package com.compomics.util.gui.parameters.identification_parameters.algorithm_settings;
import com.compomics.util.examples.BareBonesBrowserLaunch;
import com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter;
import com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters;
import com.compomics.util.gui.GuiUtilities;
import com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog;
import java.awt.Dialog;
import javax.swing.SwingConstants;
/**
* Dialog for editing the DirecTag advanced settings.
*
* @author Harald Barsnes
*/
public class DirecTagSettingsDialog extends javax.swing.JDialog implements AlgorithmSettingsDialog {
/**
* True if the dialog was canceled by the user.
*/
private boolean canceled = false;
/**
* Boolean indicating whether the settings can be edited by the user.
*/
private boolean editable;
/**
* Creates a new DirecTagSettingsDialog with a frame as owner.
*
* @param parent the parent frame
* @param direcTagParameters the DirecTag parameters
* @param editable boolean indicating whether the settings can be edited by
* the user
*/
public DirecTagSettingsDialog(java.awt.Frame parent, DirecTagParameters direcTagParameters, boolean editable) {
super(parent, true);
this.editable = editable;
initComponents();
setUpGUI();
populateGUI(direcTagParameters);
setLocationRelativeTo(parent);
setVisible(true);
}
/**
* Creates a new DirecTagSettingsDialog with a dialog as owner.
*
* @param owner the dialog owner
* @param parent the parent frame
* @param direcTagParameters the DirecTag parameters
* @param editable boolean indicating whether the settings can be edited by
* the user
*/
public DirecTagSettingsDialog(Dialog owner, java.awt.Frame parent, DirecTagParameters direcTagParameters, boolean editable) {
super(owner, true);
this.editable = editable;
initComponents();
setUpGUI();
populateGUI(direcTagParameters);
setLocationRelativeTo(owner);
setVisible(true);
}
/**
* Sets up the GUI.
*/
private void setUpGUI() {
duplicateSpectraPerChargeCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
adjustPrecursorMassCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
useSpectrumChargeStateCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
tagLengthTextField.setEditable(editable);
tagLengthTextField.setEnabled(editable);
numVariableModsTextField.setEditable(editable);
numVariableModsTextField.setEnabled(editable);
numberOfChargeStatesTextField.setEditable(editable);
numberOfChargeStatesTextField.setEnabled(editable);
duplicateSpectraPerChargeCmb.setEnabled(editable);
isotopeToleranceTextField.setEditable(editable);
isotopeToleranceTextField.setEnabled(editable);
deisptopingModeTextField.setEditable(editable);
deisptopingModeTextField.setEnabled(editable);
numberOfIntensityClassesTextField.setEditable(editable);
numberOfIntensityClassesTextField.setEnabled(editable);
outputSuffixTextField.setEditable(editable);
outputSuffixTextField.setEnabled(editable);
ticCutoffTextField.setEditable(editable);
ticCutoffTextField.setEnabled(editable);
complementToleranceTextField.setEditable(editable);
complementToleranceTextField.setEnabled(editable);
precursorAdjustmentStepTextField.setEditable(editable);
precursorAdjustmentStepTextField.setEnabled(editable);
minPrecursorAdjustmentTextField.setEditable(editable);
minPrecursorAdjustmentTextField.setEnabled(editable);
maxPrecursorAdjustmentTextField.setEditable(editable);
maxPrecursorAdjustmentTextField.setEnabled(editable);
intensityScoreWeightTextField.setEditable(editable);
intensityScoreWeightTextField.setEnabled(editable);
mzFidelityScoreWeightTextField.setEditable(editable);
mzFidelityScoreWeightTextField.setEnabled(editable);
complementScoreWeightTextField.setEditable(editable);
complementScoreWeightTextField.setEnabled(editable);
}
/**
* Populates the GUI using the given settings.
*
* @param direcTagParameters the search parameters
*/
private void populateGUI(DirecTagParameters direcTagParameters) {
tagLengthTextField.setText(String.valueOf(direcTagParameters.getTagLength()));
numVariableModsTextField.setText(String.valueOf(direcTagParameters.getMaxDynamicMods()));
numberOfChargeStatesTextField.setText(String.valueOf(direcTagParameters.getNumChargeStates()));
if (direcTagParameters.isDuplicateSpectra()) {
duplicateSpectraPerChargeCmb.setSelectedIndex(0);
} else {
duplicateSpectraPerChargeCmb.setSelectedIndex(1);
}
deisptopingModeTextField.setText(String.valueOf(direcTagParameters.getDeisotopingMode()));
isotopeToleranceTextField.setText(String.valueOf(direcTagParameters.getIsotopeMzTolerance()));
numberOfIntensityClassesTextField.setText(String.valueOf(direcTagParameters.getNumIntensityClasses()));
outputSuffixTextField.setText(String.valueOf(direcTagParameters.getOutputSuffix()));
maxPeakCountTextField.setText(String.valueOf(direcTagParameters.getMaxPeakCount()));
ticCutoffTextField.setText(String.valueOf(direcTagParameters.getTicCutoffPercentage()));
complementToleranceTextField.setText(String.valueOf(direcTagParameters.getComplementMzTolerance()));
precursorAdjustmentStepTextField.setText(String.valueOf(direcTagParameters.getPrecursorAdjustmentStep()));
minPrecursorAdjustmentTextField.setText(String.valueOf(direcTagParameters.getMinPrecursorAdjustment()));
maxPrecursorAdjustmentTextField.setText(String.valueOf(direcTagParameters.getMaxPrecursorAdjustment()));
intensityScoreWeightTextField.setText(String.valueOf(direcTagParameters.getIntensityScoreWeight()));
mzFidelityScoreWeightTextField.setText(String.valueOf(direcTagParameters.getMzFidelityScoreWeight()));
complementScoreWeightTextField.setText(String.valueOf(direcTagParameters.getComplementScoreWeight()));
maxTagCountSpinner.setValue(direcTagParameters.getMaxTagCount());
if (direcTagParameters.isAdjustPrecursorMass()) {
adjustPrecursorMassCmb.setSelectedIndex(0);
} else {
adjustPrecursorMassCmb.setSelectedIndex(1);
}
if (direcTagParameters.isUseChargeStateFromMS()) {
useSpectrumChargeStateCmb.setSelectedIndex(0);
} else {
useSpectrumChargeStateCmb.setSelectedIndex(1);
}
}
/**
* 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();
okButton = new javax.swing.JButton();
directTagPanel = new javax.swing.JPanel();
numberOfChargeStatesLabel = new javax.swing.JLabel();
duplicateSpectraLabel = new javax.swing.JLabel();
deisotopingModeLabel = new javax.swing.JLabel();
isotopeToleranceLabel = new javax.swing.JLabel();
complementToleranceLabel = new javax.swing.JLabel();
tagLengthLabel = new javax.swing.JLabel();
numVariableModsLabel = new javax.swing.JLabel();
intensityScoreWeightLabel = new javax.swing.JLabel();
mzFidelityScoreWeightLabel = new javax.swing.JLabel();
complementScoreWeightLabel = new javax.swing.JLabel();
numberOfChargeStatesTextField = new javax.swing.JTextField();
ticCutoffLabel = new javax.swing.JLabel();
maxPeakCountTextField = new javax.swing.JTextField();
maxPeakCountLabel = new javax.swing.JLabel();
numberOfIntensityClassesTextField = new javax.swing.JTextField();
numberOfIntensityClassesLabel = new javax.swing.JLabel();
minPrecursorAdjustmentLabel = new javax.swing.JLabel();
minPrecursorAdjustmentTextField = new javax.swing.JTextField();
maxPrecursorAdjustmentLabel = new javax.swing.JLabel();
maxPrecursorAdjustmentTextField = new javax.swing.JTextField();
precursorAdjustmentStepLabel = new javax.swing.JLabel();
precursorAdjustmentStepTextField = new javax.swing.JTextField();
outputSuffixLabel = new javax.swing.JLabel();
outputSuffixTextField = new javax.swing.JTextField();
duplicateSpectraPerChargeCmb = new javax.swing.JComboBox();
deisptopingModeTextField = new javax.swing.JTextField();
isotopeToleranceTextField = new javax.swing.JTextField();
complementToleranceTextField = new javax.swing.JTextField();
tagLengthTextField = new javax.swing.JTextField();
numVariableModsTextField = new javax.swing.JTextField();
intensityScoreWeightTextField = new javax.swing.JTextField();
mzFidelityScoreWeightTextField = new javax.swing.JTextField();
complementScoreWeightTextField = new javax.swing.JTextField();
ticCutoffTextField = new javax.swing.JTextField();
maxTagCountLabel = new javax.swing.JLabel();
maxTagCountSpinner = new javax.swing.JSpinner();
adjustPrecursorMassLabel = new javax.swing.JLabel();
adjustPrecursorMassCmb = new javax.swing.JComboBox();
useSpectrumChargeStateLabel = new javax.swing.JLabel();
useSpectrumChargeStateCmb = new javax.swing.JComboBox();
cancelButton = new javax.swing.JButton();
openDialogHelpJButton = new javax.swing.JButton();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
setTitle("DirecTag Advanced Settings");
addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent evt) {
formWindowClosing(evt);
}
});
backgroundPanel.setBackground(new java.awt.Color(230, 230, 230));
okButton.setText("OK");
okButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
okButtonActionPerformed(evt);
}
});
directTagPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("DirecTag Settings"));
directTagPanel.setOpaque(false);
numberOfChargeStatesLabel.setText("Number of Charge States");
duplicateSpectraLabel.setText("Duplicate Spectra per Charge");
deisotopingModeLabel.setText("Deisptoping Mode");
isotopeToleranceLabel.setText("Isotope MZ Tolerance (Da)");
complementToleranceLabel.setText("Complement MZ Tolerance (Da)");
tagLengthLabel.setText("Tag Length");
numVariableModsLabel.setText("Max Number of Variable PTMs");
intensityScoreWeightLabel.setText("Intensity Score Weight");
mzFidelityScoreWeightLabel.setText("MZ Fidelity Score Weight");
complementScoreWeightLabel.setText("Complement Score Weight");
numberOfChargeStatesTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
numberOfChargeStatesTextField.setText("3");
numberOfChargeStatesTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyPressed(java.awt.event.KeyEvent evt) {
numberOfChargeStatesTextFieldKeyPressed(evt);
}
});
ticCutoffLabel.setText("TIC Cutoff Percentage");
maxPeakCountTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
maxPeakCountTextField.setText("400");
maxPeakCountTextField.setEnabled(false);
maxPeakCountTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
maxPeakCountTextFieldKeyReleased(evt);
}
});
maxPeakCountLabel.setText("Max Peak Count");
numberOfIntensityClassesTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
numberOfIntensityClassesTextField.setText("3");
numberOfIntensityClassesTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
numberOfIntensityClassesTextFieldKeyReleased(evt);
}
});
numberOfIntensityClassesLabel.setText("Number of Intensity Classes");
minPrecursorAdjustmentLabel.setText("Min Precursor Adjustment");
minPrecursorAdjustmentTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
minPrecursorAdjustmentTextField.setText("-2.5");
minPrecursorAdjustmentTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
minPrecursorAdjustmentTextFieldKeyReleased(evt);
}
});
maxPrecursorAdjustmentLabel.setText("Max Precursor Adjustment");
maxPrecursorAdjustmentTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
maxPrecursorAdjustmentTextField.setText("2.5");
maxPrecursorAdjustmentTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
maxPrecursorAdjustmentTextFieldKeyReleased(evt);
}
});
precursorAdjustmentStepLabel.setText("Precursor Adjustment Step");
precursorAdjustmentStepTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
precursorAdjustmentStepTextField.setText("0.1");
precursorAdjustmentStepTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
precursorAdjustmentStepTextFieldKeyReleased(evt);
}
});
outputSuffixLabel.setText("Output Suffix");
outputSuffixTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
outputSuffixTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
outputSuffixTextFieldKeyReleased(evt);
}
});
duplicateSpectraPerChargeCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
deisptopingModeTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
deisptopingModeTextField.setText("0");
deisptopingModeTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
deisptopingModeTextFieldKeyReleased(evt);
}
});
isotopeToleranceTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
isotopeToleranceTextField.setText("0.25");
isotopeToleranceTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
isotopeToleranceTextFieldKeyReleased(evt);
}
});
complementToleranceTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
complementToleranceTextField.setText("0.5");
complementToleranceTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
complementToleranceTextFieldKeyReleased(evt);
}
});
tagLengthTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
tagLengthTextField.setText("3");
tagLengthTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
tagLengthTextFieldKeyReleased(evt);
}
});
numVariableModsTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
numVariableModsTextField.setText("2");
numVariableModsTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
numVariableModsTextFieldKeyReleased(evt);
}
});
intensityScoreWeightTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
intensityScoreWeightTextField.setText("1");
intensityScoreWeightTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
intensityScoreWeightTextFieldKeyReleased(evt);
}
});
mzFidelityScoreWeightTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
mzFidelityScoreWeightTextField.setText("1");
mzFidelityScoreWeightTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
mzFidelityScoreWeightTextFieldKeyReleased(evt);
}
});
complementScoreWeightTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
complementScoreWeightTextField.setText("1");
complementScoreWeightTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
complementScoreWeightTextFieldKeyReleased(evt);
}
});
ticCutoffTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
ticCutoffTextField.setText("85");
ticCutoffTextField.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
ticCutoffTextFieldKeyReleased(evt);
}
});
maxTagCountLabel.setText("Max Tag Count");
maxTagCountSpinner.setModel(new javax.swing.SpinnerNumberModel(10, 1, 2000, 1));
adjustPrecursorMassLabel.setText("Adjust Precursor Mass");
adjustPrecursorMassCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
adjustPrecursorMassCmb.setEnabled(false);
useSpectrumChargeStateLabel.setText("Use Spectrum Charge State");
useSpectrumChargeStateCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
javax.swing.GroupLayout directTagPanelLayout = new javax.swing.GroupLayout(directTagPanel);
directTagPanel.setLayout(directTagPanelLayout);
directTagPanelLayout.setHorizontalGroup(
directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addGap(198, 198, 198)
.addComponent(tagLengthTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))
.addComponent(tagLengthLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addComponent(numVariableModsLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(numVariableModsTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(directTagPanelLayout.createSequentialGroup()
.addComponent(numberOfChargeStatesLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(numberOfChargeStatesTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addComponent(ticCutoffLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(ticCutoffTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(javax.swing.GroupLayout.Alignment.LEADING, directTagPanelLayout.createSequentialGroup()
.addComponent(precursorAdjustmentStepLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(precursorAdjustmentStepTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(directTagPanelLayout.createSequentialGroup()
.addComponent(complementToleranceLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(complementToleranceTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))))
.addGroup(directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, directTagPanelLayout.createSequentialGroup()
.addGap(0, 0, Short.MAX_VALUE)
.addComponent(duplicateSpectraLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(duplicateSpectraPerChargeCmb, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(52, 52, 52))
.addGroup(directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addComponent(isotopeToleranceLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(isotopeToleranceTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, directTagPanelLayout.createSequentialGroup()
.addComponent(numberOfIntensityClassesLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(numberOfIntensityClassesTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, directTagPanelLayout.createSequentialGroup()
.addComponent(outputSuffixLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(outputSuffixTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, directTagPanelLayout.createSequentialGroup()
.addComponent(deisotopingModeLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(deisptopingModeTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addGroup(directTagPanelLayout.createSequentialGroup()
.addComponent(maxPeakCountLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(maxPeakCountTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(directTagPanelLayout.createSequentialGroup()
.addComponent(maxTagCountLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(maxTagCountSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)))
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(minPrecursorAdjustmentLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(maxPrecursorAdjustmentLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGap(18, 18, 18)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(minPrecursorAdjustmentTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(maxPrecursorAdjustmentTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, directTagPanelLayout.createSequentialGroup()
.addComponent(complementScoreWeightLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(complementScoreWeightTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(mzFidelityScoreWeightLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(intensityScoreWeightLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGap(18, 18, 18)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(intensityScoreWeightTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(mzFidelityScoreWeightTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(adjustPrecursorMassLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(useSpectrumChargeStateLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGap(18, 18, 18)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(useSpectrumChargeStateCmb, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(adjustPrecursorMassCmb, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE))))))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
directTagPanelLayout.setVerticalGroup(
directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(ticCutoffTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(ticCutoffLabel))
.addGap(6, 6, 6)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(complementToleranceLabel)
.addComponent(complementToleranceTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(precursorAdjustmentStepLabel)
.addComponent(precursorAdjustmentStepTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(minPrecursorAdjustmentLabel)
.addComponent(minPrecursorAdjustmentTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(maxPrecursorAdjustmentLabel)
.addComponent(maxPrecursorAdjustmentTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(intensityScoreWeightLabel)
.addComponent(intensityScoreWeightTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addGroup(directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(tagLengthLabel)
.addComponent(tagLengthTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(numVariableModsLabel)
.addComponent(numVariableModsTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(numberOfChargeStatesLabel)
.addComponent(numberOfChargeStatesTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(duplicateSpectraLabel)
.addComponent(duplicateSpectraPerChargeCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(isotopeToleranceTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(isotopeToleranceLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(deisptopingModeTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(deisotopingModeLabel))))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(numberOfIntensityClassesTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(numberOfIntensityClassesLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(outputSuffixLabel)
.addComponent(outputSuffixTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(maxPeakCountLabel)
.addComponent(maxPeakCountTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(maxTagCountSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(maxTagCountLabel)))
.addGroup(directTagPanelLayout.createSequentialGroup()
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(mzFidelityScoreWeightLabel)
.addComponent(mzFidelityScoreWeightTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(complementScoreWeightLabel)
.addComponent(complementScoreWeightTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(adjustPrecursorMassCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(adjustPrecursorMassLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(directTagPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(useSpectrumChargeStateCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(useSpectrumChargeStateLabel))))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
cancelButton.setText("Cancel");
cancelButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cancelButtonActionPerformed(evt);
}
});
openDialogHelpJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help.GIF"))); // NOI18N
openDialogHelpJButton.setToolTipText("Open the DirecTag web page");
openDialogHelpJButton.setBorder(null);
openDialogHelpJButton.setBorderPainted(false);
openDialogHelpJButton.setContentAreaFilled(false);
openDialogHelpJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
openDialogHelpJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
openDialogHelpJButtonMouseExited(evt);
}
});
openDialogHelpJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
openDialogHelpJButtonActionPerformed(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(directTagPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addGap(10, 10, 10)
.addComponent(openDialogHelpJButton)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(okButton)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(cancelButton)))
.addContainerGap())
);
backgroundPanelLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {cancelButton, okButton});
backgroundPanelLayout.setVerticalGroup(
backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(directTagPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(openDialogHelpJButton)
.addComponent(okButton)
.addComponent(cancelButton))
.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.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
pack();
}// </editor-fold>//GEN-END:initComponents
/**
* Validate the settings.
*
* @param evt
*/
private void numberOfChargeStatesTextFieldKeyPressed(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_numberOfChargeStatesTextFieldKeyPressed
validateParametersInput(false);
}//GEN-LAST:event_numberOfChargeStatesTextFieldKeyPressed
/**
* Validate the settings.
*
* @param evt
*/
private void maxPeakCountTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_maxPeakCountTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_maxPeakCountTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void numberOfIntensityClassesTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_numberOfIntensityClassesTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_numberOfIntensityClassesTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void minPrecursorAdjustmentTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_minPrecursorAdjustmentTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_minPrecursorAdjustmentTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void maxPrecursorAdjustmentTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_maxPrecursorAdjustmentTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_maxPrecursorAdjustmentTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void precursorAdjustmentStepTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_precursorAdjustmentStepTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_precursorAdjustmentStepTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void outputSuffixTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_outputSuffixTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_outputSuffixTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void deisptopingModeTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_deisptopingModeTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_deisptopingModeTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void isotopeToleranceTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_isotopeToleranceTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_isotopeToleranceTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void complementToleranceTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_complementToleranceTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_complementToleranceTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void tagLengthTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_tagLengthTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_tagLengthTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void numVariableModsTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_numVariableModsTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_numVariableModsTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void intensityScoreWeightTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_intensityScoreWeightTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_intensityScoreWeightTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void mzFidelityScoreWeightTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_mzFidelityScoreWeightTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_mzFidelityScoreWeightTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void complementScoreWeightTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_complementScoreWeightTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_complementScoreWeightTextFieldKeyReleased
/**
* Validate the settings.
*
* @param evt
*/
private void ticCutoffTextFieldKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_ticCutoffTextFieldKeyReleased
validateParametersInput(false);
}//GEN-LAST:event_ticCutoffTextFieldKeyReleased
/**
* Save the settings and close the dialog.
*
* @param evt
*/
private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
boolean valid = validateParametersInput(true);
if (valid) {
dispose();
}
}//GEN-LAST:event_okButtonActionPerformed
/**
* Close the dialog without saving the settings.
*
* @param evt
*/
private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
canceled = true;
dispose();
}//GEN-LAST:event_cancelButtonActionPerformed
/**
* Change the cursor into a hand cursor.
*
* @param evt
*/
private void openDialogHelpJButtonMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_openDialogHelpJButtonMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_openDialogHelpJButtonMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void openDialogHelpJButtonMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_openDialogHelpJButtonMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_openDialogHelpJButtonMouseExited
/**
* Open the DirecTag web page.
*
* @param evt
*/
private void openDialogHelpJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_openDialogHelpJButtonActionPerformed
setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag/");
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_openDialogHelpJButtonActionPerformed
/**
* Close the dialog without saving the settings.
*
* @param evt
*/
private void formWindowClosing(java.awt.event.WindowEvent evt) {//GEN-FIRST:event_formWindowClosing
cancelButtonActionPerformed(null);
}//GEN-LAST:event_formWindowClosing
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JComboBox adjustPrecursorMassCmb;
private javax.swing.JLabel adjustPrecursorMassLabel;
private javax.swing.JPanel backgroundPanel;
private javax.swing.JButton cancelButton;
private javax.swing.JLabel complementScoreWeightLabel;
private javax.swing.JTextField complementScoreWeightTextField;
private javax.swing.JLabel complementToleranceLabel;
private javax.swing.JTextField complementToleranceTextField;
private javax.swing.JLabel deisotopingModeLabel;
private javax.swing.JTextField deisptopingModeTextField;
private javax.swing.JPanel directTagPanel;
private javax.swing.JLabel duplicateSpectraLabel;
private javax.swing.JComboBox duplicateSpectraPerChargeCmb;
private javax.swing.JLabel intensityScoreWeightLabel;
private javax.swing.JTextField intensityScoreWeightTextField;
private javax.swing.JLabel isotopeToleranceLabel;
private javax.swing.JTextField isotopeToleranceTextField;
private javax.swing.JLabel maxPeakCountLabel;
private javax.swing.JTextField maxPeakCountTextField;
private javax.swing.JLabel maxPrecursorAdjustmentLabel;
private javax.swing.JTextField maxPrecursorAdjustmentTextField;
private javax.swing.JLabel maxTagCountLabel;
private javax.swing.JSpinner maxTagCountSpinner;
private javax.swing.JLabel minPrecursorAdjustmentLabel;
private javax.swing.JTextField minPrecursorAdjustmentTextField;
private javax.swing.JLabel mzFidelityScoreWeightLabel;
private javax.swing.JTextField mzFidelityScoreWeightTextField;
private javax.swing.JLabel numVariableModsLabel;
private javax.swing.JTextField numVariableModsTextField;
private javax.swing.JLabel numberOfChargeStatesLabel;
private javax.swing.JTextField numberOfChargeStatesTextField;
private javax.swing.JLabel numberOfIntensityClassesLabel;
private javax.swing.JTextField numberOfIntensityClassesTextField;
private javax.swing.JButton okButton;
private javax.swing.JButton openDialogHelpJButton;
private javax.swing.JLabel outputSuffixLabel;
private javax.swing.JTextField outputSuffixTextField;
private javax.swing.JLabel precursorAdjustmentStepLabel;
private javax.swing.JTextField precursorAdjustmentStepTextField;
private javax.swing.JLabel tagLengthLabel;
private javax.swing.JTextField tagLengthTextField;
private javax.swing.JLabel ticCutoffLabel;
private javax.swing.JTextField ticCutoffTextField;
private javax.swing.JComboBox useSpectrumChargeStateCmb;
private javax.swing.JLabel useSpectrumChargeStateLabel;
// End of variables declaration//GEN-END:variables
/**
* Inspects the parameters validity.
*
* @param showMessage if true an error messages are shown to the users
* @return a boolean indicating if the parameters are valid
*/
public boolean validateParametersInput(boolean showMessage) {
boolean valid = true;
valid = GuiUtilities.validateIntegerInput(this, tagLengthLabel, tagLengthTextField, "tag length", "Tag Length Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, numVariableModsLabel, numVariableModsTextField, "number of variable modifications", "Variable Modifications Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, numberOfChargeStatesLabel, numberOfChargeStatesTextField, "number of charge states", "Charge States Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, deisotopingModeLabel, deisptopingModeTextField, "deisotoping mode", "Deisotoping Mode Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, isotopeToleranceLabel, isotopeToleranceTextField, "isotope tolerance", "Isotope Tolerance Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, numberOfIntensityClassesLabel, numberOfIntensityClassesTextField, "number of intensity classes", "Intensity Classes Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, maxPeakCountLabel, maxPeakCountTextField, "maximum peak count", "Max Peak Count Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, ticCutoffLabel, ticCutoffTextField, "TIC cutoff", "TIC Cutoff Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, complementToleranceLabel, complementToleranceTextField, "complement tolerance", "Complement Tolerance Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, precursorAdjustmentStepLabel, precursorAdjustmentStepTextField, "precursor adjustment step", "Precursor Adjustment Step Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, minPrecursorAdjustmentLabel, minPrecursorAdjustmentTextField, "minimum precursor adjustment", "Minimum Precursor Adjustment Error", false, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, maxPrecursorAdjustmentLabel, maxPrecursorAdjustmentTextField, "maximum precursor adjustment", "Maximum Precursor Adjustment Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, intensityScoreWeightLabel, intensityScoreWeightTextField, "intensity score weight", "Intensity Score Waight Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, mzFidelityScoreWeightLabel, mzFidelityScoreWeightTextField, "mz fidelity score weight", "MZ Fidelity Score Weight Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, complementScoreWeightLabel, complementScoreWeightTextField, "complement score weight", "Complement Score Weight Error", true, showMessage, valid);
okButton.setEnabled(valid);
return valid;
}
/**
* Returns the DirecTag parameters as set by the user.
*
* @return the DirecTag parameters
*/
public DirecTagParameters getInput() {
DirecTagParameters direcTagParameters = new DirecTagParameters();
direcTagParameters.setTagLength(Integer.parseInt(tagLengthTextField.getText()));
direcTagParameters.setMaxDynamicMods(Integer.parseInt(numVariableModsTextField.getText()));
direcTagParameters.setNumChargeStates(Integer.parseInt(numberOfChargeStatesTextField.getText()));
direcTagParameters.setDuplicateSpectra(duplicateSpectraPerChargeCmb.getSelectedIndex() == 0);
direcTagParameters.setDeisotopingMode(Integer.parseInt(deisptopingModeTextField.getText()));
direcTagParameters.setIsotopeMzTolerance(Double.parseDouble(isotopeToleranceTextField.getText()));
direcTagParameters.setNumIntensityClasses(Integer.parseInt(numberOfIntensityClassesTextField.getText()));
direcTagParameters.setOutputSuffix(outputSuffixTextField.getText());
direcTagParameters.setMaxPeakCount(Integer.parseInt(maxPeakCountTextField.getText()));
direcTagParameters.setTicCutoffPercentage(Double.parseDouble(ticCutoffTextField.getText()));
direcTagParameters.setComplementMzTolerance(Double.parseDouble(complementToleranceTextField.getText()));
direcTagParameters.setPrecursorAdjustmentStep(Double.parseDouble(precursorAdjustmentStepTextField.getText()));
direcTagParameters.setMinPrecursorAdjustment(Double.parseDouble(minPrecursorAdjustmentTextField.getText()));
direcTagParameters.setMaxPrecursorAdjustment(Double.parseDouble(maxPrecursorAdjustmentTextField.getText()));
direcTagParameters.setIntensityScoreWeight(Double.parseDouble(intensityScoreWeightTextField.getText()));
direcTagParameters.setMzFidelityScoreWeight(Double.parseDouble(mzFidelityScoreWeightTextField.getText()));
direcTagParameters.setComplementScoreWeight(Double.parseDouble(complementScoreWeightTextField.getText()));
direcTagParameters.setMaxTagCount((Integer) maxTagCountSpinner.getValue());
direcTagParameters.setAdjustPrecursorMass(adjustPrecursorMassCmb.getSelectedIndex() == 0);
direcTagParameters.setUseChargeStateFromMS(useSpectrumChargeStateCmb.getSelectedIndex() == 0);
return direcTagParameters;
}
@Override
public boolean isCancelled() {
return canceled;
}
@Override
public IdentificationAlgorithmParameter getParameters() {
return getInput();
}
}