* Frame for talking to the PRIDE Archive web service to select projects for

* reshaking.

*

* @author Harald Barsnes

*/

    /**

     * The PeptideShakerGUI parent.

     */

    private PeptideShakerGUI peptideShakerGUI;

    /**

     * The currently selected species.

     */

    private String currentSpecies;

    /**

     * The project table column header tooltips.

     */

    private ArrayList<String> projectsTableToolTips;

    /**

     * The assay table column header tooltips.

     */

    private ArrayList<String> assaysTableToolTips;

    /**

     * The files table column header tooltips.

     */

    private ArrayList<String> filesTableToolTips;

    /**

     * The progress dialog.

     */

    private ProgressDialogX progressDialog;

    /**

     * The URL of the current PRIDE project.

     */

    private URL currentPrideDataFileUrl;

    /**

     * The current zipped PRIDE XML file.

     */

    private File currentZippedPrideDataFile;

    /**

     * The current PRIDE XML file.

     */

    private File currentPrideDataFile;

    /**

     * The current mgf file.

     */

    private File currentMgfFile;

    /**

     * The output folder for the mgfs and spectrum properties.

     */

    private String outputFolder = "user.home";

    /**

     * The maximum precursor charge detected in the PRIDE XML files.

     */

    private Integer maxPrecursorCharge = null;

    /**

     * The minimum precursor charge detected in the PRIDE XML files.

     */

    private Integer minPrecursorCharge = null;

    /*

     * The welcome dialog parent, can be null.

     */

    private WelcomeDialog welcomeDialog;

    /**

     * The PTM factory.

     */

    private PTMFactory ptmFactory = PTMFactory.getInstance();

    /**

     * The PRIDE search parameters report.

     */

    private String prideParametersReport = "";

    /**

     * The list of all found species.

     */

    private ArrayList<String> speciesAll;

    /**

     * The list of all found instruments.

     */

    private ArrayList<String> instrumentsAll;

    /**

     * The list of all found tissues.

     */

    private ArrayList<String> tissuesAll;

    /**

     * The list of all found PTMs.

     */

    private ArrayList<String> ptmsAll;

    /**

     * The current filter values.

     */

    private String[] currentFilterValues = new String[8];

    /**

     * The assay number filter type. True means greater than, false means

     * smaller than.

     */

    private boolean assaysGreaterThanFiler = true;

    /**

     * The list of reshakeable files.

     */

    private HashMap<String, ArrayList<String>> reshakeableFiles;

    /**

     * The list of files where search settings can be extracted.

     */

    private HashMap<String, ArrayList<String>> searchSettingsFiles;

    /**

     * The web service URL.

     */

    private static final String projectServiceURL = "http://www.ebi.ac.uk/pride/ws/archive/"; // "http://wwwdev.ebi.ac.uk:80/pride/ws/archive/";

    /**

     * The data format.

     */

    private SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");

    /**

     * The user name.

     */

    private String userName = null;

    /**

     * The password.

     */

    private String password = null;

    /**

     * The Reshake setup dialog.

     */

    private PrideReshakeSetupDialog prideReshakeSetupDialog;

    /**

     * Creates a new PrideReShakeGUI2 frame.

     *

     * @param peptideShakerGUI

     */

    public PrideReshakeGUI(PeptideShakerGUI peptideShakerGUI) {

        this.peptideShakerGUI = peptideShakerGUI;

        initComponents();

        setUpGui();

        this.setExtendedState(MAXIMIZED_BOTH);

        setVisible(true);

        PrideDataTypeSelectionDialog dataTypeSelectionDialog = new PrideDataTypeSelectionDialog(this, true);

        if (dataTypeSelectionDialog.isPublic()) {

            loadPublicProjects();

        } else {

            getPrivateProjectDetails();

        }

    }

    /**

     * Set up the GUI.

     */

    private void setUpGui() {

        clearProjectFiltersLabel.setVisible(false);

        setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")));

        reshakeableFiles = new HashMap<String, ArrayList<String>>();

        reshakeableFiles.put("RESULT", new ArrayList<String>());

        reshakeableFiles.get("RESULT").add(".xml");

        reshakeableFiles.get("RESULT").add(".xml.gz");

        reshakeableFiles.put("PEAK", new ArrayList<String>());

        reshakeableFiles.get("PEAK").add(".mgf");

        reshakeableFiles.get("PEAK").add(".mgf.gz");

        // then check for incorrect labeling...

        reshakeableFiles.put("OTHER", new ArrayList<String>());

        reshakeableFiles.get("OTHER").add(".mgf");

        reshakeableFiles.get("OTHER").add(".mgf.gz");

        reshakeableFiles.put("RAW", new ArrayList<String>());

        reshakeableFiles.get("RAW").add(".mgf");

        reshakeableFiles.get("RAW").add(".mgf.gz");

        searchSettingsFiles = new HashMap<String, ArrayList<String>>();

        searchSettingsFiles.put("RESULT", new ArrayList<String>());

        searchSettingsFiles.get("RESULT").add(".xml");

        searchSettingsFiles.get("RESULT").add(".xml.gz");

        searchSettingsFiles.get("RESULT").add(".mzid");

        searchSettingsFiles.get("RESULT").add(".mzid.gz");

        projectsTable.getColumn("Accession").setMaxWidth(90);

        projectsTable.getColumn("Accession").setMinWidth(90);

        projectsTable.getColumn(" ").setMaxWidth(50);

        projectsTable.getColumn(" ").setMinWidth(50);

        assaysTable.getColumn("Accession").setMaxWidth(90);

        assaysTable.getColumn("Accession").setMinWidth(90);

        assaysTable.getColumn(" ").setMaxWidth(50);

        assaysTable.getColumn(" ").setMinWidth(50);

        filesTable.getColumn("Assay").setMaxWidth(90);

        filesTable.getColumn("Assay").setMinWidth(90);

        filesTable.getColumn(" ").setMaxWidth(50);

        filesTable.getColumn(" ").setMinWidth(50);

        filesTable.getColumn("  ").setMaxWidth(30);

        filesTable.getColumn("  ").setMinWidth(30);

        filesTable.getColumn("Download").setMaxWidth(90);

        filesTable.getColumn("Download").setMinWidth(90);

        filesTable.getColumn("Type").setMaxWidth(90);

        filesTable.getColumn("Type").setMinWidth(90);

        filesTable.getColumn("Size").setMaxWidth(90);

        filesTable.getColumn("Size").setMinWidth(90);

        // make sure that the scroll panes are see-through

        projectsScrollPane.getViewport().setOpaque(false);

        assayTableScrollPane.getViewport().setOpaque(false);

        filesTableScrollPane.getViewport().setOpaque(false);

        projectsTable.setAutoCreateRowSorter(true);

        assaysTable.setAutoCreateRowSorter(true);

        filesTable.setAutoCreateRowSorter(true);

        projectsTable.getTableHeader().setReorderingAllowed(false);

        assaysTable.getTableHeader().setReorderingAllowed(false);

        filesTable.getTableHeader().setReorderingAllowed(false);

        // correct the color for the upper right corner

        JPanel projectsCorner = new JPanel();

        projectsCorner.setBackground(projectsTable.getTableHeader().getBackground());

        projectsScrollPane.setCorner(ScrollPaneConstants.UPPER_RIGHT_CORNER, projectsCorner);

        JPanel assayCorner = new JPanel();

        assayCorner.setBackground(assaysTable.getTableHeader().getBackground());

        assayTableScrollPane.setCorner(ScrollPaneConstants.UPPER_RIGHT_CORNER, assayCorner);

        JPanel filesCorner = new JPanel();

        filesCorner.setBackground(filesTable.getTableHeader().getBackground());

        filesTableScrollPane.setCorner(ScrollPaneConstants.UPPER_RIGHT_CORNER, filesCorner);

        projectsTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        assaysTable.getColumn("Accession").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        filesTable.getColumn("Assay").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        filesTable.getColumn("Download").setCellRenderer(new HtmlLinksRenderer(TableProperties.getSelectedRowHtmlTagFontColor(), TableProperties.getNotSelectedRowHtmlTagFontColor()));

        filesTable.getColumn("  ").setCellRenderer(new TrueFalseIconRenderer(

                new ImageIcon(this.getClass().getResource("/icons/accept.png")),

                null,

                "Reshakeable", null));

        projectsTableToolTips = new ArrayList<String>();

        projectsTableToolTips.add(null);

        projectsTableToolTips.add("Project Accession Number");

        projectsTableToolTips.add("Project Title");

        projectsTableToolTips.add("Species");

        projectsTableToolTips.add("Tissue Types");

        projectsTableToolTips.add("Post-Translational Modifications");

        projectsTableToolTips.add("Instruments");

        projectsTableToolTips.add("Number of Assays");

        projectsTableToolTips.add("Project Type");

        projectsTableToolTips.add("Publication Date (yyyy-mm-dd)");

        assaysTableToolTips = new ArrayList<String>();

        assaysTableToolTips.add(null);

        assaysTableToolTips.add("Assay Accession Number");

        assaysTableToolTips.add("Assay Title");

        assaysTableToolTips.add("Species");

        assaysTableToolTips.add("Sample Details");

        assaysTableToolTips.add("Post-Translational Modifications");

        assaysTableToolTips.add("Diseases");

        assaysTableToolTips.add("Number of Proteins");

        assaysTableToolTips.add("Number of Peptides");

        assaysTableToolTips.add("Number of Spectra");

        filesTableToolTips = new ArrayList<String>();

        filesTableToolTips.add(null);

        filesTableToolTips.add("Assay Accession Numbers");

        filesTableToolTips.add("File Type");

        filesTableToolTips.add("File");

        filesTableToolTips.add("Download File");

        filesTableToolTips.add("File Size");

        filesTableToolTips.add("Reshakeable");

        ((TitledBorder) projectsPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "PRIDE Projects");

        ((TitledBorder) assaysPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Assays");

        ((TitledBorder) filesPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Files");

        reshakableCheckBoxActionPerformed(null);

    }

    /**

     * Returns the projects table.

     *

     * @return the projects table

     */

    public JTable getProjectsTable() {

        return projectsTable;

    }

    /**

     * Returns a reference to the main GUI.

     *

     * @return a reference to the main GUI

     */

    public PeptideShakerGUI getPeptideShakerGUI() {

        return peptideShakerGUI;

    }

    /**

     * Get the private project details from the user.

     */

    private void getPrivateProjectDetails() {

        PridePrivateDataDialog pridePrivateDataDialog = new PridePrivateDataDialog(this, true);