferences prefs) {
        String langStr = prefs.get(JabRefPreferences.LANGUAGE);
        String[] parts = langStr.split("_");
        String language, country;
        if (parts.length == 1) {
            language = langStr;
            country = "";
        } else {
            language = parts[0];
            country = parts[1];
        }

        Globals.setLanguage(language, country);
    }

    // Do not use this code in release version, it contains some memory leaks
    public static String getCurrentProcessExplicitAppUserModelID() {
        final PointerByReference r = new PointerByReference();

        if (JabRef.GetCurrentProcessExplicitAppUserModelID(r).longValue() == 0) {
            final Pointer p = r.getValue();

            return p.getString(0, true); // here we leak native memory by lazyness
        }
        return "N/A";
    }

    private static void setCurrentProcessExplicitAppUserModelID(final String appID) {
        if (JabRef.SetCurrentProcessExplicitAppUserModelID(new WString(appID)).longValue() != 0) {
            throw new RuntimeException("unable to set current process explicit AppUserModelID to: " + appID);
        }
    }

    private static native NativeLong GetCurrentProcessExplicitAppUserModelID(PointerByReference appID);

    private static native NativeLong SetCurrentProcessExplicitAppUserModelID(WString appID);

    static {
        if (Globals.ON_WIN) {
            Native.register("shell32");
        }
    }

    public Vector<ParserResult> processArguments(String[] args, boolean initialStartup) {

        cli = new JabRefCLI(args);

        if (initialStartup && cli.isShowVersion()) {
            cli.displayVersion();
        }

        if (initialStartup && cli.isHelp()) {
            cli.printUsage();
            return null; // TODO replace with optional one day
        }

        boolean commandMode = cli.isDisableGui() || cli.isFetcherEngine();

        // First we quickly scan the command line parameters for any that signal
        // that the GUI
        // should not be opened. This is used to decide whether we should show the
        // splash screen or not.
        if (initialStartup && !commandMode && !cli.isDisableSplash()) {
            try {
                splashScreen.show();
            } catch (Throwable ex) {
                graphicFailure = true;
                System.err.println(Globals.lang("Unable to create graphical interface") + ".");
            }
        }

        // Check if we should reset all preferences to default values:
        if (cli.isPreferencesReset()) {
            String value = cli.getPreferencesReset();
            if (value.trim().equals("all")) {
                try {
                    System.out.println(Globals.lang("Setting all preferences to default values."));
                    Globals.prefs.clear();
                } catch (BackingStoreException e) {
                    System.err.println(Globals.lang("Unable to clear preferences."));
                    e.printStackTrace();
                }
            } else {
                String[] keys = value.split(",");
                for (String key : keys) {
                    if (Globals.prefs.hasKey(key.trim())) {
                        System.out.println(Globals.lang("Resetting preference key '%0'", key.trim()));
                        Globals.prefs.clear(key.trim());
                    } else {
                        System.out.println(Globals.lang("Unknown preference key '%0'", key.trim()));
                    }
                }
            }

        }

        // Check if we should import preferences from a file:
        if (cli.isPreferencesImport()) {
            try {
                Globals.prefs.importPreferences(cli.getPreferencesImport());
                BibtexEntryType.loadCustomEntryTypes(Globals.prefs);
                ExportFormats.initAllExports();
            } catch (IOException ex) {
                Util.pr(ex.getMessage());
            }
        }

        // Set up custom or default icon theme
        // Has to be done here as openBibFile requires an initialized icon theme (due to the implementation of special fields)
        GUIGlobals.setUpIconTheme();

        // Vector to put imported/loaded database(s) in.
        Vector<ParserResult> loaded = new Vector<ParserResult>();
        Vector<String> toImport = new Vector<String>();
        if (!cli.isBlank() && (cli.getLeftOver().length > 0)) {
            for (String aLeftOver : cli.getLeftOver()) {
                // Leftover arguments that have a "bib" extension are interpreted as
                // bib files to open. Other files, and files that could not be opened
                // as bib, we try to import instead.
                boolean bibExtension = aLeftOver.toLowerCase().endsWith("bib");
                ParserResult pr = null;
                if (bibExtension) {
                    pr = JabRef.openBibFile(aLeftOver, false);
                }

                if ((pr == null) || (pr == ParserResult.INVALID_FORMAT)) {
                    // We will try to import this file. Normally we
                    // will import it into a new tab, but if this import has
                    // been initiated by another instance through the remote
                    // listener, we will instead import it into the current database.
                    // This will enable easy integration with web browers that can
                    // open a reference file in JabRef.
                    if (initialStartup) {
                        toImport.add(aLeftOver);
                    } else {
                        ParserResult res = JabRef.importToOpenBase(aLeftOver);
                        if (res != null) {
                            loaded.add(res);
                        } else {
                            loaded.add(ParserResult.INVALID_FORMAT);
                        }
                    }
                } else if (pr != ParserResult.FILE_LOCKED) {
                    loaded.add(pr);
                }

            }
        }

        if (!cli.isBlank() && cli.isFileImport()) {
            toImport.add(cli.getFileImport());
        }

        for (String filenameString : toImport) {
            ParserResult pr = JabRef.importFile(filenameString);
            if (pr != null) {
                loaded.add(pr);
            }
        }

        if (!cli.isBlank() && cli.isImportToOpenBase()) {
            ParserResult res = JabRef.importToOpenBase(cli.getImportToOpenBase());
            if (res != null) {
                loaded.add(res);
            }
        }

        if (!cli.isBlank() && cli.isFetcherEngine()) {
            ParserResult res = fetch(cli.getFetcherEngine());
            if (res != null) {
                loaded.add(res);
            }
        }

        if (cli.isExportMatches()) {
            if (loaded.size() > 0) {
                String[] data = cli.getExportMatches().split(",");
                String searchTerm = data[0].replace("\\$", " "); //enables blanks within the search term:
                                                                 //? stands for a blank
                ParserResult pr = loaded.elementAt(loaded.size() - 1);
                BibtexDatabase dataBase = pr.getDatabase();
                SearchManagerNoGUI smng = new SearchManagerNoGUI(searchTerm, dataBase);
                BibtexDatabase newBase = smng.getDBfromMatches(); //newBase contains only match entries

                //export database
                if ((newBase != null) && (newBase.getEntryCount() > 0)) {
                    String formatName = null;
                    IExportFormat format;

                    //read in the export format, take default format if no format entered
                    switch (data.length) {
                    case (3): {
                        formatName = data[2];
                        break;
                    }
                    case (2): {
                        //default ExportFormat: HTML table (with Abstract & BibTeX)
                        formatName = "tablerefsabsbib";
                        break;
                    }
                    default: {
                        System.err.println(
                                Globals.lang("Output file missing").concat(". \n \t ").concat("Usage").concat(": ")
                                        + JabRefCLI.getExportMatchesSyntax());
                        return null; // TODO replace with optional one day
                    }
                    } //end switch

                    //export new database
                    format = ExportFormats.getExportFormat(formatName);
                    if (format != null) {
                        // We have an ExportFormat instance:
                        try {
                            System.out.println(Globals.lang("Exporting") + ": " + data[1]);
                            format.performExport(newBase, pr.getMetaData(), data[1], pr.getEncoding(), null);
                        } catch (Exception ex) {
                            System.err.println(Globals.lang("Could not export file") + " '" + data[1] + "': "
                                    + ex.getMessage());
                        }
                    } else {
                        System.err.println(Globals.lang("Unknown export format") + ": " + formatName);
                    }
                } /*end if newBase != null*/else {
                    System.err.println(Globals.lang("No search matches."));
                }
            } else {
                System.err.println(Globals.lang("The output option depends on a valid input option."));
            } //end if(loaded.size > 0)
        } //end exportMatches invoked 

        if (cli.isFileExport()) {
            if (loaded.size() > 0) {
                String[] data = cli.getFileExport().split(",");

                if (data.length == 1) {
                    // This signals that the latest import should be stored in BibTeX
                    // format to the given file.
                    if (loaded.size() > 0) {
                        ParserResult pr = loaded.elementAt(loaded.size() - 1);
                        if (!pr.isInvalid()) {
                            try {
                                System.out.println(Globals.lang("Saving") + ": " + data[0]);
                                SaveSession session = FileActions.saveDatabase(pr.getDatabase(), pr.getMetaData(),
                                        new File(data[0]), Globals.prefs, false, false,
                                        Globals.prefs.get(JabRefPreferences.DEFAULT_ENCODING), false);
                                // Show just a warning message if encoding didn't work for all characters:
                                if (!session.getWriter().couldEncodeAll()) {
                                    System.err.println(Globals.lang("Warning") + ": " + Globals.lang(
                                            "The chosen encoding '%0' could not encode the following characters: ",
                                            session.getEncoding()) + session.getWriter().getProblemCharacters());
                                }
                                session.commit();
                            } catch (SaveException ex) {
                                System.err.println(Globals.lang("Could not save file") + " '" + data[0] + "': "
                                        + ex.getMessage());
                            }
                        }
                    } else {
                        System.err.println(Globals.lang("The output option depends on a valid import option."));
                    }
                } else if (data.length == 2) {
                    // This signals that the latest import should be stored in the given
                    // format to the given file.
                    ParserResult pr = loaded.elementAt(loaded.size() - 1);

                    // Set the global variable for this database's file directory before exporting,
                    // so formatters can resolve linked files correctly.
                    // (This is an ugly hack!)
                    File theFile = pr.getFile();
                    if (!theFile.isAbsolute()) {
                        theFile = theFile.getAbsoluteFile();
                    }
                    MetaData metaData = pr.getMetaData();
                    metaData.setFile(theFile);
                    Globals.prefs.fileDirForDatabase = metaData.getFileDirectory(GUIGlobals.FILE_FIELD);
                    Globals.prefs.databaseFile = metaData.getFile();
                    System.out.println(Globals.lang("Exporting") + ": " + data[0]);
                    IExportFormat format = ExportFormats.getExportFormat(data[1]);
                    if (format != null) {
                        // We have an ExportFormat instance:
                        try {
                            format.performExport(pr.getDatabase(), pr.getMetaData(), data[0], pr.getEncoding(),
                                    null);
                        } catch (Exception ex) {
                            System.err.println(Globals.lang("Could not export file") + " '" + data[0] + "': "
                                    + ex.getMessage());
                        }
                    } else {
                        System.err.println(Globals.lang("Unknown export format") + ": " + data[1]);
                    }

                }
            } else {
                System.err.println(Globals.lang("The output option depends on a valid import option."));
            }
        }

        //Util.pr(": Finished export");

        if (cli.isPreferencesExport()) {
            try {
                Globals.prefs.exportPreferences(cli.getPreferencesExport());
            } catch (IOException ex) {
                Util.pr(ex.getMessage());
            }
        }

        if (!cli.isBlank() && cli.isAuxImport()) {
            boolean usageMsg = false;

            if (loaded.size() > 0) // bibtex file loaded
            {
                String[] data = cli.getAuxImport().split(",");

                if (data.length == 2) {
                    ParserResult pr = loaded.firstElement();
                    AuxCommandLine acl = new AuxCommandLine(data[0], pr.getDatabase());
                    BibtexDatabase newBase = acl.perform();

                    boolean notSavedMsg = false;

                    // write an output, if something could be resolved
                    if (newBase != null) {
                        if (newBase.getEntryCount() > 0) {
                            String subName = StringUtil.getCorrectFileName(data[1], "bib");

                            try {
                                System.out.println(Globals.lang("Saving") + ": " + subName);
                                SaveSession session = FileActions.saveDatabase(newBase, new MetaData(), // no Metadata
                                        new File(subName), Globals.prefs, false, false,
                                        Globals.prefs.get(JabRefPreferences.DEFAULT_ENCODING), false);
                                // Show just a warning message if encoding didn't work for all characters:
                                if (!session.getWriter().couldEncodeAll()) {
                                    System.err.println(Globals.lang("Warning") + ": " + Globals.lang(
                                            "The chosen encoding '%0' could not encode the following characters: ",
                                            session.getEncoding()) + session.getWriter().getProblemCharacters());
                                }
                                session.commit();
                            } catch (SaveException ex) {
                                System.err.println(Globals.lang("Could not save file") + " '" + subName + "': "
                                        + ex.getMessage());
                            }

                            notSavedMsg = true;
                        }
                    }

                    if (!notSavedMsg) {
                        System.out.println(Globals.lang("no database generated"));
                    }
                } else {
                    usageMsg = true;
                }
            } else {
                usageMsg = true;
            }

            if (usageMsg) {
                System.out.println(Globals.lang("no base-bibtex-file specified"));
                System.out.println(Globals.lang("usage") + " :");
                System.out.println("jabref --aux infile[.aux],outfile[.bib] base-bibtex-file");
            }
        }

        return loaded;
    }

    /**
     * Run an entry fetcher from the command line.
     * 
     * Note that this only works headlessly if the EntryFetcher does not show
     * any GUI.
     * 
     * @param fetchCommand
     *            A string containing both the fetcher to use (id of
     *            EntryFetcherExtension minus Fetcher) and the search query,
     *            separated by a :
     * @return A parser result containing the entries fetched or null if an
     *         error occurred.
     */
    private ParserResult fetch(String fetchCommand) {

        if ((fetchCommand == null) || !fetchCommand.contains(":") || (fetchCommand.split(":").length != 2)) {
            System.out.println(Globals.lang("Expected syntax for --fetch='<name of fetcher>:<query>'"));
            System.out.println(Globals.lang("The following fetchers are available:"));
            return null;
        }

        String engine = fetchCommand.split(":")[0];
        String query = fetchCommand.split(":")[1];

        EntryFetcher fetcher = null;
        for (EntryFetcherExtension e : JabRefPlugin.getInstance(PluginCore.getManager())
                .getEntryFetcherExtensions()) {
            if (engine.toLowerCase().equals(e.getId().replaceAll("Fetcher", "").toLowerCase())) {
                fetcher = e.getEntryFetcher();
            }
        }

        if (fetcher == null) {
            System.out.println(Globals.lang("Could not find fetcher '%0'", engine));
            System.out.println(Globals.lang("The following fetchers are available:"));
            for (EntryFetcherExtension e : JabRefPlugin.getInstance(PluginCore.getManager())
                    .getEntryFetcherExtensions()) {
                System.out.println("  " + e.getId().replaceAll("Fetcher", "").toLowerCase());
            }
            return null;
        }

        System.out.println(Globals.lang("Running Query '%0' with fetcher '%1'.", query, engine) + " "
                + Globals.lang("Please wait..."));
        Collection<BibtexEntry> result = new ImportInspectionCommandLine().query(query, fetcher);

        if ((result == null) || (result.size() == 0)) {
            System.out.println(
                    Globals.lang("Query '%0' with fetcher '%1' did not return any results.", query, engine));
            return null;
        }

        return new ParserResult(result);
    }

    private void setLookAndFeel() {
        try {
            String lookFeel;
            String systemLnF = UIManager.getSystemLookAndFeelClassName();

            if (Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_LOOK_AND_FEEL)) {
                // Use system Look & Feel by default
                lookFeel = systemLnF;
            } else {
                lookFeel = Globals.prefs.get(JabRefPreferences.WIN_LOOK_AND_FEEL);
            }

            // At all cost, avoid ending up with the Metal look and feel:
            if (lookFeel.equals("javax.swing.plaf.metal.MetalLookAndFeel")) {
                Plastic3DLookAndFeel lnf = new Plastic3DLookAndFeel();
                Plastic3DLookAndFeel.setCurrentTheme(new SkyBluer());
                com.jgoodies.looks.Options.setPopupDropShadowEnabled(true);
                UIManager.setLookAndFeel(lnf);
            } else {
                try {
                    UIManager.setLookAndFeel(lookFeel);
                } catch (Exception e) { // javax.swing.UnsupportedLookAndFeelException (sure; see bug #1278) or ClassNotFoundException (unsure) may be thrown
                    // specified look and feel does not exist on the classpath, so use system l&f
                    UIManager.setLookAndFeel(systemLnF);
                    // also set system l&f as default
                    Globals.prefs.put(JabRefPreferences.WIN_LOOK_AND_FEEL, systemLnF);
                    // notify the user
                    JOptionPane.showMessageDialog(JabRef.jrf,
                            Globals.lang(
                                    "Unable to find the requested Look & Feel and thus the default one is used."),
                            Globals.lang("Warning"), JOptionPane.WARNING_MESSAGE);
                }
            }
        } catch (Exception e) {
            e.printStackTrace();
        }

        // In JabRef v2.8, we did it only on NON-Mac. Now, we try on all platforms
        boolean overrideDefaultFonts = Globals.prefs.getBoolean(JabRefPreferences.OVERRIDE_DEFAULT_FONTS);
        if (overrideDefaultFonts) {
            int fontSize = Globals.prefs.getInt(JabRefPreferences.MENU_FONT_SIZE);
            UIDefaults defaults = UIManager.getDefaults();
            Enumeration<Object> keys = defaults.keys();
            Double zoomLevel = null;
            while (keys.hasMoreElements()) {
                Object key = keys.nextElement();
                if ((key instanceof String) && (((String) key).endsWith(".font"))) {
                    FontUIResource font = (FontUIResource) UIManager.get(key);
                    if (zoomLevel == null) {
                        // zoomLevel not yet set, calculate it based on the first found font
                        zoomLevel = (double) fontSize / (double) font.getSize();
                    }
                    font = new FontUIResource(font.getName(), font.getStyle(), fontSize);
                    defaults.put(key, font);
                }
            }
            if (zoomLevel != null) {
                GUIGlobals.zoomLevel = zoomLevel;
            }
        }
    }

    private void openWindow(Vector<ParserResult> loaded) {
        // Call the method performCompatibilityUpdate(), which does any
        // necessary changes for users with a preference set from an older
        // Jabref version.
        Util.performCompatibilityUpdate();

        // Set up custom or default icon theme:
        // This is now done at processArguments

        // TODO: remove temporary registering of external file types?
        Globals.prefs.updateExternalFileTypes();

        // This property is set to make the Mac OSX Java VM move the menu bar to
        // the top of the screen, where Mac users expect it to be.
        System.setProperty("apple.laf.useScreenMenuBar", "true");

        // Set antialiasing on everywhere. This only works in JRE >= 1.5.
        // Or... it doesn't work, period.
        // TODO test and maybe remove this! I found this commented out with no additional info ( payload@lavabit.com )
        // Enabled since JabRef 2.11 beta 4
        System.setProperty("swing.aatext", "true");
        // Default is "on".
        // "lcd" instead of "on" because of http://wiki.netbeans.org/FaqFontRendering and http://docs.oracle.com/javase/6/docs/technotes/guides/2d/flags.html#aaFonts 
        System.setProperty("awt.useSystemAAFontSettings", "lcd");

        // Set the Look & Feel for Swing.
        try {
            setLookAndFeel();
        } catch (Throwable e) {
            e.printStackTrace();
        }

        // If the option is enabled, open the last edited databases, if any.
        if (!cli.isBlank() && Globals.prefs.getBoolean(JabRefPreferences.OPEN_LAST_EDITED)
                && (Globals.prefs.get(JabRefPreferences.LAST_EDITED) != null)) {
            // How to handle errors in the databases to open?
            String[] names = Globals.prefs.getStringArray(JabRefPreferences.LAST_EDITED);
            lastEdLoop: for (String name : names) {
                File fileToOpen = new File(name);

                for (int j = 0; j < loaded.size(); j++) {
                    ParserResult pr = loaded.elementAt(j);

                    if ((pr.getFile() != null) && pr.getFile().equals(fileToOpen)) {
                        continue lastEdLoop;
                    }
                }

                if (fileToOpen.exists()) {
                    ParserResult pr = JabRef.openBibFile(name, false);

                    if (pr != null) {

                        if (pr == ParserResult.INVALID_FORMAT) {
                            System.out.println(
                                    Globals.lang("Error opening file") + " '" + fileToOpen.getPath() + "'");
                        } else if (pr != ParserResult.FILE_LOCKED) {
                            loaded.add(pr);
                        }

                    }
                }
            }
        }

        GUIGlobals.init();
        GUIGlobals.CURRENTFONT = new Font(Globals.prefs.get(JabRefPreferences.FONT_FAMILY),
                Globals.prefs.getInt(JabRefPreferences.FONT_STYLE),
                Globals.prefs.getInt(JabRefPreferences.FONT_SIZE));

        //Util.pr(": Initializing frame");
        JabRef.jrf = new JabRefFrame(this);

        // Add all loaded databases to the frame:

        boolean first = true;
        List<File> postponed = new ArrayList<File>();
        List<ParserResult> failed = new ArrayList<ParserResult>();
        List<ParserResult> toOpenTab = new ArrayList<ParserResult>();
        if (loaded.size() > 0) {
            for (Iterator<ParserResult> i = loaded.iterator(); i.hasNext();) {
                ParserResult pr = i.next();
                if (pr.isInvalid()) {
                    failed.add(pr);
                    i.remove();
                } else if (!pr.isPostponedAutosaveFound()) {
                    if (pr.toOpenTab()) {
                        // things to be appended to an opened tab should be done after opening all tabs
                        // add them to the list
                        toOpenTab.add(pr);
                    } else {
                        JabRef.jrf.addParserResult(pr, first);
                        first = false;
                    }
                } else {
                    i.remove();
                    postponed.add(pr.getFile());
                }
            }
        }

        // finally add things to the currently opened tab
        for (ParserResult pr : toOpenTab) {
            JabRef.jrf.addParserResult(pr, first);
            first = false;
        }

        if (cli.isLoadSession()) {
            JabRef.jrf.loadSessionAction.actionPerformed(new java.awt.event.ActionEvent(JabRef.jrf, 0, ""));
        }

        splashScreen.hide();

        /*JOptionPane.showMessageDialog(null, Globals.lang("Please note that this "
        +"is an early beta version. Do not use it without backing up your files!"),
            Globals.lang("Beta version"), JOptionPane.WARNING_MESSAGE);*/

        // Start auto save timer:
        if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_SAVE)) {
            Globals.startAutoSaveManager(JabRef.jrf);
        }

        // If we are set to remember the window location, we also remember the maximised
        // state. This needs to be set after the window has been made visible, so we
        // do it here:
        if (Globals.prefs.getBoolean(JabRefPreferences.WINDOW_MAXIMISED)) {
            JabRef.jrf.setExtendedState(JFrame.MAXIMIZED_BOTH);
        }

        JabRef.jrf.setVisible(true);

        if (Globals.prefs.getBoolean(JabRefPreferences.WINDOW_MAXIMISED)) {
            JabRef.jrf.setExtendedState(JFrame.MAXIMIZED_BOTH);
        }

        // TEST TEST TEST TEST TEST TEST
        startSidePanePlugins(JabRef.jrf);

        for (ParserResult pr : failed) {
            String message = "<html>" + Globals.lang("Error opening file '%0'.", pr.getFile().getName()) + "<p>"
                    + pr.getErrorMessage() + "</html>";

            JOptionPane.showMessageDialog(JabRef.jrf, message, Globals.lang("Error opening file"),
                    JOptionPane.ERROR_MESSAGE);
        }

        for (int i = 0; i < loaded.size(); i++) {
            ParserResult pr = loaded.elementAt(i);
            if (Globals.prefs.getBoolean(JabRefPreferences.DISPLAY_KEY_WARNING_DIALOG_AT_STARTUP)
                    && pr.hasWarnings()) {
                String[] wrns = pr.warnings();
                StringBuilder wrn = new StringBuilder();
                for (int j = 0; j < Math.min(JabRef.MAX_DIALOG_WARNINGS, wrns.length); j++) {
                    wrn.append(j + 1).append(". ").append(wrns[j]).append("\n");
                }
                if (wrns.length > JabRef.MAX_DIALOG_WARNINGS) {
                    wrn.append("... ");
                    wrn.append(Globals.lang("%0 warnings", String.valueOf(wrns.length)));
                } else if (wrn.length() > 0) {
                    wrn.deleteCharAt(wrn.length() - 1);
                }
                JabRef.jrf.showBaseAt(i);
                JOptionPane.showMessageDialog(JabRef.jrf, wrn.toString(),
                        Globals.lang("Warnings") + " (" + pr.getFile().getName() + ")",
                        JOptionPane.WARNING_MESSAGE);
            }
        }

        // After adding the databases, go through each and see if
        // any post open actions need to be done. For instance, checking
        // if we found new entry types that can be imported, or checking
        // if the database contents should be modified due to new features
        // in this version of JabRef.
        // Note that we have to check whether i does not go over baseCount().
        // This is because importToOpen might have been used, which adds to
        // loaded, but not to baseCount()
        for (int i = 0; (i < loaded.size()) && (i < JabRef.jrf.baseCount()); i++) {
            ParserResult pr = loaded.elementAt(i);
            BasePanel panel = JabRef.jrf.baseAt(i);
            OpenDatabaseAction.performPostOpenActions(panel, pr, true);
        }

        //Util.pr(": Finished adding panels");

        // If any database loading was postponed due to an autosave, schedule them
        // for handing now:
        if (postponed.size() > 0) {
            AutosaveStartupPrompter asp = new AutosaveStartupPrompter(JabRef.jrf, postponed);
            SwingUtilities.invokeLater(asp);
        }

        if (loaded.size() > 0) {
            JabRef.jrf.tabbedPane.setSelectedIndex(0);
            new FocusRequester(((BasePanel) JabRef.jrf.tabbedPane.getComponentAt(0)).mainTable);
        }
    }

    /**
     * Go through all registered instances of SidePanePlugin, and register them
     * in the SidePaneManager.
     *
     * @param jrf The JabRefFrame.
     */
    private void startSidePanePlugins(JabRefFrame jrf) {

        JabRefPlugin jabrefPlugin = JabRefPlugin.getInstance(PluginCore.getManager());
        List<_JabRefPlugin.SidePanePluginExtension> plugins = jabrefPlugin.getSidePanePluginExtensions();
        for (_JabRefPlugin.SidePanePluginExtension extension : plugins) {
            SidePanePlugin plugin = extension.getSidePanePlugin();
            plugin.init(jrf, jrf.sidePaneManager);
            SidePaneComponent comp = plugin.getSidePaneComponent();
            jrf.sidePaneManager.register(comp.getName(), comp);
            jrf.addPluginMenuItem(plugin.getMenuItem());
        }
    }

    public static ParserResult openBibFile(String name, boolean ignoreAutosave) {
        Globals.logger(Globals.lang("Opening") + ": " + name);
        File file = new File(name);
        if (!file.exists()) {
            ParserResult pr = new ParserResult(null, null, null);
            pr.setFile(file);
            pr.setInvalid(true);
            System.err.println(Globals.lang("Error") + ": " + Globals.lang("File not found"));
            return pr;

        }
        try {

            if (!ignoreAutosave) {
                boolean autoSaveFound = AutoSaveManager.newerAutoSaveExists(file);
                if (autoSaveFound) {
                    // We have found a newer autosave. Make a note of this, so it can be
                    // handled after startup:
                    ParserResult postp = new ParserResult(null, null, null);
                    postp.setPostponedAutosaveFound(true);
                    postp.setFile(file);
                    return postp;
                }
            }

            if (!FileBasedLock.waitForFileLock(file, 10)) {
                System.out.println(Globals.lang("Error opening file") + " '" + name + "'. "
                        + "File is locked by another JabRef instance.");
                return ParserResult.FILE_LOCKED;
            }

            String encoding = Globals.prefs.get(JabRefPreferences.DEFAULT_ENCODING);
            ParserResult pr = OpenDatabaseAction.loadDatabase(file, encoding);
            if (pr == null) {
                pr = new ParserResult(null, null, null);
                pr.setFile(file);
                pr.setInvalid(true);
                return pr;

            }
            pr.setFile(file);
            if (pr.hasWarnings()) {
                String[] warn = pr.warnings();
                for (String aWarn : warn) {
                    System.out.println(Globals.lang("Warning") + ": " + aWarn);
                }

            }
            return pr;
        } catch (Throwable ex) {
            ParserResult pr = new ParserResult(null, null, null);
            pr.setFile(file);
            pr.setInvalid(true);
            pr.setErrorMessage(ex.getMessage());
            ex.printStackTrace();
            return pr;
        }

    }

    private static ParserResult importFile(String argument) {
        String[] data = argument.split(",");
        try {
            if ((data.length > 1) && !"*".equals(data[1])) {
                System.out.println(Globals.lang("Importing") + ": " + data[0]);
                try {
                    List<BibtexEntry> entries;
                    if (Globals.ON_WIN) {
                        entries = Globals.importFormatReader.importFromFile(data[1], data[0], JabRef.jrf);
                    } else {
                        entries = Globals.importFormatReader.importFromFile(data[1],
                                data[0].replaceAll("~", System.getProperty("user.home")), JabRef.jrf);
                    }
                    return new ParserResult(entries);
                } catch (IllegalArgumentException ex) {
                    System.err.println(Globals.lang("Unknown import format") + ": " + data[1]);
                    return null;
                }
            } else {
                // * means "guess the format":
                System.out.println(Globals.lang("Importing in unknown format") + ": " + data[0]);

                ImportFormatReader.UnknownFormatImport importResult;
                if (Globals.ON_WIN) {
                    importResult = Globals.importFormatReader.importUnknownFormat(data[0]);
                } else {
                    importResult = Globals.importFormatReader
                            .importUnknownFormat(data[0].replaceAll("~", System.getProperty("user.home")));
                }

                if (importResult != null) {
                    System.out.println(Globals.lang("Format used") + ": " + importResult.format);

                    return importResult.parserResult;
                } else {
                    System.out.println(Globals.lang("Could not find a suitable import format."));
                }
            }
        } catch (IOException ex) {
            System.err.println(
                    Globals.lang("Error opening file") + " '" + data[0] + "': " + ex.getLocalizedMessage());
        }
        return null;
    }

    /**
     * Will open a file (like importFile), but will also request JabRef to focus on this database 
     * @param argument See importFile.
     * @return ParserResult with setToOpenTab(true)
     */
    private static ParserResult importToOpenBase(String argument) {
        ParserResult result = JabRef.importFile(argument);

        if (result != null) {
            result.setToOpenTab(true);
        }

        return result;
    }
}