package eu.isas.peptideshaker.gui.preferencesdialogs;
import com.compomics.util.gui.error_handlers.HelpDialog;
import com.compomics.util.gui.renderers.AlignedListCellRenderer;
import com.compomics.util.preferences.PTMScoringPreferences;
import eu.isas.peptideshaker.gui.PeptideShakerGUI;
import eu.isas.peptideshaker.preferences.SpectrumCountingPreferences;
import java.awt.Toolkit;
import javax.swing.JOptionPane;
import javax.swing.JSpinner.NumberEditor;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
/**
* A dialog where the user can edit the PeptideShaker preferences.
*
* @author Harald Barsnes
* @author Marc Vaudel
*/
public class PreferencesDialog extends javax.swing.JDialog {
/**
* Instance of the main GUI class.
*/
private PeptideShakerGUI peptideShakerGUI;
/**
* The spectrum counting preferences.
*/
private SpectrumCountingPreferences spectrumCountingPreferences;
/**
* The PTM scoring preferences.
*/
private PTMScoringPreferences ptmScoringPreferences;
/**
* Creates a new PreferencesDialog.
*
* @param peptideShakerGUI
* @param modal
*/
public PreferencesDialog(PeptideShakerGUI peptideShakerGUI, boolean modal) {
super(peptideShakerGUI, modal);
initComponents();
this.peptideShakerGUI = peptideShakerGUI;
this.spectrumCountingPreferences = peptideShakerGUI.getSpectrumCountingPreferences();
this.ptmScoringPreferences = peptideShakerGUI.getPtmScoringPreferences();
// centrally align the spinner
((NumberEditor) nAASpinner.getEditor()).getTextField().setHorizontalAlignment(JTextField.CENTER);
// set the values
nAASpinner.setValue(peptideShakerGUI.getDisplayPreferences().getnAASurroundingPeptides());
methodCmb.setRenderer(new AlignedListCellRenderer(SwingConstants.CENTER));
probabilitsticScoreCalculationCmb.setRenderer(new AlignedListCellRenderer(SwingConstants.CENTER));
neutralLossesCmb.setRenderer(new AlignedListCellRenderer(SwingConstants.CENTER));
insertSpectrumCountingPreferences();
insertPTMScoringPreferences();
setLocationRelativeTo(peptideShakerGUI);
setVisible(true);
}
/**
* Update the GUI based on the spectrum counting preferences.
*/
private void insertSpectrumCountingPreferences() {
if (spectrumCountingPreferences.getSelectedMethod() == SpectrumCountingPreferences.SpectralCountingMethod.NSAF) {
methodCmb.setSelectedIndex(0);
} else {
methodCmb.setSelectedIndex(1);
}
if (spectrumCountingPreferences.isValidatedHits()) {
validatedCheck.setSelected(true);
} else {
validatedCheck.setSelected(false);
}
}
/**
* Updates the GUI based on the PTM scoring preferences.
*/
private void insertPTMScoringPreferences() {
if (ptmScoringPreferences.isProbabilitsticScoreCalculation()) {
probabilitsticScoreCalculationCmb.setSelectedIndex(0);
} else {
probabilitsticScoreCalculationCmb.setSelectedIndex(1);
}
if (ptmScoringPreferences.isProbabilisticScoreNeutralLosses()) {
neutralLossesCmb.setSelectedIndex(0);
} else {
neutralLossesCmb.setSelectedIndex(1);
}
flrThresholdTxt.setText(ptmScoringPreferences.getFlrThreshold() + "");
}
/**
* Verifies the input of the user.
*
* @return a boolean indicating whether the input can be parsed
*/
public boolean validateInput() {
try {
new Double(flrThresholdTxt.getText());
} catch (Exception e) {
JOptionPane.showMessageDialog(null, "Please verify the input for A-score threshold.",
"Input Error", JOptionPane.ERROR_MESSAGE);
return false;
}
return true;
}
/**
* This method is called from within the constructor to initialize the form.
* WARNING: Do NOT modify this code. The content of this method is always
* regenerated by the Form Editor.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
backgroundPanel = new javax.swing.JPanel();
optionsPanel1 = new javax.swing.JPanel();
jLabel1 = new javax.swing.JLabel();
methodCmb = new javax.swing.JComboBox();
validatedCheck = new javax.swing.JCheckBox();
optionsPanel = new javax.swing.JPanel();
surroundingAminoAcidsLabel = new javax.swing.JLabel();
nAASpinner = new javax.swing.JSpinner();
preferencesPanel = new javax.swing.JPanel();
flrLabel = new javax.swing.JLabel();
flrThresholdTxt = new javax.swing.JTextField();
neutralLossesLabel = new javax.swing.JLabel();
neutralLossesCmb = new javax.swing.JComboBox();
probalisticScoreCalculationLabel = new javax.swing.JLabel();
probabilitsticScoreCalculationCmb = new javax.swing.JComboBox();
helpJButton = new javax.swing.JButton();
okButton = new javax.swing.JButton();
cancelButton = new javax.swing.JButton();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
setTitle("Preferences");
setResizable(false);
backgroundPanel.setBackground(new java.awt.Color(230, 230, 230));
optionsPanel1.setBorder(javax.swing.BorderFactory.createTitledBorder("MS2 Quantification"));
optionsPanel1.setOpaque(false);
jLabel1.setText("Quantification Method");
methodCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "NSAF+", "emPAI" }));
validatedCheck.setText("validated");
validatedCheck.setToolTipText("Count only the validated hits");
validatedCheck.setIconTextGap(10);
validatedCheck.setOpaque(false);
javax.swing.GroupLayout optionsPanel1Layout = new javax.swing.GroupLayout(optionsPanel1);
optionsPanel1.setLayout(optionsPanel1Layout);
optionsPanel1Layout.setHorizontalGroup(
optionsPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(optionsPanel1Layout.createSequentialGroup()
.addContainerGap()
.addComponent(jLabel1, javax.swing.GroupLayout.PREFERRED_SIZE, 150, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(methodCmb, javax.swing.GroupLayout.PREFERRED_SIZE, 100, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(validatedCheck, javax.swing.GroupLayout.PREFERRED_SIZE, 95, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap(39, Short.MAX_VALUE))
);
optionsPanel1Layout.setVerticalGroup(
optionsPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(optionsPanel1Layout.createSequentialGroup()
.addContainerGap()
.addGroup(optionsPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(jLabel1)
.addComponent(methodCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(validatedCheck))
.addContainerGap(13, Short.MAX_VALUE))
);
optionsPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Peptide Sequence"));
optionsPanel.setOpaque(false);
surroundingAminoAcidsLabel.setText("Surrounding Amino Acids");
nAASpinner.setModel(new javax.swing.SpinnerNumberModel(2, 0, 5, 1));
javax.swing.GroupLayout optionsPanelLayout = new javax.swing.GroupLayout(optionsPanel);
optionsPanel.setLayout(optionsPanelLayout);
optionsPanelLayout.setHorizontalGroup(
optionsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(optionsPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(surroundingAminoAcidsLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 150, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(nAASpinner)
.addContainerGap())
);
optionsPanelLayout.setVerticalGroup(
optionsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(optionsPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(optionsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(surroundingAminoAcidsLabel)
.addComponent(nAASpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(14, Short.MAX_VALUE))
);
preferencesPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("PTM Scoring"));
preferencesPanel.setOpaque(false);
flrLabel.setText("False Localization Rate");
flrThresholdTxt.setEditable(false);
flrThresholdTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
flrThresholdTxt.setText("50");
neutralLossesLabel.setText("Neutral Losses Accounted");
neutralLossesCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
probalisticScoreCalculationLabel.setText("Probabilitstic Score");
probabilitsticScoreCalculationCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
javax.swing.GroupLayout preferencesPanelLayout = new javax.swing.GroupLayout(preferencesPanel);
preferencesPanel.setLayout(preferencesPanelLayout);
preferencesPanelLayout.setHorizontalGroup(
preferencesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(preferencesPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(preferencesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(preferencesPanelLayout.createSequentialGroup()
.addComponent(flrLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 150, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addGroup(preferencesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(neutralLossesCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(flrThresholdTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 242, Short.MAX_VALUE)
.addComponent(probabilitsticScoreCalculationCmb, javax.swing.GroupLayout.Alignment.TRAILING, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)))
.addGroup(preferencesPanelLayout.createSequentialGroup()
.addGroup(preferencesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(neutralLossesLabel)
.addComponent(probalisticScoreCalculationLabel))
.addGap(0, 0, Short.MAX_VALUE)))
.addContainerGap())
);
preferencesPanelLayout.setVerticalGroup(
preferencesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(preferencesPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(preferencesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(probalisticScoreCalculationLabel)
.addComponent(probabilitsticScoreCalculationCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGap(9, 9, 9)
.addGroup(preferencesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(flrLabel)
.addComponent(flrThresholdTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(preferencesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(neutralLossesLabel)
.addComponent(neutralLossesCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
helpJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help.GIF"))); // NOI18N
helpJButton.setToolTipText("Help");
helpJButton.setBorder(null);
helpJButton.setBorderPainted(false);
helpJButton.setContentAreaFilled(false);
helpJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
helpJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
helpJButtonMouseExited(evt);
}
});
helpJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
helpJButtonActionPerformed(evt);
}
});
okButton.setText("OK");
okButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
okButtonActionPerformed(evt);
}
});
cancelButton.setText("Cancel");
cancelButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cancelButtonActionPerformed(evt);
}
});
javax.swing.GroupLayout backgroundPanelLayout = new javax.swing.GroupLayout(backgroundPanel);
backgroundPanel.setLayout(backgroundPanelLayout);
backgroundPanelLayout.setHorizontalGroup(
backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(optionsPanel1, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addGap(10, 10, 10)
.addComponent(helpJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 23, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(okButton, javax.swing.GroupLayout.PREFERRED_SIZE, 65, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(cancelButton))
.addComponent(optionsPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(preferencesPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addContainerGap())
);
backgroundPanelLayout.setVerticalGroup(
backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(optionsPanel1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(optionsPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(preferencesPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(cancelButton)
.addComponent(okButton))
.addComponent(helpJButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addContainerGap())
);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(backgroundPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(backgroundPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
);
pack();
}// </editor-fold>//GEN-END:initComponents
/**
* Saves the setting and then closes the dialog.
*
* @param evt
*/
private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
if (validateInput()) {
// ptm thresholds
boolean ptmScoreThresholdChanged = false;
// delta score threshold
if (peptideShakerGUI.getPtmScoringPreferences().getFlrThreshold() != new Double(flrThresholdTxt.getText())) {
peptideShakerGUI.getPtmScoringPreferences().setFlrThreshold(new Double(flrThresholdTxt.getText()));
ptmScoreThresholdChanged = true;
}
if (peptideShakerGUI.getPtmScoringPreferences().isProbabilitsticScoreCalculation()&& probabilitsticScoreCalculationCmb.getSelectedIndex() != 0
|| !peptideShakerGUI.getPtmScoringPreferences().isProbabilitsticScoreCalculation() && probabilitsticScoreCalculationCmb.getSelectedIndex() != 1) {
peptideShakerGUI.getPtmScoringPreferences().setProbabilitsticScoreCalculation(probabilitsticScoreCalculationCmb.getSelectedIndex() == 0);
ptmScoreThresholdChanged = true;
}
if (peptideShakerGUI.getPtmScoringPreferences().isProbabilisticScoreNeutralLosses()&& neutralLossesCmb.getSelectedIndex() != 0
|| !peptideShakerGUI.getPtmScoringPreferences().isProbabilisticScoreNeutralLosses() && neutralLossesCmb.getSelectedIndex() != 1) {
peptideShakerGUI.getPtmScoringPreferences().setProbabilisticScoreNeutralLosses(neutralLossesCmb.getSelectedIndex() == 0);
ptmScoreThresholdChanged = true;
}
// spectrum counting
boolean spectrumCountingMethodChanged = false;
if (methodCmb.getSelectedIndex() == 0 && spectrumCountingPreferences.getSelectedMethod() != SpectrumCountingPreferences.SpectralCountingMethod.NSAF) {
spectrumCountingPreferences.setSelectedMethod(SpectrumCountingPreferences.SpectralCountingMethod.NSAF);
spectrumCountingMethodChanged = true;
} else if (methodCmb.getSelectedIndex() == 1 && spectrumCountingPreferences.getSelectedMethod() != SpectrumCountingPreferences.SpectralCountingMethod.EMPAI) {
spectrumCountingPreferences.setSelectedMethod(SpectrumCountingPreferences.SpectralCountingMethod.EMPAI);
spectrumCountingMethodChanged = true;
}
if (spectrumCountingPreferences.isValidatedHits() != validatedCheck.isSelected()) {
spectrumCountingPreferences.setValidatedHits(validatedCheck.isSelected());
spectrumCountingMethodChanged = true;
}
// surrounding amino acids
boolean numberOfSurroundingAminoAcidsChanged = false;
int selection = (Integer) nAASpinner.getValue();
if (selection != peptideShakerGUI.getDisplayPreferences().getnAASurroundingPeptides()) {
peptideShakerGUI.getDisplayPreferences().setnAASurroundingPeptides(selection);
numberOfSurroundingAminoAcidsChanged = true;
}
// update the ptm score threshold
if (ptmScoreThresholdChanged) {
//@TODO: update interface where needed?
}
// update the number of surrounding amino acids
if (numberOfSurroundingAminoAcidsChanged) {
peptideShakerGUI.updateSurroundingAminoAcids();
}
// update the spectrum counting method
if (spectrumCountingMethodChanged) {
peptideShakerGUI.setSpectrumCountingPreferences(spectrumCountingPreferences);
peptideShakerGUI.getIdentificationFeaturesGenerator().clearSpectrumCounting();
peptideShakerGUI.setUpdated(PeptideShakerGUI.OVER_VIEW_TAB_INDEX, false);
peptideShakerGUI.setUpdated(PeptideShakerGUI.STRUCTURES_TAB_INDEX, false);
peptideShakerGUI.setUpdated(PeptideShakerGUI.QC_PLOTS_TAB_INDEX, false);
peptideShakerGUI.updateTabbedPanes();
}
peptideShakerGUI.setDataSaved(false);
dispose();
}
}//GEN-LAST:event_okButtonActionPerformed
/**
* Closes the dialog.
*
* @param evt
*/
private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
dispose();
}//GEN-LAST:event_cancelButtonActionPerformed
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void helpJButtonMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_helpJButtonMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_helpJButtonMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void helpJButtonMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_helpJButtonMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_helpJButtonMouseExited
/**
* Open the help dialog.
*
* @param evt
*/
private void helpJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_helpJButtonActionPerformed
setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
new HelpDialog(peptideShakerGUI, getClass().getResource("/helpFiles/PreferencesDialog.html"),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/help.GIF")),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")),
"PeptideShaker - Help");
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_helpJButtonActionPerformed
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JPanel backgroundPanel;
private javax.swing.JButton cancelButton;
private javax.swing.JLabel flrLabel;
private javax.swing.JTextField flrThresholdTxt;
private javax.swing.JButton helpJButton;
private javax.swing.JLabel jLabel1;
private javax.swing.JComboBox methodCmb;
private javax.swing.JSpinner nAASpinner;
private javax.swing.JComboBox neutralLossesCmb;
private javax.swing.JLabel neutralLossesLabel;
private javax.swing.JButton okButton;
private javax.swing.JPanel optionsPanel;
private javax.swing.JPanel optionsPanel1;
private javax.swing.JPanel preferencesPanel;
private javax.swing.JComboBox probabilitsticScoreCalculationCmb;
private javax.swing.JLabel probalisticScoreCalculationLabel;
private javax.swing.JLabel surroundingAminoAcidsLabel;
private javax.swing.JCheckBox validatedCheck;
// End of variables declaration//GEN-END:variables
}