* The Protein Structures tab.

*

* @author Harald Barsnes

*/

    /**

     * Peptide keys that can be mapped to the current PDB file.

     */

    private ArrayList<String> peptidePdbArray;

    /**

     * Indexes for the three main data tables.

     */

    private enum TableIndex {

        PROTEIN_TABLE, PEPTIDE_TABLE, PDB_MATCHES, PDB_CHAINS

    };

    /**

     * If true, labels are shown for the modifications in the 3D structure.

     */

    private boolean showModificationLabels = true;

    /**

     * If true, the 3D model will be spinning.

     */

    private boolean spinModel = true;

    /**

     * If true the ribbon model is used.

     */

    private boolean ribbonModel = true;

    /**

     * If true the backbone model is used.

     */

    private boolean backboneModel = false;

    /**

     * The currently displayed PDB file.

     */

    private String currentlyDisplayedPdbFile;

    /**

     * A simple progress dialog.

     */

    private ProgressDialogX progressDialog;

    /**

     * The UniProt to PDB finder.

     */

    private FindPdbForUniprotAccessions uniProtPdb;

    /**

     * The PeptideShaker main frame.

     */

    private PeptideShakerGUI peptideShakerGUI;

    /**

     * The Jmol panel.

     */

    private JmolPanel jmolPanel;

    /**

     * The protein table column header tooltips.

     */

    private ArrayList<String> proteinTableToolTips;

    /**

     * The peptide table column header tooltips.

     */

    private ArrayList<String> peptideTableToolTips;

    /**

     * The PDB files table column header tooltips.

     */

    private ArrayList<String> pdbTableToolTips;

    /**

     * The PDB chains table column header tooltips.

     */

    private ArrayList<String> pdbChainsTableToolTips;

    /**

     * A mapping of the peptide table entries.

     */

    private HashMap<Integer, String> peptideTableMap = new HashMap<Integer, String>();

    /**

     * If true Jmol is currently displaying a structure.

     */

    private boolean jmolStructureShown = false;

    /**

     * The current PDB chains.

     */

    private PdbBlock[] chains;

    /**

     * The amino acid sequence of the current chain.

     */

    private String chainSequence;

    /**

     * The current protein sequence.

     */

    private String proteinSequence;

    /**

     * The sequence factory

     */

    private SequenceFactory sequenceFactory = SequenceFactory.getInstance();

    /**

     * The gene factory.

     */

    private GeneFactory geneFactory = GeneFactory.getInstance();

    /**

     * A list of proteins in the protein table.

     */

    private ArrayList<String> proteinKeys = new ArrayList<String>();

    /**

     * Creates a new ProteinPanel.

     *

     * @param peptideShakerGUI the PeptideShaker main frame

     */

    public ProteinStructurePanel(PeptideShakerGUI peptideShakerGUI) {

        initComponents();

        this.peptideShakerGUI = peptideShakerGUI;

        jmolPanel = new JmolPanel();

        pdbPanel.add(jmolPanel);

        setUpTableHeaderToolTips();

        setUpGUI();

    }

    /**

     * Set up the GUI.

     */

    private void setUpGUI() {

        proteinScrollPane.getViewport().setOpaque(false);

        peptideScrollPane.getViewport().setOpaque(false);

        pdbJScrollPane.getViewport().setOpaque(false);

        pdbChainsJScrollPane.getViewport().setOpaque(false);

        SelfUpdatingTableModel.addSortListener(proteinTable, new ProgressDialogX(peptideShakerGUI,

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

                Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")),

                true));

        // add scrolling listeners

        SelfUpdatingTableModel.addScrollListeners(proteinTable, proteinScrollPane, proteinScrollPane.getVerticalScrollBar());

        peptideTable.setAutoCreateRowSorter(true);

        setTableProperties();

    }

    /**

     * Set up the table header tooltips.

     */

    private void setUpTableHeaderToolTips() {

        proteinTableToolTips = new ArrayList<String>();

        proteinTableToolTips.add(null);

        proteinTableToolTips.add("Starred");

        proteinTableToolTips.add("Protein Inference Class");

        proteinTableToolTips.add("Protein Accession Number");

        proteinTableToolTips.add("Protein Description");

        proteinTableToolTips.add("Chromosome Number");

        proteinTableToolTips.add("Protein Sequence Coverage (%) (Confident / Doubtful / Not Validated / Possible)");

        proteinTableToolTips.add("Number of Peptides (Validated / Doubtful / Not Validated)");

        proteinTableToolTips.add("Number of Spectra (Validated / Doubtful / Not Validated)");

        proteinTableToolTips.add("MS2 Quantification");

        proteinTableToolTips.add("Protein Molecular Weight (kDa)");

        if (peptideShakerGUI.getDisplayPreferences().showScores()) {

            proteinTableToolTips.add("Protein Score");

        } else {

            proteinTableToolTips.add("Protein Confidence");

        }

        proteinTableToolTips.add("Validated");

        peptideTableToolTips = new ArrayList<String>();

        peptideTableToolTips.add(null);

        peptideTableToolTips.add("Starred");

        peptideTableToolTips.add("Protein Inference");

        peptideTableToolTips.add("Peptide Sequence");

        peptideTableToolTips.add("Peptide Start Index");

        peptideTableToolTips.add("In PDB Sequence");

        peptideTableToolTips.add("Validated");

        pdbTableToolTips = new ArrayList<String>();

        pdbTableToolTips.add(null);

        pdbTableToolTips.add("PDB Accession Number");

        pdbTableToolTips.add("PDB Title");

        pdbTableToolTips.add("Type of Structure");

        pdbTableToolTips.add("Number of Chains");