package com.compomics.util.gui.parameters.identification_parameters.algorithm_settings;
import com.compomics.util.examples.BareBonesBrowserLaunch;
import com.compomics.util.experiment.biology.PTM;
import com.compomics.util.experiment.biology.PTMFactory;
import com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter;
import com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters;
import com.compomics.util.gui.GuiUtilities;
import com.compomics.util.gui.error_handlers.HelpDialog;
import com.compomics.util.gui.ptm.ModificationsDialog;
import com.compomics.util.experiment.identification.identification_parameters.PtmSettings;
import com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog;
import java.awt.Color;
import java.awt.Dialog;
import java.awt.Frame;
import java.awt.Toolkit;
import java.awt.event.MouseEvent;
import java.util.ArrayList;
import java.util.Arrays;
import javax.swing.JColorChooser;
import javax.swing.JOptionPane;
import javax.swing.JTable;
import javax.swing.SwingConstants;
import javax.swing.table.DefaultTableModel;
import javax.swing.table.JTableHeader;
import no.uib.jsparklines.extra.NimbusCheckBoxRenderer;
import no.uib.jsparklines.renderers.JSparklinesBarChartTableCellRenderer;
import no.uib.jsparklines.renderers.JSparklinesColorTableCellRenderer;
import org.jfree.chart.plot.PlotOrientation;
/**
* Dialog for the X!Tandem specific settings.
*
* @author Marc Vaudel
* @author Harald Barsnes
*/
public class XTandemSettingsDialog extends javax.swing.JDialog implements AlgorithmSettingsDialog {
/**
* The modification profile used for the search.
*/
private PtmSettings modificationProfile;
/**
* The fragment ion mass accuracy.
*/
private double fragmentIonMassAccuracyInDa;
/**
* Boolean indicating whether the used canceled the editing.
*/
private boolean cancelled = false;
/**
* The modification table column header tooltips.
*/
private ArrayList<String> modificationTableToolTips;
/**
* The post translational modifications factory.
*/
private PTMFactory ptmFactory = PTMFactory.getInstance();
/**
* Boolean indicating whether the modification profile has been changed.
* Note that it only checks if the user has made changed to the selection,
* not if the end result is different or not.
*/
private boolean modProfileChanged = false;
/**
* Boolean indicating whether the settings can be edited by the user.
*/
private boolean editable;
/**
* Creates new form XtandemParametersDialog with a frame as owner.
*
* @param parent the parent frame
* @param xtandemParameters the X!Tandem parameters
* @param modificationProfile the modification profile of the search
* @param fragmentIonMassAccuracyInDa the fragment ion mass accuracy of the
* mass spectrometer
* @param editable boolean indicating whether the settings can be edited by
* the user
*/
public XTandemSettingsDialog(java.awt.Frame parent, XtandemParameters xtandemParameters, PtmSettings modificationProfile, double fragmentIonMassAccuracyInDa, boolean editable) {
super(parent, true);
this.modificationProfile = new PtmSettings(modificationProfile);
this.fragmentIonMassAccuracyInDa = fragmentIonMassAccuracyInDa;
this.editable = editable;
initComponents();
setUpGUI();
populateGUI(xtandemParameters);
setLocationRelativeTo(parent);
setVisible(true);
}
/**
* Creates new form XtandemParametersDialog with a dialog as owner.
*
* @param owner the dialog owner
* @param parent the parent frame
* @param xtandemParameters the X!Tandem parameters
* @param modificationProfile the modification profile of the search
* @param fragmentIonMassAccuracyInDa the fragment ion mass accuracy of the
* mass spectrometer
* @param editable boolean indicating whether the settings can be edited by
* the user
*/
public XTandemSettingsDialog(Dialog owner, java.awt.Frame parent, XtandemParameters xtandemParameters, PtmSettings modificationProfile, double fragmentIonMassAccuracyInDa, boolean editable) {
super(owner, true);
this.modificationProfile = new PtmSettings(modificationProfile);
this.fragmentIonMassAccuracyInDa = fragmentIonMassAccuracyInDa;
this.editable = editable;
initComponents();
setUpGUI();
populateGUI(xtandemParameters);
setLocationRelativeTo(owner);
setVisible(true);
}
/**
* Sets up the GUI.
*/
private void setUpGUI() {
noiseSuppressionCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
quickAcetylCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
quickPyroCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
stpBiasCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
outputProteinsCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
outputSequencesCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
outputSpectraCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
outputHistogramsCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
refinementCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
unanticipatedCleavageCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
semiEnzymaticCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
potentialModificationsCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
pointMutationsCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
snapsCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
spectrumSynthesisCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
outputResultsCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
modificationTableToolTips = new ArrayList<String>();
modificationTableToolTips.add(null);
modificationTableToolTips.add("Modification Name");
modificationTableToolTips.add("Modification Mass");
modificationTableToolTips.add("Variable Refinement Modification");
modificationTableToolTips.add("Fixed Refinement Modification");
modificationsJScrollPane.getViewport().setOpaque(false);
modificationsTable.getTableHeader().setReorderingAllowed(false);
setAllModificationTableProperties();
dynamicRangeTxt.setEditable(editable);
dynamicRangeTxt.setEnabled(editable);
nPeaksTxt.setEditable(editable);
nPeaksTxt.setEnabled(editable);
minFragmentMzTxt.setEditable(editable);
minFragmentMzTxt.setEnabled(editable);
minPeaksTxt.setEditable(editable);
minPeaksTxt.setEnabled(editable);
noiseSuppressionCmb.setEnabled(editable);
minPrecMassTxt.setEditable(editable);
minPrecMassTxt.setEnabled(editable);
quickAcetylCmb.setEnabled(editable);
quickPyroCmb.setEnabled(editable);
stpBiasCmb.setEnabled(editable);
eValueTxt.setEditable(editable);
eValueTxt.setEnabled(editable);
outputProteinsCmb.setEnabled(editable);
outputSequencesCmb.setEnabled(editable);
outputSpectraCmb.setEnabled(editable);
outputHistogramsCmb.setEnabled(editable);
skylineTxt.setEditable(editable);
skylineTxt.setEnabled(editable);
refinementCmb.setEnabled(editable);
maxEValueRefineTxt.setEditable(editable);
maxEValueRefineTxt.setEnabled(editable);
unanticipatedCleavageCmb.setEnabled(editable);
semiEnzymaticCmb.setEnabled(editable);
potentialModificationsCmb.setEnabled(editable);
pointMutationsCmb.setEnabled(editable);
snapsCmb.setEnabled(editable);
spectrumSynthesisCmb.setEnabled(editable);
ptmComplexityTxt.setEnabled(editable);
}
/**
* Sets the properties of the all modification table.
*/
private void setAllModificationTableProperties() {
modificationsTable.getColumn(" ").setCellRenderer(new JSparklinesColorTableCellRenderer());
modificationsTable.getColumn(" ").setMaxWidth(35);
modificationsTable.getColumn(" ").setMinWidth(35);
modificationsTable.getColumn("Mass").setMaxWidth(100);
modificationsTable.getColumn("Mass").setMinWidth(100);
modificationsTable.getColumn("F").setCellRenderer(new NimbusCheckBoxRenderer());
modificationsTable.getColumn("V").setCellRenderer(new NimbusCheckBoxRenderer());
modificationsTable.getColumn("F").setMaxWidth(30);
modificationsTable.getColumn("F").setMinWidth(30);
modificationsTable.getColumn("V").setMaxWidth(30);
modificationsTable.getColumn("V").setMinWidth(30);
}
/**
* Populates the GUI using the given settings.
*
* @param xtandemParameters the parameters to display
*/
private void populateGUI(XtandemParameters xtandemParameters) {
if (xtandemParameters.getDynamicRange() != null) {
dynamicRangeTxt.setText(xtandemParameters.getDynamicRange() + "");
}
if (xtandemParameters.getnPeaks() != null) {
nPeaksTxt.setText(xtandemParameters.getnPeaks() + "");
}
if (xtandemParameters.getMinFragmentMz() != null) {
minFragmentMzTxt.setText(xtandemParameters.getMinFragmentMz() + "");
}
if (xtandemParameters.getMinPeaksPerSpectrum() != null) {
minPeaksTxt.setText(xtandemParameters.getMinPeaksPerSpectrum() + "");
}
if (xtandemParameters.isUseNoiseSuppression()) {
noiseSuppressionCmb.setSelectedIndex(0);
minPrecMassTxt.setEnabled(true);
} else {
noiseSuppressionCmb.setSelectedIndex(1);
minPrecMassTxt.setEnabled(false);
}
if (xtandemParameters.getMinPrecursorMass() != null) {
minPrecMassTxt.setText(xtandemParameters.getMinPrecursorMass() + "");
}
if (xtandemParameters.isProteinQuickAcetyl()) {
quickAcetylCmb.setSelectedIndex(0);
} else {
quickAcetylCmb.setSelectedIndex(1);
}
if (xtandemParameters.isQuickPyrolidone()) {
quickPyroCmb.setSelectedIndex(0);
} else {
quickPyroCmb.setSelectedIndex(1);
}
if (xtandemParameters.isStpBias()) {
stpBiasCmb.setSelectedIndex(0);
} else {
stpBiasCmb.setSelectedIndex(1);
}
if (xtandemParameters.isRefine()) {
refinementCmb.setSelectedIndex(0);
maxEValueRefineTxt.setEnabled(true);
unanticipatedCleavageCmb.setEnabled(true);
semiEnzymaticCmb.setEnabled(true);
potentialModificationsCmb.setEnabled(true);
pointMutationsCmb.setEnabled(true);
snapsCmb.setEnabled(true);
spectrumSynthesisCmb.setEnabled(true);
} else {
refinementCmb.setSelectedIndex(1);
maxEValueRefineTxt.setEnabled(false);
unanticipatedCleavageCmb.setEnabled(false);
semiEnzymaticCmb.setEnabled(false);
potentialModificationsCmb.setEnabled(false);
pointMutationsCmb.setEnabled(false);
snapsCmb.setEnabled(false);
spectrumSynthesisCmb.setEnabled(false);
}
if (xtandemParameters.getMaximumExpectationValueRefinement() != null) {
maxEValueRefineTxt.setText(xtandemParameters.getMaximumExpectationValueRefinement() + "");
}
if (xtandemParameters.isRefineUnanticipatedCleavages()) {
unanticipatedCleavageCmb.setSelectedIndex(0);
} else {
unanticipatedCleavageCmb.setSelectedIndex(1);
}
if (xtandemParameters.isRefineSemi()) {
semiEnzymaticCmb.setSelectedIndex(0);
} else {
semiEnzymaticCmb.setSelectedIndex(1);
}
if (xtandemParameters.isPotentialModificationsForFullRefinment()) {
potentialModificationsCmb.setSelectedIndex(0);
} else {
potentialModificationsCmb.setSelectedIndex(1);
}
if (xtandemParameters.isRefinePointMutations()) {
pointMutationsCmb.setSelectedIndex(0);
} else {
pointMutationsCmb.setSelectedIndex(1);
}
if (xtandemParameters.isRefineSnaps()) {
snapsCmb.setSelectedIndex(0);
} else {
snapsCmb.setSelectedIndex(1);
}
if (xtandemParameters.isRefineSpectrumSynthesis()) {
spectrumSynthesisCmb.setSelectedIndex(0);
} else {
spectrumSynthesisCmb.setSelectedIndex(1);
}
if (xtandemParameters.getMaxEValue() != null) {
eValueTxt.setText(xtandemParameters.getMaxEValue() + "");
}
if (xtandemParameters.isOutputProteins()) {
outputProteinsCmb.setSelectedIndex(0);
outputSequencesCmb.setEnabled(true);
if (xtandemParameters.isOutputSequences()) {
outputSequencesCmb.setSelectedIndex(0);
} else {
outputSequencesCmb.setSelectedIndex(1);
}
} else {
outputProteinsCmb.setSelectedIndex(1);
outputSequencesCmb.setEnabled(false);
outputSequencesCmb.setSelectedIndex(1);
}
outputResultsCmb.setSelectedItem(xtandemParameters.getOutputResults());
if (xtandemParameters.isOutputSpectra()) {
outputSpectraCmb.setSelectedIndex(0);
} else {
outputSpectraCmb.setSelectedIndex(1);
}
if (xtandemParameters.isOutputHistograms()) {
outputHistogramsCmb.setSelectedIndex(0);
} else {
outputHistogramsCmb.setSelectedIndex(1);
}
if (xtandemParameters.getSkylinePath() != null) {
skylineTxt.setText(xtandemParameters.getSkylinePath() + "");
}
ptmComplexityTxt.setText(xtandemParameters.getProteinPtmComplexity() + "");
// load the ptms
updateModificationList();
}
@Override
public boolean isCancelled() {
return cancelled;
}
@Override
public IdentificationAlgorithmParameter getParameters() {
return getInput();
}
/**
* Returns the user selection as X!tandem parameters object.
*
* @return the user selection
*/
public XtandemParameters getInput() {
XtandemParameters result = new XtandemParameters();
String input = dynamicRangeTxt.getText().trim();
if (!input.equals("")) {
result.setDynamicRange(new Double(input));
}
input = nPeaksTxt.getText().trim();
if (!input.equals("")) {
result.setnPeaks(new Integer(input));
}
input = minFragmentMzTxt.getText().trim();
if (!input.equals("")) {
result.setMinFragmentMz(new Double(input));
}
input = minPeaksTxt.getText().trim();
if (!input.equals("")) {
result.setMinPeaksPerSpectrum(new Integer(input));
}
result.setUseNoiseSuppression(noiseSuppressionCmb.getSelectedIndex() == 0);
input = minPrecMassTxt.getText().trim();
if (!input.equals("")) {
result.setMinPrecursorMass(new Double(input));
}
result.setProteinQuickAcetyl(quickAcetylCmb.getSelectedIndex() == 0);
result.setQuickPyrolidone(quickPyroCmb.getSelectedIndex() == 0);
result.setStpBias(stpBiasCmb.getSelectedIndex() == 0);
result.setRefine(refinementCmb.getSelectedIndex() == 0);
input = maxEValueRefineTxt.getText().trim();
if (!input.equals("")) {
result.setMaximumExpectationValueRefinement(new Double(input));
}
result.setRefineUnanticipatedCleavages(unanticipatedCleavageCmb.getSelectedIndex() == 0);
result.setRefineSemi(semiEnzymaticCmb.getSelectedIndex() == 0);
result.setPotentialModificationsForFullRefinment(potentialModificationsCmb.getSelectedIndex() == 0);
result.setRefinePointMutations(pointMutationsCmb.getSelectedIndex() == 0);
result.setRefineSnaps(snapsCmb.getSelectedIndex() == 0);
result.setRefineSpectrumSynthesis(spectrumSynthesisCmb.getSelectedIndex() == 0);
input = eValueTxt.getText().trim();
if (!input.equals("")) {
result.setMaxEValue(new Double(input));
}
result.setOutputResults((String) outputResultsCmb.getSelectedItem());
result.setOutputProteins(outputProteinsCmb.getSelectedIndex() == 0);
result.setOutputSequences(outputSequencesCmb.getSelectedIndex() == 0);
result.setOutputSpectra(outputSpectraCmb.getSelectedIndex() == 0);
result.setOutputHistograms(outputHistogramsCmb.getSelectedIndex() == 0);
input = skylineTxt.getText().trim();
if (!input.equals("")) {
result.setSkylinePath(input);
}
input = ptmComplexityTxt.getText().trim();
if (!input.equals("")) {
result.setProteinPtmComplexity(new Double(input));
}
return result;
}
/**
* Returns the modification profile corresponding to the input by the user.
*
* @return the modification profile corresponding to the input by the user
*/
public PtmSettings getModificationProfile() {
return modificationProfile;
}
/**
* Returns true if the user edited the modification profile. Note that it
* only checks if the user has made changed to the selection, not if the end
* result is different or not.
*
* @return true if the user edited the modification profile
*/
public boolean modProfileEdited() {
return modProfileChanged;
}
/**
* 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();
tabbedPane = new javax.swing.JTabbedPane();
spectrumImportSettingsPanel = new javax.swing.JPanel();
dynamicRangeLbl = new javax.swing.JLabel();
dynamicRangeTxt = new javax.swing.JTextField();
nPeaksTxt = new javax.swing.JTextField();
nPeaksLbl = new javax.swing.JLabel();
minFragMzLbl = new javax.swing.JLabel();
minFragmentMzTxt = new javax.swing.JTextField();
minPeaksLbl = new javax.swing.JLabel();
minPeaksTxt = new javax.swing.JTextField();
minPrecMassLbl = new javax.swing.JLabel();
minPrecMassTxt = new javax.swing.JTextField();
noiseSuppressionCmb = new javax.swing.JComboBox();
noiseSuppressionLabel = new javax.swing.JLabel();
advancedSearchSettingsPanel = new javax.swing.JPanel();
quickPyroCmb = new javax.swing.JComboBox();
quickAcetylCmb = new javax.swing.JComboBox();
quickAcetylLabel = new javax.swing.JLabel();
quickPyroLabel = new javax.swing.JLabel();
stpBiasLabel = new javax.swing.JLabel();
stpBiasCmb = new javax.swing.JComboBox();
ptmComplexityLbl = new javax.swing.JLabel();
ptmComplexityTxt = new javax.swing.JTextField();
outputSettingsPanel = new javax.swing.JPanel();
eValueLbl = new javax.swing.JLabel();
eValueTxt = new javax.swing.JTextField();
outputSequencesLabel = new javax.swing.JLabel();
outputSequencesCmb = new javax.swing.JComboBox();
outputProteinsCmb = new javax.swing.JComboBox();
outputProteinsLabel = new javax.swing.JLabel();
outputSpectraLabel = new javax.swing.JLabel();
outputSpectraCmb = new javax.swing.JComboBox();
skylineTxt = new javax.swing.JTextField();
skylinePathValueLbl = new javax.swing.JLabel();
outputHistogramsCmb = new javax.swing.JComboBox();
outputHistogramsLabel = new javax.swing.JLabel();
outputResultsLabel = new javax.swing.JLabel();
outputResultsCmb = new javax.swing.JComboBox();
refinementSettingsPanel = new javax.swing.JPanel();
refinementCmb = new javax.swing.JComboBox();
refinementLabel = new javax.swing.JLabel();
semiEnzymaticLabel = new javax.swing.JLabel();
semiEnzymaticCmb = new javax.swing.JComboBox();
maxEValueRefineTxt = new javax.swing.JTextField();
maxEValueRefinmentLbl = new javax.swing.JLabel();
pointMutationLabel = new javax.swing.JLabel();
pointMutationsCmb = new javax.swing.JComboBox();
snapsLabel = new javax.swing.JLabel();
snapsCmb = new javax.swing.JComboBox();
spectrumSynthesisCmb = new javax.swing.JComboBox();
spectrumSynthesisLabel = new javax.swing.JLabel();
unanticipatedCleavageCmb = new javax.swing.JComboBox();
unanticipatedCleavageLabel = new javax.swing.JLabel();
usePotentialModsLabel = new javax.swing.JLabel();
potentialModificationsCmb = new javax.swing.JComboBox();
refinementModificationsJPanel = new javax.swing.JPanel();
refinementModificationsLabel = new javax.swing.JLabel();
openModificationSettingsJButton = new javax.swing.JButton();
modificationsJScrollPane = new javax.swing.JScrollPane();
modificationsTable = new JTable() {
protected JTableHeader createDefaultTableHeader() {
return new JTableHeader(columnModel) {
public String getToolTipText(MouseEvent e) {
java.awt.Point p = e.getPoint();
int index = columnModel.getColumnIndexAtX(p.x);
int realIndex = columnModel.getColumn(index).getModelIndex();
String tip = (String) modificationTableToolTips.get(realIndex);
return tip;
}
};
}
};
openDialogHelpJButton = new javax.swing.JButton();
advancedSettingsWarningLabel = new javax.swing.JLabel();
okButton = new javax.swing.JButton();
closeButton = new javax.swing.JButton();
jSeparator1 = new javax.swing.JSeparator();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
setTitle("X!Tandem Advanced Settings");
setMinimumSize(new java.awt.Dimension(600, 550));
setPreferredSize(new java.awt.Dimension(638, 600));
backgroundPanel.setBackground(new java.awt.Color(230, 230, 230));
tabbedPane.setBackground(new java.awt.Color(230, 230, 230));
tabbedPane.setOpaque(true);
spectrumImportSettingsPanel.setBackground(new java.awt.Color(230, 230, 230));
dynamicRangeLbl.setText("Dynamic Range (Da) (?)");
dynamicRangeLbl.setToolTipText("Open X!Tandem parameter details");
dynamicRangeLbl.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
dynamicRangeLblMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
dynamicRangeLblMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
dynamicRangeLblMouseExited(evt);
}
});
dynamicRangeTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
dynamicRangeTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
dynamicRangeTxtKeyReleased(evt);
}
});
nPeaksTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
nPeaksTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
nPeaksTxtKeyReleased(evt);
}
});
nPeaksLbl.setText("Number of Peaks (?)");
nPeaksLbl.setToolTipText("Open X!Tandem parameter details");
nPeaksLbl.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
nPeaksLblMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
nPeaksLblMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
nPeaksLblMouseExited(evt);
}
});
minFragMzLbl.setText("Minimum Fragment m/z (?)");
minFragMzLbl.setToolTipText("Open X!Tandem parameter details");
minFragMzLbl.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
minFragMzLblMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
minFragMzLblMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
minFragMzLblMouseExited(evt);
}
});
minFragmentMzTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
minFragmentMzTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
minFragmentMzTxtKeyReleased(evt);
}
});
minPeaksLbl.setText("Minimum Peaks (?)");
minPeaksLbl.setToolTipText("Open X!Tandem parameter details");
minPeaksLbl.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
minPeaksLblMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
minPeaksLblMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
minPeaksLblMouseExited(evt);
}
});
minPeaksTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
minPeaksTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
minPeaksTxtKeyReleased(evt);
}
});
minPrecMassLbl.setText("Minimum Precursor Mass (?)");
minPrecMassLbl.setToolTipText("Open X!Tandem parameter details");
minPrecMassLbl.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
minPrecMassLblMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
minPrecMassLblMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
minPrecMassLblMouseExited(evt);
}
});
minPrecMassTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
minPrecMassTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
minPrecMassTxtKeyReleased(evt);
}
});
noiseSuppressionCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
noiseSuppressionCmb.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
noiseSuppressionCmbActionPerformed(evt);
}
});
noiseSuppressionLabel.setText("Noise Suppression (?)");
noiseSuppressionLabel.setToolTipText("Open X!Tandem parameter details");
noiseSuppressionLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
noiseSuppressionLabelMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
noiseSuppressionLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
noiseSuppressionLabelMouseExited(evt);
}
});
javax.swing.GroupLayout spectrumImportSettingsPanelLayout = new javax.swing.GroupLayout(spectrumImportSettingsPanel);
spectrumImportSettingsPanel.setLayout(spectrumImportSettingsPanelLayout);
spectrumImportSettingsPanelLayout.setHorizontalGroup(
spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(spectrumImportSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(spectrumImportSettingsPanelLayout.createSequentialGroup()
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(minPrecMassLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(noiseSuppressionLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(minPrecMassTxt)
.addComponent(noiseSuppressionCmb, 0, 294, Short.MAX_VALUE)))
.addGroup(spectrumImportSettingsPanelLayout.createSequentialGroup()
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(dynamicRangeLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(nPeaksLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(nPeaksTxt)
.addComponent(dynamicRangeTxt)))
.addGroup(spectrumImportSettingsPanelLayout.createSequentialGroup()
.addComponent(minPeaksLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(minPeaksTxt))
.addGroup(spectrumImportSettingsPanelLayout.createSequentialGroup()
.addComponent(minFragMzLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(minFragmentMzTxt)))
.addGap(25, 25, 25))
);
spectrumImportSettingsPanelLayout.setVerticalGroup(
spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(spectrumImportSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(dynamicRangeLbl)
.addComponent(dynamicRangeTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(nPeaksTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(nPeaksLbl))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(minFragmentMzTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(minFragMzLbl))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(minPeaksTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(minPeaksLbl))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(noiseSuppressionCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(noiseSuppressionLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(spectrumImportSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(minPrecMassTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(minPrecMassLbl))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
tabbedPane.addTab("Spectrum Import", spectrumImportSettingsPanel);
advancedSearchSettingsPanel.setBackground(new java.awt.Color(230, 230, 230));
quickPyroCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
quickPyroCmb.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
quickPyroCmbActionPerformed(evt);
}
});
quickAcetylCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
quickAcetylCmb.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
quickAcetylCmbActionPerformed(evt);
}
});
quickAcetylLabel.setText("Quick Acetyl (?)");
quickAcetylLabel.setToolTipText("Open X!Tandem parameter details");
quickAcetylLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
quickAcetylLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
quickAcetylLabelMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
quickAcetylLabelMouseReleased(evt);
}
});
quickPyroLabel.setText("Quick Pyrolidone (?)");
quickPyroLabel.setToolTipText("Open X!Tandem parameter details");
quickPyroLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
quickPyroLabelMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
quickPyroLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
quickPyroLabelMouseExited(evt);
}
});
stpBiasLabel.setText("stP bias (?)");
stpBiasLabel.setToolTipText("Open X!Tandem parameter details");
stpBiasLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
stpBiasLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
stpBiasLabelMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
stpBiasLabelMouseReleased(evt);
}
});
stpBiasCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
ptmComplexityLbl.setText("PTM Complexity (?)");
ptmComplexityLbl.setToolTipText("Open X!Tandem parameter details");
ptmComplexityLbl.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
ptmComplexityLblMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
ptmComplexityLblMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
ptmComplexityLblMouseReleased(evt);
}
});
ptmComplexityTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
ptmComplexityTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
ptmComplexityTxtKeyReleased(evt);
}
});
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)
.addGroup(advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(advancedSearchSettingsPanelLayout.createSequentialGroup()
.addComponent(ptmComplexityLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(ptmComplexityTxt))
.addGroup(advancedSearchSettingsPanelLayout.createSequentialGroup()
.addGroup(advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(quickPyroLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(quickAcetylLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(stpBiasLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(quickPyroCmb, 0, 294, Short.MAX_VALUE)
.addComponent(stpBiasCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(quickAcetylCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))))
.addGap(25, 25, 25))
);
advancedSearchSettingsPanelLayout.setVerticalGroup(
advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(advancedSearchSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(quickAcetylLabel)
.addComponent(quickAcetylCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(quickPyroCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(quickPyroLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(stpBiasCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(stpBiasLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(advancedSearchSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(ptmComplexityLbl)
.addComponent(ptmComplexityTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(314, Short.MAX_VALUE))
);
tabbedPane.addTab("Advanced Search", advancedSearchSettingsPanel);
outputSettingsPanel.setBackground(new java.awt.Color(230, 230, 230));
eValueLbl.setText("E-value Cutoff (?)");
eValueLbl.setToolTipText("Open X!Tandem parameter details");
eValueLbl.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
eValueLblMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
eValueLblMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
eValueLblMouseReleased(evt);
}
});
eValueTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
eValueTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
eValueTxtKeyReleased(evt);
}
});
outputSequencesLabel.setText("Output Sequences (?)");
outputSequencesLabel.setToolTipText("Open X!Tandem parameter details");
outputSequencesLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
outputSequencesLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
outputSequencesLabelMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
outputSequencesLabelMouseReleased(evt);
}
});
outputSequencesCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
outputProteinsCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
outputProteinsCmb.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
outputProteinsCmbActionPerformed(evt);
}
});
outputProteinsLabel.setText("Output Proteins (?)");
outputProteinsLabel.setToolTipText("Open X!Tandem parameter details");
outputProteinsLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
outputProteinsLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
outputProteinsLabelMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
outputProteinsLabelMouseReleased(evt);
}
});
outputSpectraLabel.setText("Output Spectra (?)");
outputSpectraLabel.setToolTipText("Open X!Tandem parameter details");
outputSpectraLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
outputSpectraLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
outputSpectraLabelMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
outputSpectraLabelMouseReleased(evt);
}
});
outputSpectraCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
skylineTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
skylinePathValueLbl.setText("Skyline Path (?)");
skylinePathValueLbl.setToolTipText("Open X!Tandem parameter details");
skylinePathValueLbl.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
skylinePathValueLblMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
skylinePathValueLblMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
skylinePathValueLblMouseReleased(evt);
}
});
outputHistogramsCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
outputHistogramsLabel.setText("Output Histograms (?)");
outputHistogramsLabel.setToolTipText("Open X!Tandem parameter details");
outputHistogramsLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
outputHistogramsLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
outputHistogramsLabelMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
outputHistogramsLabelMouseReleased(evt);
}
});
outputResultsLabel.setText("Output Results (?)");
outputResultsLabel.setToolTipText("Open X!Tandem parameter details");
outputResultsLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
outputResultsLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
outputResultsLabelMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
outputResultsLabelMouseReleased(evt);
}
});
outputResultsCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "all", "valid", "stochastic" }));
outputResultsCmb.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
outputResultsCmbActionPerformed(evt);
}
});
javax.swing.GroupLayout outputSettingsPanelLayout = new javax.swing.GroupLayout(outputSettingsPanel);
outputSettingsPanel.setLayout(outputSettingsPanelLayout);
outputSettingsPanelLayout.setHorizontalGroup(
outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, outputSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(eValueLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(outputResultsLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(outputProteinsLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(outputSequencesLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(outputSpectraLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(skylinePathValueLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(outputHistogramsLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(outputResultsCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(eValueTxt)
.addComponent(skylineTxt)
.addComponent(outputProteinsCmb, javax.swing.GroupLayout.Alignment.TRAILING, 0, 294, Short.MAX_VALUE)
.addComponent(outputSequencesCmb, javax.swing.GroupLayout.Alignment.TRAILING, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(outputSpectraCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(outputHistogramsCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addGap(25, 25, 25))
);
outputSettingsPanelLayout.setVerticalGroup(
outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(outputSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(outputResultsLabel)
.addComponent(outputResultsCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(eValueLbl)
.addComponent(eValueTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(outputProteinsLabel)
.addComponent(outputProteinsCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(outputSequencesCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(outputSequencesLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(outputSpectraCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(outputSpectraLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(outputHistogramsCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(outputHistogramsLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(outputSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(skylinePathValueLbl)
.addComponent(skylineTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(236, Short.MAX_VALUE))
);
tabbedPane.addTab("Output", outputSettingsPanel);
refinementSettingsPanel.setBackground(new java.awt.Color(230, 230, 230));
refinementCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
refinementCmb.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
refinementCmbActionPerformed(evt);
}
});
refinementLabel.setText("Refinement (?)");
refinementLabel.setToolTipText("Open X!Tandem parameter details");
refinementLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
refinementLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
refinementLabelMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
refinementLabelMouseReleased(evt);
}
});
semiEnzymaticLabel.setText("Semi-Enzymatic Cleavage (?)");
semiEnzymaticLabel.setToolTipText("Open X!Tandem parameter details");
semiEnzymaticLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
semiEnzymaticLabelMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
semiEnzymaticLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
semiEnzymaticLabelMouseExited(evt);
}
});
semiEnzymaticCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
maxEValueRefineTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
maxEValueRefineTxt.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
maxEValueRefineTxtKeyReleased(evt);
}
});
maxEValueRefinmentLbl.setText("Maximum Valid Expectation Value (?)");
maxEValueRefinmentLbl.setToolTipText("Open X!Tandem parameter details");
maxEValueRefinmentLbl.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
maxEValueRefinmentLblMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
maxEValueRefinmentLblMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
maxEValueRefinmentLblMouseReleased(evt);
}
});
pointMutationLabel.setText("Point Mutations (?)");
pointMutationLabel.setToolTipText("Open X!Tandem parameter details");
pointMutationLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
pointMutationLabelMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
pointMutationLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
pointMutationLabelMouseExited(evt);
}
});
pointMutationsCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
snapsLabel.setText("snAPs (?)");
snapsLabel.setToolTipText("Open X!Tandem parameter details");
snapsLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
snapsLabelMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
snapsLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
snapsLabelMouseExited(evt);
}
});
snapsCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
spectrumSynthesisCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
spectrumSynthesisLabel.setText("Spectrum Synthesis (?)");
spectrumSynthesisLabel.setToolTipText("Open X!Tandem parameter details");
spectrumSynthesisLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
spectrumSynthesisLabelMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
spectrumSynthesisLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
spectrumSynthesisLabelMouseExited(evt);
}
});
unanticipatedCleavageCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
unanticipatedCleavageLabel.setText("Unanticipated Cleavage (?)");
unanticipatedCleavageLabel.setToolTipText("Open X!Tandem parameter details");
unanticipatedCleavageLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
unanticipatedCleavageLabelMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
unanticipatedCleavageLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
unanticipatedCleavageLabelMouseExited(evt);
}
});
usePotentialModsLabel.setText("Potential Modifications for Full Refinement (?)");
usePotentialModsLabel.setToolTipText("Open X!Tandem parameter details");
usePotentialModsLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
usePotentialModsLabelMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
usePotentialModsLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
usePotentialModsLabelMouseExited(evt);
}
});
potentialModificationsCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));
refinementModificationsJPanel.setOpaque(false);
refinementModificationsLabel.setText("Refinement Modifications (?)");
refinementModificationsLabel.setToolTipText("Open X!Tandem parameter details");
refinementModificationsLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
refinementModificationsLabelMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
refinementModificationsLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
refinementModificationsLabelMouseExited(evt);
}
});
openModificationSettingsJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/edit_gray.png"))); // NOI18N
openModificationSettingsJButton.setToolTipText("Edit Modifications");
openModificationSettingsJButton.setBorder(null);
openModificationSettingsJButton.setBorderPainted(false);
openModificationSettingsJButton.setContentAreaFilled(false);
openModificationSettingsJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/edit.png"))); // NOI18N
openModificationSettingsJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
openModificationSettingsJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
openModificationSettingsJButtonMouseExited(evt);
}
});
openModificationSettingsJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
openModificationSettingsJButtonActionPerformed(evt);
}
});
modificationsJScrollPane.setPreferredSize(new java.awt.Dimension(100, 60));
modificationsTable.setModel(new javax.swing.table.DefaultTableModel(
new Object [][] {
},
new String [] {
" ", "Name", "Mass", "V", "F"
}
) {
Class[] types = new Class [] {
java.lang.Object.class, java.lang.String.class, java.lang.Double.class, java.lang.Boolean.class, java.lang.Boolean.class
};
boolean[] canEdit = new boolean [] {
false, false, false, true, true
};
public Class getColumnClass(int columnIndex) {
return types [columnIndex];
}
public boolean isCellEditable(int rowIndex, int columnIndex) {
return canEdit [columnIndex];
}
});
modificationsTable.addMouseMotionListener(new java.awt.event.MouseMotionAdapter() {
public void mouseMoved(java.awt.event.MouseEvent evt) {
modificationsTableMouseMoved(evt);
}
});
modificationsTable.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseExited(java.awt.event.MouseEvent evt) {
modificationsTableMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
modificationsTableMouseReleased(evt);
}
});
modificationsJScrollPane.setViewportView(modificationsTable);
javax.swing.GroupLayout refinementModificationsJPanelLayout = new javax.swing.GroupLayout(refinementModificationsJPanel);
refinementModificationsJPanel.setLayout(refinementModificationsJPanelLayout);
refinementModificationsJPanelLayout.setHorizontalGroup(
refinementModificationsJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(refinementModificationsJPanelLayout.createSequentialGroup()
.addComponent(refinementModificationsLabel, javax.swing.GroupLayout.DEFAULT_SIZE, 296, Short.MAX_VALUE)
.addGap(246, 246, 246)
.addComponent(openModificationSettingsJButton)
.addGap(2, 2, 2))
.addComponent(modificationsJScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
refinementModificationsJPanelLayout.setVerticalGroup(
refinementModificationsJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(refinementModificationsJPanelLayout.createSequentialGroup()
.addGroup(refinementModificationsJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(refinementModificationsLabel)
.addComponent(openModificationSettingsJButton))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(modificationsJScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 145, Short.MAX_VALUE)
.addContainerGap())
);
javax.swing.GroupLayout refinementSettingsPanelLayout = new javax.swing.GroupLayout(refinementSettingsPanel);
refinementSettingsPanel.setLayout(refinementSettingsPanelLayout);
refinementSettingsPanelLayout.setHorizontalGroup(
refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(refinementSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(refinementModificationsJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGroup(refinementSettingsPanelLayout.createSequentialGroup()
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(refinementLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(maxEValueRefinmentLbl, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(unanticipatedCleavageLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(semiEnzymaticLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(usePotentialModsLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(pointMutationLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(snapsLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(spectrumSynthesisLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(spectrumSynthesisCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(snapsCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(pointMutationsCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(potentialModificationsCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(semiEnzymaticCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(unanticipatedCleavageCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(maxEValueRefineTxt)
.addComponent(refinementCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))))
.addGap(25, 25, 25))
);
refinementSettingsPanelLayout.setVerticalGroup(
refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(refinementSettingsPanelLayout.createSequentialGroup()
.addGap(25, 25, 25)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(refinementCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(refinementLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(maxEValueRefineTxt, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(maxEValueRefinmentLbl))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(unanticipatedCleavageCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(unanticipatedCleavageLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(semiEnzymaticCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(semiEnzymaticLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(potentialModificationsCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(usePotentialModsLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(pointMutationsCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(pointMutationLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(snapsCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(snapsLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(refinementSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(spectrumSynthesisCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(spectrumSynthesisLabel))
.addGap(18, 18, 18)
.addComponent(refinementModificationsJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addContainerGap())
);
tabbedPane.addTab("Refinement", refinementSettingsPanel);
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);
}
});
advancedSettingsWarningLabel.setText("Note: The advanced settings are for expert use only. See the help for details.");
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);
}
});
javax.swing.GroupLayout backgroundPanelLayout = new javax.swing.GroupLayout(backgroundPanel);
backgroundPanel.setLayout(backgroundPanelLayout);
backgroundPanelLayout.setHorizontalGroup(
backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, backgroundPanelLayout.createSequentialGroup()
.addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(jSeparator1))
.addGroup(javax.swing.GroupLayout.Alignment.LEADING, backgroundPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(tabbedPane))
.addGroup(javax.swing.GroupLayout.Alignment.LEADING, backgroundPanelLayout.createSequentialGroup()
.addGap(19, 19, 19)
.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)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jSeparator1, javax.swing.GroupLayout.PREFERRED_SIZE, 2, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(openDialogHelpJButton)
.addComponent(okButton)
.addComponent(closeButton)
.addComponent(advancedSettingsWarningLabel))
.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
/**
* Close the dialog without saving the settings.
*
* @param evt
*/
private void closeButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_closeButtonActionPerformed
cancelled = true;
dispose();
}//GEN-LAST:event_closeButtonActionPerformed
/**
* Save the settings and then 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
/**
* Enable/disable the output sequence combo box.
*
* @param evt
*/
private void outputProteinsCmbActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_outputProteinsCmbActionPerformed
if (outputProteinsCmb.getSelectedIndex() == 0) {
outputSequencesCmb.setEnabled(true);
} else {
outputSequencesCmb.setSelectedIndex(1);
outputSequencesCmb.setEnabled(false);
}
}//GEN-LAST:event_outputProteinsCmbActionPerformed
/**
* Validate the input.
*
* @param evt
*/
private void eValueTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_eValueTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_eValueTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void maxEValueRefineTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_maxEValueRefineTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_maxEValueRefineTxtKeyReleased
/**
* Enable/disable the refinement setting.
*
* @param evt
*/
private void refinementCmbActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_refinementCmbActionPerformed
if (refinementCmb.getSelectedIndex() == 0) {
maxEValueRefineTxt.setEnabled(true);
unanticipatedCleavageCmb.setEnabled(true);
semiEnzymaticCmb.setEnabled(true);
potentialModificationsCmb.setEnabled(true);
pointMutationsCmb.setEnabled(true);
snapsCmb.setEnabled(true);
spectrumSynthesisCmb.setEnabled(true);
} else {
maxEValueRefineTxt.setEnabled(false);
unanticipatedCleavageCmb.setEnabled(false);
semiEnzymaticCmb.setEnabled(false);
potentialModificationsCmb.setEnabled(false);
pointMutationsCmb.setEnabled(false);
snapsCmb.setEnabled(false);
spectrumSynthesisCmb.setEnabled(false);
}
}//GEN-LAST:event_refinementCmbActionPerformed
/**
* Check for quick acetyl conflict.
*
* @param evt
*/
private void quickAcetylCmbActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_quickAcetylCmbActionPerformed
if (quickAcetylCmb.getSelectedIndex() == 0) {
for (String modName : modificationProfile.getFixedModifications()) {
PTM ptm = ptmFactory.getPTM(modName);
if ((ptm.getType() == PTM.MODNP || ptm.getType() == PTM.MODNPAA || ptm.getType() == PTM.MODN || ptm.getType() == PTM.MODNAA)
&& Math.abs(ptm.getMass() - 42.010565) < fragmentIonMassAccuracyInDa) {
JOptionPane.showMessageDialog(this, "The quick acetyl option might conflict with " + modName + ".",
"Modification Conflict", JOptionPane.ERROR_MESSAGE);
quickAcetylCmb.setSelectedIndex(1);
break;
}
}
}
}//GEN-LAST:event_quickAcetylCmbActionPerformed
/**
* Check for quick pyrolidone conflict.
*
* @param evt
*/
private void quickPyroCmbActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_quickPyroCmbActionPerformed
if (quickPyroCmb.getSelectedIndex() == 0) {
for (String modName : modificationProfile.getFixedModifications()) {
PTM ptm = ptmFactory.getPTM(modName);
if ((ptm.getType() == PTM.MODNP || ptm.getType() == PTM.MODNPAA || ptm.getType() == PTM.MODN || ptm.getType() == PTM.MODNAA)
&& Math.abs(ptm.getMass() + 17.026549) < fragmentIonMassAccuracyInDa) {
JOptionPane.showMessageDialog(this, "The quick pyrolidone option might conflict with " + modName + ".",
"Modification Conflict", JOptionPane.ERROR_MESSAGE);
quickAcetylCmb.setSelectedIndex(1);
break;
}
}
}
}//GEN-LAST:event_quickPyroCmbActionPerformed
/**
* Enable/disable the noise min precursor mass.
*
* @param evt
*/
private void noiseSuppressionCmbActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_noiseSuppressionCmbActionPerformed
if (noiseSuppressionCmb.getSelectedIndex() == 0) {
minPrecMassTxt.setEnabled(true);
} else {
minPrecMassTxt.setEnabled(false);
}
}//GEN-LAST:event_noiseSuppressionCmbActionPerformed
/**
* Validate the input.
*
* @param evt
*/
private void minPrecMassTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_minPrecMassTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_minPrecMassTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void minPeaksTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_minPeaksTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_minPeaksTxtKeyReleased
/**
* Validate the input.
*
* @param evt
*/
private void minFragmentMzTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_minFragmentMzTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_minFragmentMzTxtKeyReleased
/**
* 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 dynamicRangeTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_dynamicRangeTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_dynamicRangeTxtKeyReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void dynamicRangeLblMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_dynamicRangeLblMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_dynamicRangeLblMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void dynamicRangeLblMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_dynamicRangeLblMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_dynamicRangeLblMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void dynamicRangeLblMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_dynamicRangeLblMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/sdr.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_dynamicRangeLblMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void minFragMzLblMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_minFragMzLblMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_minFragMzLblMouseEntered
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void minFragMzLblMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_minFragMzLblMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_minFragMzLblMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void minFragMzLblMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_minFragMzLblMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/smfmz.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_minFragMzLblMouseReleased
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void nPeaksLblMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_nPeaksLblMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_nPeaksLblMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void nPeaksLblMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_nPeaksLblMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/stp.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_nPeaksLblMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void nPeaksLblMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_nPeaksLblMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_nPeaksLblMouseEntered
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void minPeaksLblMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_minPeaksLblMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_minPeaksLblMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void minPeaksLblMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_minPeaksLblMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_minPeaksLblMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void minPeaksLblMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_minPeaksLblMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/smp.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_minPeaksLblMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void noiseSuppressionLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_noiseSuppressionLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_noiseSuppressionLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void noiseSuppressionLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_noiseSuppressionLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_noiseSuppressionLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void noiseSuppressionLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_noiseSuppressionLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/suns.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_noiseSuppressionLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void minPrecMassLblMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_minPrecMassLblMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_minPrecMassLblMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void minPrecMassLblMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_minPrecMassLblMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_minPrecMassLblMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void minPrecMassLblMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_minPrecMassLblMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/smpmh.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_minPrecMassLblMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void quickAcetylLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_quickAcetylLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_quickAcetylLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void quickAcetylLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_quickAcetylLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_quickAcetylLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void quickAcetylLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_quickAcetylLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/pqa.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_quickAcetylLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void quickPyroLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_quickPyroLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_quickPyroLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void quickPyroLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_quickPyroLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_quickPyroLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void quickPyroLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_quickPyroLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/pqp.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_quickPyroLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void stpBiasLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_stpBiasLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_stpBiasLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void stpBiasLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_stpBiasLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_stpBiasLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void stpBiasLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_stpBiasLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/pstpb.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_stpBiasLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void eValueLblMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_eValueLblMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_eValueLblMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void eValueLblMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_eValueLblMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_eValueLblMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void eValueLblMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_eValueLblMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/omvev.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_eValueLblMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void outputProteinsLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputProteinsLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_outputProteinsLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void outputProteinsLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputProteinsLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputProteinsLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void outputProteinsLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputProteinsLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/oprot.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputProteinsLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void outputSequencesLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputSequencesLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_outputSequencesLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void outputSequencesLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputSequencesLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputSequencesLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void outputSequencesLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputSequencesLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/osequ.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputSequencesLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void outputSpectraLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputSpectraLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_outputSpectraLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void outputSpectraLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputSpectraLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputSpectraLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void outputSpectraLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputSpectraLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/ospec.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputSpectraLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void outputHistogramsLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputHistogramsLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_outputHistogramsLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void outputHistogramsLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputHistogramsLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputHistogramsLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void outputHistogramsLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputHistogramsLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/ohist.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputHistogramsLabelMouseReleased
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void skylinePathValueLblMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_skylinePathValueLblMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_skylinePathValueLblMouseExited
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void skylinePathValueLblMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_skylinePathValueLblMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_skylinePathValueLblMouseEntered
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void skylinePathValueLblMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_skylinePathValueLblMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/ssp.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_skylinePathValueLblMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void refinementLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_refinementLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_refinementLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void refinementLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_refinementLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_refinementLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void refinementLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_refinementLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/refine.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_refinementLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void maxEValueRefinmentLblMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_maxEValueRefinmentLblMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_maxEValueRefinmentLblMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void maxEValueRefinmentLblMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_maxEValueRefinmentLblMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_maxEValueRefinmentLblMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void maxEValueRefinmentLblMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_maxEValueRefinmentLblMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/refmvev.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_maxEValueRefinmentLblMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void unanticipatedCleavageLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_unanticipatedCleavageLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_unanticipatedCleavageLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void unanticipatedCleavageLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_unanticipatedCleavageLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_unanticipatedCleavageLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void unanticipatedCleavageLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_unanticipatedCleavageLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/ruc.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_unanticipatedCleavageLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void semiEnzymaticLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_semiEnzymaticLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_semiEnzymaticLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void semiEnzymaticLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_semiEnzymaticLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_semiEnzymaticLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void semiEnzymaticLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_semiEnzymaticLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/rcsemi.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_semiEnzymaticLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void usePotentialModsLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_usePotentialModsLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_usePotentialModsLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void usePotentialModsLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_usePotentialModsLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_usePotentialModsLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void usePotentialModsLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_usePotentialModsLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/rupmffr.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_usePotentialModsLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void pointMutationLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_pointMutationLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_pointMutationLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void pointMutationLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_pointMutationLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_pointMutationLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void pointMutationLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_pointMutationLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/rpm.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_pointMutationLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void snapsLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_snapsLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_snapsLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void snapsLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_snapsLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_snapsLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void snapsLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_snapsLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/rsaps.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_snapsLabelMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void spectrumSynthesisLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_spectrumSynthesisLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_spectrumSynthesisLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void spectrumSynthesisLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_spectrumSynthesisLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_spectrumSynthesisLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void spectrumSynthesisLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_spectrumSynthesisLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/rss.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_spectrumSynthesisLabelMouseReleased
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void modificationsTableMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_modificationsTableMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_modificationsTableMouseExited
/**
* Opens a color chooser where the color for the PTM can be changed, or
* allows the users to change of a PTM is in the most used PTMs list.
*
* @param evt
*/
private void modificationsTableMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_modificationsTableMouseReleased
int row = modificationsTable.rowAtPoint(evt.getPoint());
int column = modificationsTable.columnAtPoint(evt.getPoint());
if (row != -1) {
if (column == modificationsTable.getColumn(" ").getModelIndex()) {
Color newColor = JColorChooser.showDialog(this, "Pick a Color", (Color) modificationsTable.getValueAt(row, column));
if (newColor != null) {
ptmFactory.setColor((String) modificationsTable.getValueAt(row, 1), newColor);
modificationsTable.setValueAt(newColor, row, 0);
((DefaultTableModel) modificationsTable.getModel()).fireTableDataChanged();
modificationsTable.repaint();
}
} else if (column == modificationsTable.getColumn("V").getModelIndex()
&& modificationsTable.getValueAt(row, column) != null) {
boolean selected = (Boolean) modificationsTable.getValueAt(row, column);
String ptmName = (String) modificationsTable.getValueAt(row, 1);
// add/remove the ptm as a refinement ptm
if (selected) {
// add as refinement ptm
if (!modificationProfile.getRefinementVariableModifications().contains(ptmName)) {
modificationProfile.addRefinementVariableModification(ptmFactory.getPTM(ptmName));
modProfileChanged = true;
}
} else {
// remove the ptm as refinement ptm
modificationProfile.removeRefinementVariableModification(ptmName);
modProfileChanged = true;
}
updateModificationList();
if (row < modificationsTable.getRowCount()) {
modificationsTable.setRowSelectionInterval(row, row);
} else if (row - 1 < modificationsTable.getRowCount() && row >= 0) {
modificationsTable.setRowSelectionInterval(row - 1, row - 1);
}
} else if (column == modificationsTable.getColumn("F").getModelIndex()
&& modificationsTable.getValueAt(row, column) != null) {
boolean selected = (Boolean) modificationsTable.getValueAt(row, column);
String ptmName = (String) modificationsTable.getValueAt(row, 1);
// add/remove the ptm as a refinement ptm
if (selected) {
// add as refinement ptm
if (!modificationProfile.getRefinementFixedModifications().contains(ptmName)) {
modificationProfile.addRefinementFixedModification(ptmFactory.getPTM(ptmName));
modProfileChanged = true;
}
} else {
// remove the ptm as refinement ptm
modificationProfile.removeRefinementFixedModification(ptmName);
modProfileChanged = true;
}
updateModificationList();
if (row < modificationsTable.getRowCount()) {
modificationsTable.setRowSelectionInterval(row, row);
} else if (row - 1 < modificationsTable.getRowCount() && row >= 0) {
modificationsTable.setRowSelectionInterval(row - 1, row - 1);
}
}
}
}//GEN-LAST:event_modificationsTableMouseReleased
private void modificationsTableMouseMoved(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_modificationsTableMouseMoved
int row = modificationsTable.rowAtPoint(evt.getPoint());
int column = modificationsTable.columnAtPoint(evt.getPoint());
if (row != -1) {
if (column == modificationsTable.getColumn(" ").getModelIndex()) {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
} else {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
}
}//GEN-LAST:event_modificationsTableMouseMoved
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void openModificationSettingsJButtonMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_openModificationSettingsJButtonMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_openModificationSettingsJButtonMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void openModificationSettingsJButtonMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_openModificationSettingsJButtonMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_openModificationSettingsJButtonMouseExited
/**
* Open the ModificationsDialog.
*
* @param evt
*/
private void openModificationSettingsJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_openModificationSettingsJButtonActionPerformed
new ModificationsDialog((Frame) this.getParent(), true);
updateModificationList();
}//GEN-LAST:event_openModificationSettingsJButtonActionPerformed
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void refinementModificationsLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_refinementModificationsLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_refinementModificationsLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void refinementModificationsLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_refinementModificationsLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_refinementModificationsLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void refinementModificationsLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_refinementModificationsLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/refpmm.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_refinementModificationsLabelMouseReleased
/**
* 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/XTandemSettingsDialog.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
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void outputResultsLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputResultsLabelMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_outputResultsLabelMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void outputResultsLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputResultsLabelMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputResultsLabelMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void outputResultsLabelMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_outputResultsLabelMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/api/oresu.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_outputResultsLabelMouseReleased
/**
* Enable or disable the e-value cutoff option.
*
* @param evt
*/
private void outputResultsCmbActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_outputResultsCmbActionPerformed
eValueTxt.setEnabled(!((String) outputResultsCmb.getSelectedItem()).equalsIgnoreCase("all"));
}//GEN-LAST:event_outputResultsCmbActionPerformed
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void ptmComplexityLblMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_ptmComplexityLblMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_ptmComplexityLblMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void ptmComplexityLblMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_ptmComplexityLblMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_ptmComplexityLblMouseExited
/**
* Open the link to the X!Tandem help pages.
*
* @param evt
*/
private void ptmComplexityLblMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_ptmComplexityLblMouseReleased
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.thegpm.org/TANDEM/release.html");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_ptmComplexityLblMouseReleased
/**
* Validate the input.
*
* @param evt
*/
private void ptmComplexityTxtKeyReleased(java.awt.event.KeyEvent evt) {//GEN-FIRST:event_ptmComplexityTxtKeyReleased
validateInput(false);
}//GEN-LAST:event_ptmComplexityTxtKeyReleased
/**
* 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, eValueLbl, eValueTxt, "e-value cutoff", "E-value Cutoff Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, dynamicRangeLbl, dynamicRangeTxt, "dynamic range cutoff", "Dynamic Range Cutoff Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, nPeaksLbl, nPeaksTxt, "number of peaks", "Number of Peaks Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, minFragMzLbl, minFragmentMzTxt, "minimal fragment m/z", "Minimal Fragment MZ Error", true, showMessage, valid);
valid = GuiUtilities.validateIntegerInput(this, minPeaksLbl, minPeaksTxt, "minimal number of peaks", "Minimal Number of Peaks Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, minPrecMassLbl, minPrecMassTxt, "minimal precursor mass", "Minimal Precursor Mass Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, maxEValueRefinmentLbl, maxEValueRefineTxt, "maximal e-value for the refinement", "Maximal Refinement E-Value Error", true, showMessage, valid);
valid = GuiUtilities.validateDoubleInput(this, ptmComplexityLbl, ptmComplexityTxt, "PTM complexity", "PTM Complexity Error", true, showMessage, valid);
// check if the ptm complexity value is in the range (0.0-12.0)
if (valid) {
try {
Double value = new Double(ptmComplexityTxt.getText());
if (value > 12) {
if (showMessage && valid) {
JOptionPane.showMessageDialog(this, "Please select a number in the range (0.0-12.0) for PTM complexity.",
"PTM Complexity Error", JOptionPane.WARNING_MESSAGE);
}
valid = false;
ptmComplexityLbl.setForeground(Color.RED);
ptmComplexityLbl.setToolTipText("Please select a number in the range (0.0-12.0)");
}
} catch (NumberFormatException e) {
// ignore, already caught above
}
}
okButton.setEnabled(valid);
return valid;
}
/**
* Updates the modification list.
*/
private void updateModificationList() {
ArrayList<String> allModificationsList = ptmFactory.getPTMs();
String[] allModificationsAsArray = new String[allModificationsList.size()];
for (int i = 0; i < allModificationsList.size(); i++) {
allModificationsAsArray[i] = allModificationsList.get(i);
}
Arrays.sort(allModificationsAsArray);
modificationsTable.setModel(new javax.swing.table.DefaultTableModel(
new Object[][]{},
new String[]{
" ", "Name", "Mass", "V", "F"
}
) {
Class[] types = new Class[]{
java.lang.Object.class, java.lang.String.class, java.lang.Double.class, java.lang.Boolean.class, java.lang.Boolean.class
};
boolean[] canEdit = new boolean[]{
false, false, false, true, true
};
public Class getColumnClass(int columnIndex) {
return types[columnIndex];
}
public boolean isCellEditable(int rowIndex, int columnIndex) {
return canEdit[columnIndex] && editable;
}
});
for (String mod : allModificationsAsArray) {
((DefaultTableModel) modificationsTable.getModel()).addRow(
new Object[]{ptmFactory.getColor(mod),
mod,
ptmFactory.getPTM(mod).getMass(),
modificationProfile.getRefinementVariableModifications().contains(mod),
modificationProfile.getRefinementFixedModifications().contains(mod)});
}
((DefaultTableModel) modificationsTable.getModel()).fireTableDataChanged();
modificationsTable.repaint();
// get the min and max values for the mass sparklines
double maxMass = Double.MIN_VALUE;
double minMass = Double.MAX_VALUE;
for (String ptm : ptmFactory.getPTMs()) {
if (ptmFactory.getPTM(ptm).getMass() > maxMass) {
maxMass = ptmFactory.getPTM(ptm).getMass();
}
if (ptmFactory.getPTM(ptm).getMass() < minMass) {
minMass = ptmFactory.getPTM(ptm).getMass();
}
}
setAllModificationTableProperties();
modificationsTable.getColumn("Mass").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, minMass, maxMass));
((JSparklinesBarChartTableCellRenderer) modificationsTable.getColumn("Mass").getCellRenderer()).showNumberAndChart(true, 50);
if (modificationsTable.getRowCount() > 0) {
modificationsTable.setRowSelectionInterval(0, 0);
}
}
// 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.JButton closeButton;
private javax.swing.JLabel dynamicRangeLbl;
private javax.swing.JTextField dynamicRangeTxt;
private javax.swing.JLabel eValueLbl;
private javax.swing.JTextField eValueTxt;
private javax.swing.JSeparator jSeparator1;
private javax.swing.JTextField maxEValueRefineTxt;
private javax.swing.JLabel maxEValueRefinmentLbl;
private javax.swing.JLabel minFragMzLbl;
private javax.swing.JTextField minFragmentMzTxt;
private javax.swing.JLabel minPeaksLbl;
private javax.swing.JTextField minPeaksTxt;
private javax.swing.JLabel minPrecMassLbl;
private javax.swing.JTextField minPrecMassTxt;
private javax.swing.JScrollPane modificationsJScrollPane;
private javax.swing.JTable modificationsTable;
private javax.swing.JLabel nPeaksLbl;
private javax.swing.JTextField nPeaksTxt;
private javax.swing.JComboBox noiseSuppressionCmb;
private javax.swing.JLabel noiseSuppressionLabel;
private javax.swing.JButton okButton;
private javax.swing.JButton openDialogHelpJButton;
private javax.swing.JButton openModificationSettingsJButton;
private javax.swing.JComboBox outputHistogramsCmb;
private javax.swing.JLabel outputHistogramsLabel;
private javax.swing.JComboBox outputProteinsCmb;
private javax.swing.JLabel outputProteinsLabel;
private javax.swing.JComboBox outputResultsCmb;
private javax.swing.JLabel outputResultsLabel;
private javax.swing.JComboBox outputSequencesCmb;
private javax.swing.JLabel outputSequencesLabel;
private javax.swing.JPanel outputSettingsPanel;
private javax.swing.JComboBox outputSpectraCmb;
private javax.swing.JLabel outputSpectraLabel;
private javax.swing.JLabel pointMutationLabel;
private javax.swing.JComboBox pointMutationsCmb;
private javax.swing.JComboBox potentialModificationsCmb;
private javax.swing.JLabel ptmComplexityLbl;
private javax.swing.JTextField ptmComplexityTxt;
private javax.swing.JComboBox quickAcetylCmb;
private javax.swing.JLabel quickAcetylLabel;
private javax.swing.JComboBox quickPyroCmb;
private javax.swing.JLabel quickPyroLabel;
private javax.swing.JComboBox refinementCmb;
private javax.swing.JLabel refinementLabel;
private javax.swing.JPanel refinementModificationsJPanel;
private javax.swing.JLabel refinementModificationsLabel;
private javax.swing.JPanel refinementSettingsPanel;
private javax.swing.JComboBox semiEnzymaticCmb;
private javax.swing.JLabel semiEnzymaticLabel;
private javax.swing.JLabel skylinePathValueLbl;
private javax.swing.JTextField skylineTxt;
private javax.swing.JComboBox snapsCmb;
private javax.swing.JLabel snapsLabel;
private javax.swing.JPanel spectrumImportSettingsPanel;
private javax.swing.JComboBox spectrumSynthesisCmb;
private javax.swing.JLabel spectrumSynthesisLabel;
private javax.swing.JComboBox stpBiasCmb;
private javax.swing.JLabel stpBiasLabel;
private javax.swing.JTabbedPane tabbedPane;
private javax.swing.JComboBox unanticipatedCleavageCmb;
private javax.swing.JLabel unanticipatedCleavageLabel;
private javax.swing.JLabel usePotentialModsLabel;
// End of variables declaration//GEN-END:variables
}