package com.compomics.util.gui.parameters.identification_parameters.algorithm_settings;
import com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter;
import com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters;
import com.compomics.util.experiment.massspectrometry.Charge;
import com.compomics.util.gui.GuiUtilities;
import com.compomics.util.gui.JOptionEditorPane;
import com.compomics.util.gui.error_handlers.HelpDialog;
import com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog;
import java.awt.Dialog;
import java.awt.Toolkit;
import javax.swing.DefaultComboBoxModel;
import javax.swing.JOptionPane;
import javax.swing.SwingConstants;
import javax.swing.SwingUtilities;
/**
* Dialog for the OMSSA specific parameters.
*
* @author Marc Vaudel
* @author Harald Barsnes
*/
public class OmssaSettingsDialog extends javax.swing.JDialog implements AlgorithmSettingsDialog {
/**
* Boolean indicating whether the used canceled the editing.
*/
private boolean cancelled = false;
/**
* Boolean indicating whether the settings can be edited by the user.
*/
private boolean editable;
/**
* Creates new form OmssaParametersDialog with a frame as owner.
*
* @param parent the parent frame
* @param omssaParameters the OMSSA parameters
* @param editable boolean indicating whether the settings can be edited by the user
*/
public OmssaSettingsDialog(java.awt.Frame parent, OmssaParameters omssaParameters, boolean editable) {
super(parent, true);
this.editable = editable;
initComponents();
setUpGui();
populateGUI(omssaParameters);
validateInput(false);
setLocationRelativeTo(parent);
setVisible(true);
}
/**
* Creates new form OmssaParametersDialog with a dialog as owner.
*
* @param owner the dialog owner
* @param parent the parent frame
* @param omssaParameters the OMSSA parameters
* @param editable boolean indicating whether the settings can be edited by the user
*/
public OmssaSettingsDialog(Dialog owner, java.awt.Frame parent, OmssaParameters omssaParameters, boolean editable) {
super(owner, true);
this.editable = editable;
initComponents();
setUpGui();
populateGUI(omssaParameters);
validateInput(false);
setLocationRelativeTo(owner);
setVisible(true);
}
/**
* Sets up the GUI.
*/
private void setUpGui() {
eliminatePrecursorCombo.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
chargeEstimationCombo.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
plusOneChargeCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
precursorScalingCombo.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
sequenceMappingCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
cleaveNterminalMethionineCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
searchPositiveIonsCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
forwardIonsFirstCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
cTermIonsCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
correlationCorrectionScoreCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
omssaOutputFormatComboBox.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
lowIntensityTxt.setEditable(editable);
lowIntensityTxt.setEnabled(editable);
highIntensityTxt.setEditable(editable);
highIntensityTxt.setEnabled(editable);
intensityIncrementTxt.setEditable(editable);
intensityIncrementTxt.setEnabled(editable);
nPeaksTxt.setEditable(editable);
nPeaksTxt.setEnabled(editable);
eliminatePrecursorCombo.setEnabled(editable);
chargeEstimationCombo.setEnabled(editable);
plusOneChargeCmb.setEnabled(editable);
fractionChargeTxt.setEditable(editable);
fractionChargeTxt.setEnabled(editable);
minPrecPerSpectrumTxt.setEditable(editable);
minPrecPerSpectrumTxt.setEnabled(editable);
precursorScalingCombo.setEnabled(editable);
sequenceMappingCmb.setEnabled(editable);
cleaveNterminalMethionineCmb.setEnabled(editable);
minPrecChargeMultipleChargedFragmentsTxt.setEditable(editable);
minPrecChargeMultipleChargedFragmentsTxt.setEnabled(editable);
neutronTxt.setEditable(editable);
neutronTxt.setEnabled(editable);
singlyChargedWindowWidthTxt.setEditable(editable);
singlyChargedWindowWidthTxt.setEnabled(editable);
doublyChargedWindowWidthTxt.setEditable(editable);
doublyChargedWindowWidthTxt.setEnabled(editable);
singlyChargedNpeaksTxt.setEditable(editable);
singlyChargedNpeaksTxt.setEnabled(editable);
doublyChargedNpeaksTxt.setEditable(editable);
doublyChargedNpeaksTxt.setEnabled(editable);
minAnnotatedPeaksTxt.setEditable(editable);
minAnnotatedPeaksTxt.setEnabled(editable);
maxLaddersTxt.setEditable(editable);
maxLaddersTxt.setEnabled(editable);
maxFragmentChargeTxt.setEditable(editable);
maxFragmentChargeTxt.setEnabled(editable);
searchPositiveIonsCmb.setEnabled(editable);
cTermIonsCmb.setEnabled(editable);
maxFragmentsPerSeriesTxt.setEditable(editable);
maxFragmentsPerSeriesTxt.setEnabled(editable);
correlationCorrectionScoreCmb.setEnabled(editable);
consecutiveIonProbabilityTxt.setEditable(editable);
consecutiveIonProbabilityTxt.setEnabled(editable);
nHitsPerSpectrumPerChargeTxt.setEditable(editable);
nHitsPerSpectrumPerChargeTxt.setEnabled(editable);
iterativeSequenceEvalueTxt.setEditable(editable);
iterativeSequenceEvalueTxt.setEnabled(editable);
iterativeSpectraEvalueTxt.setEditable(editable);
iterativeSpectraEvalueTxt.setEnabled(editable);
iterativeReplaceEvalueTxt.setEditable(editable);
iterativeReplaceEvalueTxt.setEnabled(editable);
minPepLengthTxt.setEditable(editable);
minPepLengthTxt.setEnabled(editable);
maxPepLengthTxt.setEditable(editable);
maxPepLengthTxt.setEnabled(editable);
maxEvalueTxt.setEditable(editable);
maxEvalueTxt.setEnabled(editable);
hitlistTxt.setEditable(editable);
hitlistTxt.setEnabled(editable);
omssaOutputFormatComboBox.setEnabled(editable);
}
/**
* Populates the GUI using the given settings.
*
* @param omssaParameters the parameters to display
*/
private void populateGUI(OmssaParameters omssaParameters) {
if (omssaParameters.getLowIntensityCutOff() != null) {
lowIntensityTxt.setText(omssaParameters.getLowIntensityCutOff() + "");
}
if (omssaParameters.getHighIntensityCutOff() != null) {
highIntensityTxt.setText(omssaParameters.getHighIntensityCutOff() + "");
}
if (omssaParameters.getIntensityCutOffIncrement() != null) {
intensityIncrementTxt.setText(omssaParameters.getIntensityCutOffIncrement() + "");
}
if (omssaParameters.getMinPeaks() != null) {
nPeaksTxt.setText(omssaParameters.getMinPeaks() + "");
}
if (omssaParameters.isRemovePrecursor() != null) {
if (omssaParameters.isRemovePrecursor()) {
eliminatePrecursorCombo.setSelectedIndex(0);
} else {
eliminatePrecursorCombo.setSelectedIndex(1);
}
}
if (omssaParameters.isEstimateCharge() != null) {
if (omssaParameters.isEstimateCharge()) {
chargeEstimationCombo.setSelectedIndex(0);
} else {
chargeEstimationCombo.setSelectedIndex(1);
}
}
if (omssaParameters.isDetermineChargePlusOneAlgorithmically() != null) {
if (omssaParameters.isDetermineChargePlusOneAlgorithmically()) {
plusOneChargeCmb.setSelectedIndex(0);
} else {
plusOneChargeCmb.setSelectedIndex(1);
}
}
if (omssaParameters.getFractionOfPeaksForChargeEstimation() != null) {
fractionChargeTxt.setText(omssaParameters.getFractionOfPeaksForChargeEstimation() + "");
}
if (omssaParameters.getMinPrecPerSpectrum() != null) {
minPrecPerSpectrumTxt.setText(omssaParameters.getMinPrecPerSpectrum() + "");
}
if (omssaParameters.isScalePrecursor() != null) {
if (omssaParameters.isScalePrecursor()) {
precursorScalingCombo.setSelectedIndex(0);
} else {
precursorScalingCombo.setSelectedIndex(1);
}
} else {
precursorScalingCombo.setSelectedIndex(1);
}
if (omssaParameters.isMemoryMappedSequenceLibraries() != null) {
if (omssaParameters.isMemoryMappedSequenceLibraries()) {
sequenceMappingCmb.setSelectedIndex(0);
} else {
sequenceMappingCmb.setSelectedIndex(1);
}
} else {
sequenceMappingCmb.setSelectedIndex(1);
}
if (omssaParameters.isCleaveNterMethionine() != null) {
if (omssaParameters.isCleaveNterMethionine()) {
cleaveNterminalMethionineCmb.setSelectedIndex(0);
} else {
cleaveNterminalMethionineCmb.setSelectedIndex(1);
}
} else {
cleaveNterminalMethionineCmb.setSelectedIndex(1);
}
if (omssaParameters.getMinPeptideLength() != null) {
minPepLengthTxt.setText(omssaParameters.getMinPeptideLength() + "");
}
if (omssaParameters.getMaxPeptideLength() != null) {
maxPepLengthTxt.setText(omssaParameters.getMaxPeptideLength() + "");
}
if (omssaParameters.getMaxEValue() != null) {
maxEvalueTxt.setText(omssaParameters.getMaxEValue() + "");
}
if (omssaParameters.getHitListLength() != null) {
hitlistTxt.setText(omssaParameters.getHitListLength() + "");
}
omssaOutputFormatComboBox.setSelectedItem(omssaParameters.getSelectedOutput());
if (omssaParameters.getMinimalChargeForMultipleChargedFragments() != null) {
minPrecChargeMultipleChargedFragmentsTxt.setText(omssaParameters.getMinimalChargeForMultipleChargedFragments().value + "");
}
if (omssaParameters.getNeutronThreshold() != null) {
neutronTxt.setText(omssaParameters.getNeutronThreshold() + "");
}
if (omssaParameters.getSingleChargeWindow() != null) {
singlyChargedWindowWidthTxt.setText(omssaParameters.getSingleChargeWindow() + "");
}
if (omssaParameters.getDoubleChargeWindow() != null) {
doublyChargedWindowWidthTxt.setText(omssaParameters.getDoubleChargeWindow() + "");
}
if (omssaParameters.getnPeaksInSingleChargeWindow() != null) {
singlyChargedNpeaksTxt.setText(omssaParameters.getnPeaksInSingleChargeWindow() + "");
}
if (omssaParameters.getnPeaksInDoubleChargeWindow() != null) {
doublyChargedNpeaksTxt.setText(omssaParameters.getnPeaksInDoubleChargeWindow() + "");
}
if (omssaParameters.getnAnnotatedMostIntensePeaks() != null) {
minAnnotatedMostIntensePeaksTxt.setText(omssaParameters.getnAnnotatedMostIntensePeaks() + "");
}
if (omssaParameters.getnAnnotatedMostIntensePeaks() != null) {
minAnnotatedPeaksTxt.setText(omssaParameters.getMinAnnotatedPeaks() + "");
}
if (omssaParameters.getMaxMzLadders() != null) {
maxLaddersTxt.setText(omssaParameters.getMaxMzLadders() + "");
}
if (omssaParameters.getMaxFragmentCharge() != null) {
maxFragmentChargeTxt.setText(omssaParameters.getMaxFragmentCharge() + "");
}
if (omssaParameters.isSearchPositiveIons() != null) {
if (omssaParameters.isSearchPositiveIons()) {
searchPositiveIonsCmb.setSelectedIndex(0);
} else {
searchPositiveIonsCmb.setSelectedIndex(1);
}
} else {
searchPositiveIonsCmb.setSelectedIndex(1);
}
if (omssaParameters.isSearchForwardFragmentFirst() != null) {
if (omssaParameters.isSearchForwardFragmentFirst()) {
forwardIonsFirstCmb.setSelectedIndex(0);
} else {
forwardIonsFirstCmb.setSelectedIndex(1);
}
} else {
forwardIonsFirstCmb.setSelectedIndex(1);
}
if (omssaParameters.isSearchRewindFragments() != null) {
if (omssaParameters.isSearchRewindFragments()) {
cTermIonsCmb.setSelectedIndex(0);
} else {
cTermIonsCmb.setSelectedIndex(1);
}
} else {
cTermIonsCmb.setSelectedIndex(1);
}
if (omssaParameters.getMaxFragmentPerSeries() != null) {
maxFragmentsPerSeriesTxt.setText(omssaParameters.getMaxFragmentPerSeries() + "");
}
if (omssaParameters.isUseCorrelationCorrectionScore() != null) {
if (omssaParameters.isUseCorrelationCorrectionScore()) {
correlationCorrectionScoreCmb.setSelectedIndex(0);
} else {
correlationCorrectionScoreCmb.setSelectedIndex(1);
}
} else {
correlationCorrectionScoreCmb.setSelectedIndex(1);
}
if (omssaParameters.getConsecutiveIonProbability() != null) {
consecutiveIonProbabilityTxt.setText(omssaParameters.getConsecutiveIonProbability() + "");
}
if (omssaParameters.getIterativeSequenceEvalue() != null) {
iterativeSequenceEvalueTxt.setText(omssaParameters.getIterativeSequenceEvalue() + "");
}
if (omssaParameters.getIterativeSpectrumEvalue() != null) {
iterativeSpectraEvalueTxt.setText(omssaParameters.getIterativeSpectrumEvalue() + "");
}
if (omssaParameters.getIterativeReplaceEvalue() != null) {
iterativeReplaceEvalueTxt.setText(omssaParameters.getIterativeReplaceEvalue() + "");
}
if (omssaParameters.getMaxHitsPerSpectrumPerCharge() != null) {
nHitsPerSpectrumPerChargeTxt.setText(omssaParameters.getMaxHitsPerSpectrumPerCharge() + "");
}
}
@Override
public boolean isCancelled() {
return cancelled;
}
@Override
public IdentificationAlgorithmParameter getParameters() {
return getInput();
}
/**
* Returns the user selection as OMSSA parameters object.
*
* @return the user selection
*/
public OmssaParameters getInput() {
OmssaParameters tempOmssaParameters = new OmssaParameters();
String input = lowIntensityTxt.getText().trim();
tempOmssaParameters.setLowIntensityCutOff(new Double(input));
input = highIntensityTxt.getText().trim();
tempOmssaParameters.setHighIntensityCutOff(new Double(input));
input = intensityIncrementTxt.getText().trim();
tempOmssaParameters.setIntensityCutOffIncrement(new Double(input));
input = nPeaksTxt.getText().trim();
tempOmssaParameters.setIntensityCutOffIncrement(new Double(input));
tempOmssaParameters.setRemovePrecursor(eliminatePrecursorCombo.getSelectedIndex() == 0);
tempOmssaParameters.setEstimateCharge(chargeEstimationCombo.getSelectedIndex() == 0);
tempOmssaParameters.setDetermineChargePlusOneAlgorithmically(plusOneChargeCmb.getSelectedIndex() == 0);
input = fractionChargeTxt.getText().trim();
tempOmssaParameters.setFractionOfPeaksForChargeEstimation(new Double(input));
input = minPrecPerSpectrumTxt.getText().trim();
tempOmssaParameters.setMinPrecPerSpectrum(new Integer(input));
tempOmssaParameters.setScalePrecursor(precursorScalingCombo.getSelectedIndex() == 0);
tempOmssaParameters.setMemoryMappedSequenceLibraries(sequenceMappingCmb.getSelectedIndex() == 0);
tempOmssaParameters.setCleaveNterMethionine(cleaveNterminalMethionineCmb.getSelectedIndex() == 0);
input = minPepLengthTxt.getText().trim();
if (!input.equals("")) {
tempOmssaParameters.setMinPeptideLength(new Integer(input));
}
input = maxPepLengthTxt.getText().trim();
if (!input.equals("")) {
tempOmssaParameters.setMaxPeptideLength(new Integer(input));
}
input = maxEvalueTxt.getText().trim();
tempOmssaParameters.setMaxEValue(new Double(input));
input = hitlistTxt.getText().trim();
tempOmssaParameters.setHitListLength(new Integer(input));
tempOmssaParameters.setSelectedOutput(omssaOutputFormatComboBox.getSelectedItem().toString());
input = minPrecChargeMultipleChargedFragmentsTxt.getText().trim();
int charge = new Integer(input);
tempOmssaParameters.setMinimalChargeForMultipleChargedFragments(new Charge(Charge.PLUS, charge));
input = neutronTxt.getText().trim();
tempOmssaParameters.setNeutronThreshold(new Double(input));
input = singlyChargedWindowWidthTxt.getText().trim();
tempOmssaParameters.setSingleChargeWindow(new Integer(input));
input = doublyChargedWindowWidthTxt.getText().trim();
tempOmssaParameters.setDoubleChargeWindow(new Integer(input));
input = singlyChargedNpeaksTxt.getText().trim();
tempOmssaParameters.setnPeaksInSingleChargeWindow(new Integer(input));
input = doublyChargedNpeaksTxt.getText().trim();
tempOmssaParameters.setnPeaksInDoubleChargeWindow(new Integer(input));
input = minAnnotatedMostIntensePeaksTxt.getText().trim();
tempOmssaParameters.setnAnnotatedMostIntensePeaks(new Integer(input));
input = minAnnotatedPeaksTxt.getText().trim();
tempOmssaParameters.setMinAnnotatedPeaks(new Integer(input));
input = nHitsPerSpectrumPerChargeTxt.getText().trim();
tempOmssaParameters.setMaxHitsPerSpectrumPerCharge(new Integer(input));
input = maxLaddersTxt.getText().trim();
tempOmssaParameters.setMaxMzLadders(new Integer(input));
input = maxFragmentChargeTxt.getText().trim();
tempOmssaParameters.setMaxFragmentCharge(new Integer(input));
tempOmssaParameters.setSearchPositiveIons(searchPositiveIonsCmb.getSelectedIndex() == 0);
tempOmssaParameters.setSearchForwardFragmentFirst(forwardIonsFirstCmb.getSelectedIndex() == 0);
tempOmssaParameters.setSearchRewindFragments(cTermIonsCmb.getSelectedIndex() == 0);
input = maxFragmentsPerSeriesTxt.getText().trim();
tempOmssaParameters.setMaxFragmentPerSeries(new Integer(input));
tempOmssaParameters.setUseCorrelationCorrectionScore(correlationCorrectionScoreCmb.getSelectedIndex() == 0);
input = consecutiveIonProbabilityTxt.getText().trim();
tempOmssaParameters.setConsecutiveIonProbability(new Double(input));
input = iterativeSequenceEvalueTxt.getText().trim();
tempOmssaParameters.setIterativeSequenceEvalue(new Double(input));
input = iterativeSpectraEvalueTxt.getText().trim();
tempOmssaParameters.setIterativeSpectrumEvalue(new Double(input));
input = iterativeReplaceEvalueTxt.getText().trim();
tempOmssaParameters.setIterativeReplaceEvalue(new Double(input));
return tempOmssaParameters;
}
/**
* 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();
openDialogHelpJButton = new javax.swing.JButton();
okButton = new javax.swing.JButton();
closeButton = new javax.swing.JButton();
advancedSettingsWarningLabel = new javax.swing.JLabel();
tabbedPane = new javax.swing.JTabbedPane();
spectrumProcessingPanel = new javax.swing.JPanel();
lowIntensityLbl = new javax.swing.JLabel();
highIntensityLbl = new javax.swing.JLabel();
intensityIncrementLbl = new javax.swing.JLabel();
lowIntensityTxt = new javax.swing.JTextField();
nPeaksLbl = new javax.swing.JLabel();
highIntensityTxt = new javax.swing.JTextField();
intensityIncrementTxt = new javax.swing.JTextField();
nPeaksTxt = new javax.swing.JTextField();
chargeReductionLabel = new javax.swing.JLabel();
eliminatePrecursorCombo = new javax.swing.JComboBox();
chargeEstimationCombo = new javax.swing.JComboBox();
precursorChargeEstimationLabel = new javax.swing.JLabel();
plusOneChargeCmb = new javax.swing.JComboBox();
plusOneChargeAutomaticLbl = new javax.swing.JLabel();
fractionChargeLbl = new javax.swing.JLabel();
fractionChargeTxt = new javax.swing.JTextField();
minPrecPerSpectrumLbl = new javax.swing.JLabel();
minPrecPerSpectrumTxt = new javax.swing.JTextField();
precursorMassScalingLabel = new javax.swing.JLabel();
precursorScalingCombo = new javax.swing.JComboBox();
databaseProcessingPanel = new javax.swing.JPanel();
sequenceMappingLbl = new javax.swing.JLabel();
sequenceMappingCmb = new javax.swing.JComboBox();
cleaveNterminalMethionineCmb = new javax.swing.JComboBox();
cleaveNterminalMethionineLbl = new javax.swing.JLabel();
advancedSearchSettingsPanel = new javax.swing.JPanel();
searchSettingsScrollPane = new javax.swing.JScrollPane();
searchSettingsPanel = new javax.swing.JPanel();
minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel = new javax.swing.JLabel();
minPrecChargeMultipleChargedFragmentsTxt = new javax.swing.JTextField();
neutronLbl = new javax.swing.JLabel();
neutronTxt = new javax.swing.JTextField();
singlyChargedWindowWidthLbl = new javax.swing.JLabel();
singlyChargedWindowWidthTxt = new javax.swing.JTextField();
doublyChargedWindowWidthLbl = new javax.swing.JLabel();
doublyChargedWindowWidthTxt = new javax.swing.JTextField();
singlyChargedNpeaksTxt = new javax.swing.JTextField();
singlyChargedNPeaksLbl = new javax.swing.JLabel();
doublyChargedNPeaksLbl = new javax.swing.JLabel();
doublyChargedNpeaksTxt = new javax.swing.JTextField();
minAnnotatedMostIntensePeaksLbl = new javax.swing.JLabel();
minAnnotatedMostIntensePeaksTxt = new javax.swing.JTextField();
minAnnotatedPeaksLbl = new javax.swing.JLabel();
minAnnotatedPeaksTxt = new javax.swing.JTextField();
maxLaddersLbl = new javax.swing.JLabel();
maxLaddersTxt = new javax.swing.JTextField();
maxFragmentChargeTxt = new javax.swing.JTextField();
maxFragmentChargeLbl = new javax.swing.JLabel();
searchPositiveIonsLbl = new javax.swing.JLabel();
searchPositiveIonsCmb = new javax.swing.JComboBox();
forwardIonsFirstLbl = new javax.swing.JLabel();
forwardIonsFirstCmb = new javax.swing.JComboBox();
cTermIonsLbl = new javax.swing.JLabel();
cTermIonsCmb = new javax.swing.JComboBox();
maxFragmentsPerSeriesLbl = new javax.swing.JLabel();
maxFragmentsPerSeriesTxt = new javax.swing.JTextField();
correlationCorrectionScoreCmb = new javax.swing.JComboBox();
correlationCorrectionScoreLbl = new javax.swing.JLabel();
consecutiveIonProbabilityTxt = new javax.swing.JTextField();
consecutiveIonProbabilityLbl = new javax.swing.JLabel();
nHitsPerSpectrumPerChargeLbl = new javax.swing.JLabel();
nHitsPerSpectrumPerChargeTxt = new javax.swing.JTextField();
iterativeSearchSettingsPanel = new javax.swing.JPanel();
iterativeSequenceEvalueLbl = new javax.swing.JLabel();
iterativeSequenceEvalueTxt = new javax.swing.JTextField();
iterativeSpectraEvalueLbl = new javax.swing.JLabel();
iterativeSpectraEvalueTxt = new javax.swing.JTextField();
iterativeReplaceEvalueLbl = new javax.swing.JLabel();
iterativeReplaceEvalueTxt = new javax.swing.JTextField();
semiEnzymaticParametersPanel = new javax.swing.JPanel();
maxPepLengthTxt = new javax.swing.JTextField();
peptideLengthDividerLabel1 = new javax.swing.JLabel();
minPepLengthTxt = new javax.swing.JTextField();
peptideLengthJLabel = new javax.swing.JLabel();
outputParametersPanel = new javax.swing.JPanel();
omssaOutputFormatComboBox = new javax.swing.JComboBox();
omssaOutputFormatLabel = new javax.swing.JLabel();
eValueLbl = new javax.swing.JLabel();
hitListLbl = new javax.swing.JLabel();
maxEvalueTxt = new javax.swing.JTextField();
hitlistTxt = new javax.swing.JTextField();
jSeparator1 = new javax.swing.JSeparator();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
setTitle("OMSSA Advanced Settings");
setMinimumSize(new java.awt.Dimension(600, 500));
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));
openDialogHelpJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help.GIF"))); // NOI18N
openDialogHelpJButton.setToolTipText("Help");
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);
}
});
okButton.setText("OK");
okButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
okButtonActionPerformed(evt);
}
});
closeButton.setText("Close");
closeButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
closeButtonActionPerformed(evt);
}
});
advancedSettingsWarningLabel.setText("Note: The advanced settings are for expert use only. See the help for details.");
tabbedPane.setBackground(new java.awt.Color(230, 230, 230));
tabbedPane.setOpaque(true);
spectrumProcessingPanel.setBackground(new java.awt.Color(230, 230, 230));
spectrumProcessingPanel.setPreferredSize(new java.awt.Dimension(518, 143));
lowIntensityLbl.setText("Low Intensity Cutoff (percent of most intense peak)");
highIntensityLbl.setText("High Intensity Cutoff (percent of most intense peak)");
intensityIncrementLbl.setText("Intensity Cutoff Increment");
lowIntensityTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
lowIntensityTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
lowIntensityTxtKeyReleased(evt);
}
});
nPeaksLbl.setText("Minimal Number of Peaks");
highIntensityTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
highIntensityTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
highIntensityTxtKeyReleased(evt);
}
});
intensityIncrementTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
intensityIncrementTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
intensityIncrementTxtKeyReleased(evt);
}
});
nPeaksTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
nPeaksTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
nPeaksTxtKeyReleased(evt);
}
});
chargeReductionLabel.setText("Eliminate Charge Reduced Precursors in Spectra");
eliminatePrecursorCombo.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
chargeEstimationCombo.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Use Range", "Believe Input File" }));
precursorChargeEstimationLabel.setText("Precursor Charge Estimation");
plusOneChargeCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
plusOneChargeAutomaticLbl.setText("Plus One Charge Estimated Algorithmically");
fractionChargeLbl.setText("Fraction of Precursor m/z for Charge One Estimation");
fractionChargeTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
fractionChargeTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
fractionChargeTxtKeyReleased(evt);
}
});
minPrecPerSpectrumLbl.setText("Minimal Number of Precursors per Spectrum");
minPrecPerSpectrumTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
minPrecPerSpectrumTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
minPrecPerSpectrumTxtKeyReleased(evt);
}
});
precursorMassScalingLabel.setText("Precursor Mass Scaling");
precursorScalingCombo.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
javax.swing.GroupLayout spectrumProcessingPanelLayout = new javax.swing.GroupLayout(spectrumProcessingPanel);
spectrumProcessingPanel.setLayout(spectrumProcessingPanelLayout);
spectrumProcessingPanelLayout.setHorizontalGroup(
spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(spectrumProcessingPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(intensityIncrementLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
.addComponent(nPeaksLbl, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 370, Short.MAX_VALUE)
.addComponent(chargeReductionLabel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 370, Short.MAX_VALUE))
.addComponent(highIntensityLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
.addComponent(minPrecPerSpectrumLbl, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(fractionChargeLbl, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(plusOneChargeAutomaticLbl, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(precursorChargeEstimationLabel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 370, Short.MAX_VALUE))
.addComponent(lowIntensityLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(precursorMassScalingLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(lowIntensityTxt)
.addComponent(highIntensityTxt, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 179, Short.MAX_VALUE)
.addComponent(nPeaksTxt, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 179, Short.MAX_VALUE)
.addComponent(eliminatePrecursorCombo, javax.swing.GroupLayout.Alignment.TRAILING, 0, 179, Short.MAX_VALUE)
.addComponent(chargeEstimationCombo, javax.swing.GroupLayout.Alignment.TRAILING, 0, 179, Short.MAX_VALUE)
.addComponent(plusOneChargeCmb, javax.swing.GroupLayout.Alignment.TRAILING, 0, 179, Short.MAX_VALUE)
.addComponent(fractionChargeTxt, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 179, Short.MAX_VALUE)
.addComponent(minPrecPerSpectrumTxt, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 179, Short.MAX_VALUE)
.addComponent(intensityIncrementTxt, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 179, Short.MAX_VALUE)
.addComponent(precursorScalingCombo, javax.swing.GroupLayout.Alignment.TRAILING, 0, 179, Short.MAX_VALUE))
.addGap(25, 25, 25))
);
spectrumProcessingPanelLayout.setVerticalGroup(
spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(spectrumProcessingPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(lowIntensityLbl)
.addComponent(lowIntensityTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(highIntensityLbl)
.addComponent(highIntensityTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(intensityIncrementLbl)
.addComponent(intensityIncrementTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(nPeaksLbl)
.addComponent(nPeaksTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(chargeReductionLabel)
.addComponent(eliminatePrecursorCombo, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(precursorChargeEstimationLabel)
.addComponent(chargeEstimationCombo, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(plusOneChargeAutomaticLbl)
.addComponent(plusOneChargeCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(fractionChargeLbl)
.addComponent(fractionChargeTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(minPrecPerSpectrumLbl)
.addComponent(minPrecPerSpectrumTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(precursorScalingCombo, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(precursorMassScalingLabel))
.addContainerGap(378, Short.MAX_VALUE))
);
tabbedPane.addTab("Spectrum", spectrumProcessingPanel);
databaseProcessingPanel.setBackground(new java.awt.Color(230, 230, 230));
sequenceMappingLbl.setText("Sequences Mapping in Memory");
sequenceMappingCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
cleaveNterminalMethionineCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
cleaveNterminalMethionineLbl.setText("Cleave N-terminal Methionine");
javax.swing.GroupLayout databaseProcessingPanelLayout = new javax.swing.GroupLayout(databaseProcessingPanel);
databaseProcessingPanel.setLayout(databaseProcessingPanelLayout);
databaseProcessingPanelLayout.setHorizontalGroup(
databaseProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(databaseProcessingPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(databaseProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(sequenceMappingLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(cleaveNterminalMethionineLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(databaseProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(cleaveNterminalMethionineCmb, 0, 180, Short.MAX_VALUE)
.addComponent(sequenceMappingCmb, 0, 180, Short.MAX_VALUE))
.addGap(25, 25, 25))
);
databaseProcessingPanelLayout.setVerticalGroup(
databaseProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, databaseProcessingPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(databaseProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(sequenceMappingLbl)
.addComponent(sequenceMappingCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(databaseProcessingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(cleaveNterminalMethionineLbl)
.addComponent(cleaveNterminalMethionineCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
tabbedPane.addTab("Database", databaseProcessingPanel);
advancedSearchSettingsPanel.setBackground(new java.awt.Color(230, 230, 230));
advancedSearchSettingsPanel.setPreferredSize(new java.awt.Dimension(518, 143));
searchSettingsScrollPane.setBorder(null);
searchSettingsPanel.setBackground(new java.awt.Color(230, 230, 230));
minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel.setText("Minimum Precursor Charge for Multiply Charged Fragments");
minPrecChargeMultipleChargedFragmentsTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
minPrecChargeMultipleChargedFragmentsTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
minPrecChargeMultipleChargedFragmentsTxtKeyReleased(evt);
}
});
neutronLbl.setText("Mass Threshold to Consider Exact Neutron Mass");
neutronTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
neutronTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
neutronTxtKeyReleased(evt);
}
});
singlyChargedWindowWidthLbl.setText("Singly Charged Window Width (Da)");
singlyChargedWindowWidthTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
singlyChargedWindowWidthTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
singlyChargedWindowWidthTxtKeyReleased(evt);
}
});
doublyChargedWindowWidthLbl.setText("Doubly Charged Window Width (Da)");
doublyChargedWindowWidthTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
doublyChargedWindowWidthTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
doublyChargedWindowWidthTxtKeyReleased(evt);
}
});
singlyChargedNpeaksTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
singlyChargedNpeaksTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
singlyChargedNpeaksTxtKeyReleased(evt);
}
});
singlyChargedNPeaksLbl.setText("Number of Peaks in Singly Charged Windows");
doublyChargedNPeaksLbl.setText("Number of Peaks in Doubly Charged Windows");
doublyChargedNpeaksTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
doublyChargedNpeaksTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
doublyChargedNpeaksTxtKeyReleased(evt);
}
});
minAnnotatedMostIntensePeaksLbl.setText("Minimum Annotated Peaks Among the Most Intense Ones");
minAnnotatedMostIntensePeaksTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
minAnnotatedMostIntensePeaksTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
minAnnotatedMostIntensePeaksTxtKeyReleased(evt);
}
});
minAnnotatedPeaksLbl.setText("Minimum Number of Annotated Peaks");
minAnnotatedPeaksTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
minAnnotatedPeaksTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
minAnnotatedPeaksTxtKeyReleased(evt);
}
});
maxLaddersLbl.setText("Maximum m/z Ladders");
maxLaddersTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
maxLaddersTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
maxLaddersTxtKeyReleased(evt);
}
});
maxFragmentChargeTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
maxFragmentChargeTxt.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
maxFragmentChargeTxtActionPerformed(evt);
}
});
maxFragmentChargeTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
maxFragmentChargeTxtKeyReleased(evt);
}
});
maxFragmentChargeLbl.setText("Maximum Fragment Charge");
searchPositiveIonsLbl.setText("Search Positive Ions");
searchPositiveIonsCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
forwardIonsFirstLbl.setText("Search First Forward Ion (b1)");
forwardIonsFirstCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
cTermIonsLbl.setText("Search Rewind (C-terminal) Ions");
cTermIonsCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
maxFragmentsPerSeriesLbl.setText("Maximum Fragments per Series");
maxFragmentsPerSeriesTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
maxFragmentsPerSeriesTxt.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
maxFragmentsPerSeriesTxtActionPerformed(evt);
}
});
maxFragmentsPerSeriesTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
maxFragmentsPerSeriesTxtKeyReleased(evt);
}
});
correlationCorrectionScoreCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
correlationCorrectionScoreLbl.setText("Use Correlation Correction Score");
consecutiveIonProbabilityTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
consecutiveIonProbabilityTxt.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
consecutiveIonProbabilityTxtActionPerformed(evt);
}
});
consecutiveIonProbabilityTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
consecutiveIonProbabilityTxtKeyReleased(evt);
}
});
consecutiveIonProbabilityLbl.setText("Consecutive Ion Probability");
nHitsPerSpectrumPerChargeLbl.setText("Number of Hits per Spectrum per Charge");
nHitsPerSpectrumPerChargeTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
nHitsPerSpectrumPerChargeTxt.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
nHitsPerSpectrumPerChargeTxtActionPerformed(evt);
}
});
nHitsPerSpectrumPerChargeTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
nHitsPerSpectrumPerChargeTxtKeyReleased(evt);
}
});
javax.swing.GroupLayout searchSettingsPanelLayout = new javax.swing.GroupLayout(searchSettingsPanel);
searchSettingsPanel.setLayout(searchSettingsPanelLayout);
searchSettingsPanelLayout.setHorizontalGroup(
searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(minPrecChargeMultipleChargedFragmentsTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(neutronLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(neutronTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(singlyChargedWindowWidthLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(singlyChargedWindowWidthTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(doublyChargedWindowWidthLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(doublyChargedWindowWidthTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(singlyChargedNPeaksLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(singlyChargedNpeaksTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(doublyChargedNPeaksLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(doublyChargedNpeaksTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(minAnnotatedMostIntensePeaksLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(minAnnotatedMostIntensePeaksTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(minAnnotatedPeaksLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(minAnnotatedPeaksTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(maxLaddersLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(maxLaddersTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(maxFragmentChargeLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(searchPositiveIonsLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(searchPositiveIonsCmb, 0, 180, Short.MAX_VALUE)
.addComponent(maxFragmentChargeTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE)))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(forwardIonsFirstLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(forwardIonsFirstCmb, 0, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(cTermIonsLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(cTermIonsCmb, 0, 180, Short.MAX_VALUE))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, searchSettingsPanelLayout.createSequentialGroup()
.addComponent(maxFragmentsPerSeriesLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(maxFragmentsPerSeriesTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, searchSettingsPanelLayout.createSequentialGroup()
.addComponent(correlationCorrectionScoreLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(correlationCorrectionScoreCmb, 0, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(consecutiveIonProbabilityLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(consecutiveIonProbabilityTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addComponent(nHitsPerSpectrumPerChargeLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(nHitsPerSpectrumPerChargeTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE))
);
searchSettingsPanelLayout.setVerticalGroup(
searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(searchSettingsPanelLayout.createSequentialGroup()
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel)
.addComponent(minPrecChargeMultipleChargedFragmentsTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(neutronLbl)
.addComponent(neutronTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(singlyChargedWindowWidthLbl)
.addComponent(singlyChargedWindowWidthTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(doublyChargedWindowWidthLbl)
.addComponent(doublyChargedWindowWidthTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(singlyChargedNPeaksLbl)
.addComponent(singlyChargedNpeaksTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(doublyChargedNPeaksLbl)
.addComponent(doublyChargedNpeaksTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(minAnnotatedMostIntensePeaksLbl)
.addComponent(minAnnotatedMostIntensePeaksTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(minAnnotatedPeaksLbl)
.addComponent(minAnnotatedPeaksTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(maxLaddersLbl)
.addComponent(maxLaddersTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(maxFragmentChargeLbl)
.addComponent(maxFragmentChargeTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(searchPositiveIonsLbl)
.addComponent(searchPositiveIonsCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(forwardIonsFirstLbl)
.addComponent(forwardIonsFirstCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(cTermIonsLbl)
.addComponent(cTermIonsCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(maxFragmentsPerSeriesLbl)
.addComponent(maxFragmentsPerSeriesTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(correlationCorrectionScoreLbl)
.addComponent(correlationCorrectionScoreCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(consecutiveIonProbabilityLbl)
.addComponent(consecutiveIonProbabilityTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(searchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(nHitsPerSpectrumPerChargeLbl)
.addComponent(nHitsPerSpectrumPerChargeTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap())
);
searchSettingsScrollPane.setViewportView(searchSettingsPanel);
javax.swing.GroupLayout advancedSearchSettingsPanelLayout = new javax.swing.GroupLayout(advancedSearchSettingsPanel);
advancedSearchSettingsPanel.setLayout(advancedSearchSettingsPanelLayout);
advancedSearchSettingsPanelLayout.setHorizontalGroup(
advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(advancedSearchSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addComponent(searchSettingsScrollPane)
.addGap(25, 25, 25))
);
advancedSearchSettingsPanelLayout.setVerticalGroup(
advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(advancedSearchSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addComponent(searchSettingsScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 621, Short.MAX_VALUE)
.addContainerGap())
);
tabbedPane.addTab("Search", advancedSearchSettingsPanel);
iterativeSearchSettingsPanel.setBackground(new java.awt.Color(230, 230, 230));
iterativeSequenceEvalueLbl.setText("E-value Cutoff for Sequences (0 means all)");
iterativeSequenceEvalueTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
iterativeSequenceEvalueTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
iterativeSequenceEvalueTxtKeyReleased(evt);
}
});
iterativeSpectraEvalueLbl.setText("E-value Cutoff for Spectra (0 means all)");
iterativeSpectraEvalueTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
iterativeSpectraEvalueTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
iterativeSpectraEvalueTxtKeyReleased(evt);
}
});
iterativeReplaceEvalueLbl.setText("E-value Cutoff to Replace a Hit (0 means keep best)");
iterativeReplaceEvalueTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
iterativeReplaceEvalueTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
iterativeReplaceEvalueTxtKeyReleased(evt);
}
});
javax.swing.GroupLayout iterativeSearchSettingsPanelLayout = new javax.swing.GroupLayout(iterativeSearchSettingsPanel);
iterativeSearchSettingsPanel.setLayout(iterativeSearchSettingsPanelLayout);
iterativeSearchSettingsPanelLayout.setHorizontalGroup(
iterativeSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(iterativeSearchSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(iterativeSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(iterativeSequenceEvalueLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(iterativeSpectraEvalueLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 374, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(iterativeReplaceEvalueLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 374, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGap(0, 0, 0)
.addGroup(iterativeSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(iterativeReplaceEvalueTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE)
.addComponent(iterativeSequenceEvalueTxt, javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(iterativeSpectraEvalueTxt, javax.swing.GroupLayout.Alignment.TRAILING))
.addGap(25, 25, 25))
);
iterativeSearchSettingsPanelLayout.setVerticalGroup(
iterativeSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(iterativeSearchSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(iterativeSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(iterativeSequenceEvalueLbl)
.addComponent(iterativeSequenceEvalueTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(iterativeSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(iterativeSpectraEvalueLbl)
.addComponent(iterativeSpectraEvalueTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(iterativeSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(iterativeReplaceEvalueLbl)
.addComponent(iterativeReplaceEvalueTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
tabbedPane.addTab("Iterative Search", iterativeSearchSettingsPanel);
semiEnzymaticParametersPanel.setBackground(new java.awt.Color(230, 230, 230));
maxPepLengthTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
maxPepLengthTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
maxPepLengthTxtKeyReleased(evt);
}
});
peptideLengthDividerLabel1.setText("-");
minPepLengthTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
minPepLengthTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
minPepLengthTxtKeyReleased(evt);
}
});
peptideLengthJLabel.setText("Peptide Length (min - max)");
javax.swing.GroupLayout semiEnzymaticParametersPanelLayout = new javax.swing.GroupLayout(semiEnzymaticParametersPanel);
semiEnzymaticParametersPanel.setLayout(semiEnzymaticParametersPanelLayout);
semiEnzymaticParametersPanelLayout.setHorizontalGroup(
semiEnzymaticParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, semiEnzymaticParametersPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addComponent(peptideLengthJLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(minPepLengthTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 84, Short.MAX_VALUE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(peptideLengthDividerLabel1, javax.swing.GroupLayout.PREFERRED_SIZE, 4, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(maxPepLengthTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 84, Short.MAX_VALUE)
.addGap(25, 25, 25))
);
semiEnzymaticParametersPanelLayout.setVerticalGroup(
semiEnzymaticParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(semiEnzymaticParametersPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(semiEnzymaticParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(peptideLengthJLabel)
.addComponent(minPepLengthTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(maxPepLengthTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(peptideLengthDividerLabel1))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
tabbedPane.addTab("Semi-Enzymatic", semiEnzymaticParametersPanel);
outputParametersPanel.setBackground(new java.awt.Color(230, 230, 230));
omssaOutputFormatComboBox.setModel(new DefaultComboBoxModel(OmssaParameters.getOmssaOutputTypes()));
omssaOutputFormatComboBox.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
omssaOutputFormatComboBoxActionPerformed(evt);
}
});
omssaOutputFormatLabel.setText("OMSSA Output Format");
eValueLbl.setText("E-value Cutoff");
hitListLbl.setText("Maximum HitList Length (0 means all)");
maxEvalueTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
maxEvalueTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
maxEvalueTxtKeyReleased(evt);
}
});
hitlistTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
hitlistTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
hitlistTxtKeyReleased(evt);
}
});
javax.swing.GroupLayout outputParametersPanelLayout = new javax.swing.GroupLayout(outputParametersPanel);
outputParametersPanel.setLayout(outputParametersPanelLayout);
outputParametersPanelLayout.setHorizontalGroup(
outputParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(outputParametersPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(outputParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(omssaOutputFormatLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(hitListLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(eValueLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 370, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(hitlistTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE)
.addComponent(maxEvalueTxt, javax.swing.GroupLayout.DEFAULT_SIZE, 180, Short.MAX_VALUE)
.addComponent(omssaOutputFormatComboBox, 0, 180, Short.MAX_VALUE))
.addGap(25, 25, 25))
);
outputParametersPanelLayout.setVerticalGroup(
outputParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, outputParametersPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(outputParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(eValueLbl)
.addComponent(maxEvalueTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(hitListLbl)
.addComponent(hitlistTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputParametersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(omssaOutputFormatComboBox, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(omssaOutputFormatLabel))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
tabbedPane.addTab("Output", outputParametersPanel);
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(tabbedPane)
.addComponent(jSeparator1)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addGap(10, 10, 10)
.addComponent(openDialogHelpJButton)
.addGap(18, 18, 18)
.addComponent(advancedSettingsWarningLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(okButton, javax.swing.GroupLayout.PREFERRED_SIZE, 59, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(closeButton)))
.addContainerGap())
);
backgroundPanelLayout.setVerticalGroup(
backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(tabbedPane, javax.swing.GroupLayout.DEFAULT_SIZE, 685, Short.MAX_VALUE)
.addGap(0, 0, 0)
.addComponent(jSeparator1, 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.CENTER)
.addComponent(openDialogHelpJButton)
.addComponent(advancedSettingsWarningLabel)
.addComponent(okButton)
.addComponent(closeButton))
.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 input.
*
* @param evt
*/
private void minPrecChargeMultipleChargedFragmentsTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_minPrecChargeMultipleChargedFragmentsTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_minPrecChargeMultipleChargedFragmentsTxtKeyReleased
/**
* Save the settings and close the dialog.
*
* @param evt
*/
private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
if (validateInput(true)) {
dispose();
}
}//GEN-LAST:event_okButtonActionPerformed
/**
* Close the without saving.
*
* @param evt
*/
private void closeButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_closeButtonActionPerformed
cancelled = true;
dispose();
}//GEN-LAST:event_closeButtonActionPerformed
/**
* Change the cursor to 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 help dialog.
*
* @param evt
*/
private void openDialogHelpJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_openDialogHelpJButtonActionPerformed
setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
new HelpDialog(this, getClass().getResource("/helpFiles/OmssaSettingsDialog.html"),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/help.GIF")),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/searchgui.gif")),
"SearchGUI - Help", 500, 50);
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_openDialogHelpJButtonActionPerformed
/**
* Validate the input.
*
* @param evt
*/
private void omssaOutputFormatComboBoxActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_omssaOutputFormatComboBoxActionPerformed
if (!((String) omssaOutputFormatComboBox.getSelectedItem()).equalsIgnoreCase("OMX") && this.isVisible()) {
// invoke later to give time for components to update
SwingUtilities.invokeLater(new Runnable() {
public void run() {
JOptionPane.showMessageDialog(OmssaSettingsDialog.this, JOptionEditorPane.getJOptionEditorPane(
"Note that the OMSSA " + (String) omssaOutputFormatComboBox.getSelectedItem()
+ " format is not compatible with <a href=\"http://compomics.github.io/projects/peptide-shaker.html\">PeptideShaker</a>."),
"Format Warning", JOptionPane.WARNING_MESSAGE);
}
});
}
validateInput(false);
}//GEN-LAST:event_omssaOutputFormatComboBoxActionPerformed
/**
* Validate the input.
*
* @param evt
*/
private void maxEvalueTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_maxEvalueTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_maxEvalueTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void hitlistTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_hitlistTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_hitlistTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void maxPepLengthTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_maxPepLengthTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_maxPepLengthTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void minPepLengthTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_minPepLengthTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_minPepLengthTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void iterativeSequenceEvalueTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_iterativeSequenceEvalueTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_iterativeSequenceEvalueTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void iterativeSpectraEvalueTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_iterativeSpectraEvalueTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_iterativeSpectraEvalueTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void iterativeReplaceEvalueTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_iterativeReplaceEvalueTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_iterativeReplaceEvalueTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void neutronTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_neutronTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_neutronTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void singlyChargedWindowWidthTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_singlyChargedWindowWidthTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_singlyChargedWindowWidthTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void doublyChargedWindowWidthTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_doublyChargedWindowWidthTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_doublyChargedWindowWidthTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void singlyChargedNpeaksTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_singlyChargedNpeaksTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_singlyChargedNpeaksTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void doublyChargedNpeaksTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_doublyChargedNpeaksTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_doublyChargedNpeaksTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void minAnnotatedMostIntensePeaksTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_minAnnotatedMostIntensePeaksTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_minAnnotatedMostIntensePeaksTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void minAnnotatedPeaksTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_minAnnotatedPeaksTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_minAnnotatedPeaksTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void maxLaddersTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_maxLaddersTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_maxLaddersTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void maxFragmentChargeTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_maxFragmentChargeTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_maxFragmentChargeTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void maxFragmentChargeTxtActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_maxFragmentChargeTxtActionPerformed
validateInput(false);
}//GEN-LAST:event_maxFragmentChargeTxtActionPerformed
/**
* Validate the input.
*
* @param evt
*/
private void maxFragmentsPerSeriesTxtActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_maxFragmentsPerSeriesTxtActionPerformed
validateInput(false);
}//GEN-LAST:event_maxFragmentsPerSeriesTxtActionPerformed
/**
* Validate the input.
*
* @param evt
*/
private void maxFragmentsPerSeriesTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_maxFragmentsPerSeriesTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_maxFragmentsPerSeriesTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void consecutiveIonProbabilityTxtActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_consecutiveIonProbabilityTxtActionPerformed
validateInput(false);
}//GEN-LAST:event_consecutiveIonProbabilityTxtActionPerformed
/**
* Validate the input.
*
* @param evt
*/
private void consecutiveIonProbabilityTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_consecutiveIonProbabilityTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_consecutiveIonProbabilityTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void minPrecPerSpectrumTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_minPrecPerSpectrumTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_minPrecPerSpectrumTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void fractionChargeTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_fractionChargeTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_fractionChargeTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void nPeaksTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_nPeaksTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_nPeaksTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void intensityIncrementTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_intensityIncrementTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_intensityIncrementTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void highIntensityTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_highIntensityTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_highIntensityTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void lowIntensityTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_lowIntensityTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_lowIntensityTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void nHitsPerSpectrumPerChargeTxtActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_nHitsPerSpectrumPerChargeTxtActionPerformed
validateInput(false);
}//GEN-LAST:event_nHitsPerSpectrumPerChargeTxtActionPerformed
/**
* Validate the input.
*
* @param evt
*/
private void nHitsPerSpectrumPerChargeTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_nHitsPerSpectrumPerChargeTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_nHitsPerSpectrumPerChargeTxtKeyReleased
/**
* Close the without saving.
*
* @param evt
*/
private void formWindowClosing(java.awt.event.WindowEvent evt) {//GEN-FIRST:event_formWindowClosing
closeButtonActionPerformed(null);
}//GEN-LAST:event_formWindowClosing
/**
* 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 validateInput(boolean showMessage) {
boolean valid = true;
valid = GuiUtilities.validateDoubleInput(this, lowIntensityLbl, lowIntensityTxt, "low intensity cutoff", "Low Intensity Cutoff Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, highIntensityLbl, highIntensityTxt, "high intensity cutoff", "High Intensity Cutoff Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, intensityIncrementLbl, intensityIncrementTxt, "intensity cutoff increment", "Intensity Cutoff Increment Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, nPeaksLbl, nPeaksTxt, "number of peaks per spectrum", "Number of Peaks Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, fractionChargeLbl, fractionChargeTxt, "fraction of peaks for charge estimation", "Fraction of Peaks Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, minPrecPerSpectrumLbl, minPrecPerSpectrumTxt, "number of precursor per spectrum", "Number of Precursors Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, peptideLengthJLabel, minPepLengthTxt, "minimim peptide length", "Peptide Length Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, peptideLengthJLabel, maxPepLengthTxt, "maximum peptide length", "Peptide Length Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, eValueLbl, maxEvalueTxt, "maximal e-value", "Maximum E-Value Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, hitListLbl, hitlistTxt, "hitlist length", "Hitlist Length Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, nHitsPerSpectrumPerChargeLbl, nHitsPerSpectrumPerChargeTxt, "number of hits per spectrum and per charge", "Hits per Spectrum and per Charge Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel, minPrecChargeMultipleChargedFragmentsTxt, "minimal charge to consider multiply charged fragments", "Minimal Charge for Multiple Fragments Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, neutronLbl, neutronTxt, "mass after which the exact mass of a neutron is used", "Mass for Proton Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, singlyChargedWindowWidthLbl, singlyChargedWindowWidthTxt, "size for single charge windows", "Window Size Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, doublyChargedWindowWidthLbl, doublyChargedWindowWidthTxt, "size for double charge windows", "Window Size Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, singlyChargedNPeaksLbl, singlyChargedNpeaksTxt, "number of peaks for single charge windows", "Window Number of Peaks Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, doublyChargedNPeaksLbl, doublyChargedNpeaksTxt, "number of peaks for double charge windows", "Window Number of Peaks Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, minAnnotatedMostIntensePeaksLbl, minAnnotatedMostIntensePeaksTxt, "number for the minimal number of annotated peaks among the most intense ones", "Number of Annotated Intense Peaks Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, minAnnotatedPeaksLbl, minAnnotatedPeaksTxt, "number for the minimal number of annotated peaks", "Number of Annotated Peaks Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, maxLaddersLbl, maxLaddersTxt, "number for the maximal m/z ladder size", "Ladder Size Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, maxFragmentsPerSeriesLbl, maxFragmentsPerSeriesTxt, "number for the maximal number of fragments per series", "Fragments per Series Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, consecutiveIonProbabilityLbl, consecutiveIonProbabilityTxt, "consecutive ion probability", "Consecutive Ion Probability Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, iterativeSequenceEvalueLbl, iterativeSequenceEvalueTxt, "e-value cutoff to include sequences in the iterative search", "Iterative Search E-value Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, iterativeSpectraEvalueLbl, iterativeSpectraEvalueTxt, "e-value cutoff to include spectra in the iterative search", "Iterative Search E-value Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, iterativeReplaceEvalueLbl, iterativeReplaceEvalueTxt, "e-value cutoff to replace hits in the iterative search", "Iterative Search E-value Error", true, showMessage, valid);
okButton.setEnabled(valid);
return valid;
}
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JPanel advancedSearchSettingsPanel;
private javax.swing.JLabel advancedSettingsWarningLabel;
private javax.swing.JPanel backgroundPanel;
private javax.swing.JComboBox cTermIonsCmb;
private javax.swing.JLabel cTermIonsLbl;
private javax.swing.JComboBox chargeEstimationCombo;
private javax.swing.JLabel chargeReductionLabel;
private javax.swing.JComboBox cleaveNterminalMethionineCmb;
private javax.swing.JLabel cleaveNterminalMethionineLbl;
private javax.swing.JButton closeButton;
private javax.swing.JLabel consecutiveIonProbabilityLbl;
private javax.swing.JTextField consecutiveIonProbabilityTxt;
private javax.swing.JComboBox correlationCorrectionScoreCmb;
private javax.swing.JLabel correlationCorrectionScoreLbl;
private javax.swing.JPanel databaseProcessingPanel;
private javax.swing.JLabel doublyChargedNPeaksLbl;
private javax.swing.JTextField doublyChargedNpeaksTxt;
private javax.swing.JLabel doublyChargedWindowWidthLbl;
private javax.swing.JTextField doublyChargedWindowWidthTxt;
private javax.swing.JLabel eValueLbl;
private javax.swing.JComboBox eliminatePrecursorCombo;
private javax.swing.JComboBox forwardIonsFirstCmb;
private javax.swing.JLabel forwardIonsFirstLbl;
private javax.swing.JLabel fractionChargeLbl;
private javax.swing.JTextField fractionChargeTxt;
private javax.swing.JLabel highIntensityLbl;
private javax.swing.JTextField highIntensityTxt;
private javax.swing.JLabel hitListLbl;
private javax.swing.JTextField hitlistTxt;
private javax.swing.JLabel intensityIncrementLbl;
private javax.swing.JTextField intensityIncrementTxt;
private javax.swing.JLabel iterativeReplaceEvalueLbl;
private javax.swing.JTextField iterativeReplaceEvalueTxt;
private javax.swing.JPanel iterativeSearchSettingsPanel;
private javax.swing.JLabel iterativeSequenceEvalueLbl;
private javax.swing.JTextField iterativeSequenceEvalueTxt;
private javax.swing.JLabel iterativeSpectraEvalueLbl;
private javax.swing.JTextField iterativeSpectraEvalueTxt;
private javax.swing.JSeparator jSeparator1;
private javax.swing.JLabel lowIntensityLbl;
private javax.swing.JTextField lowIntensityTxt;
private javax.swing.JTextField maxEvalueTxt;
private javax.swing.JLabel maxFragmentChargeLbl;
private javax.swing.JTextField maxFragmentChargeTxt;
private javax.swing.JLabel maxFragmentsPerSeriesLbl;
private javax.swing.JTextField maxFragmentsPerSeriesTxt;
private javax.swing.JLabel maxLaddersLbl;
private javax.swing.JTextField maxLaddersTxt;
private javax.swing.JTextField maxPepLengthTxt;
private javax.swing.JLabel minAnnotatedMostIntensePeaksLbl;
private javax.swing.JTextField minAnnotatedMostIntensePeaksTxt;
private javax.swing.JLabel minAnnotatedPeaksLbl;
private javax.swing.JTextField minAnnotatedPeaksTxt;
private javax.swing.JTextField minPepLengthTxt;
private javax.swing.JTextField minPrecChargeMultipleChargedFragmentsTxt;
private javax.swing.JLabel minPrecPerSpectrumLbl;
private javax.swing.JTextField minPrecPerSpectrumTxt;
private javax.swing.JLabel minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel;
private javax.swing.JLabel nHitsPerSpectrumPerChargeLbl;
private javax.swing.JTextField nHitsPerSpectrumPerChargeTxt;
private javax.swing.JLabel nPeaksLbl;
private javax.swing.JTextField nPeaksTxt;
private javax.swing.JLabel neutronLbl;
private javax.swing.JTextField neutronTxt;
private javax.swing.JButton okButton;
private javax.swing.JComboBox omssaOutputFormatComboBox;
private javax.swing.JLabel omssaOutputFormatLabel;
private javax.swing.JButton openDialogHelpJButton;
private javax.swing.JPanel outputParametersPanel;
private javax.swing.JLabel peptideLengthDividerLabel1;
private javax.swing.JLabel peptideLengthJLabel;
private javax.swing.JLabel plusOneChargeAutomaticLbl;
private javax.swing.JComboBox plusOneChargeCmb;
private javax.swing.JLabel precursorChargeEstimationLabel;
private javax.swing.JLabel precursorMassScalingLabel;
private javax.swing.JComboBox precursorScalingCombo;
private javax.swing.JComboBox searchPositiveIonsCmb;
private javax.swing.JLabel searchPositiveIonsLbl;
private javax.swing.JPanel searchSettingsPanel;
private javax.swing.JScrollPane searchSettingsScrollPane;
private javax.swing.JPanel semiEnzymaticParametersPanel;
private javax.swing.JComboBox sequenceMappingCmb;
private javax.swing.JLabel sequenceMappingLbl;
private javax.swing.JLabel singlyChargedNPeaksLbl;
private javax.swing.JTextField singlyChargedNpeaksTxt;
private javax.swing.JLabel singlyChargedWindowWidthLbl;
private javax.swing.JTextField singlyChargedWindowWidthTxt;
private javax.swing.JPanel spectrumProcessingPanel;
private javax.swing.JTabbedPane tabbedPane;
// End of variables declaration//GEN-END:variables
}