/**
* Opens a file chooser for importing method settings.
*
* @param evt
*/
private void browseConfigButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_browseConfigButtonActionPerformed
if (txtConfigurationFileLocation.getText().length() > 0) {
newDialog
.getReporterGui()
.getLastSelectedFolder()
.setLastSelectedFolder(txtConfigurationFileLocation.getText());
}
File selectedFile =
Util.getUserSelectedFile(
this,
".xml",
"Reporter Method File (*.xml)",
"Select Settings File",
newDialog.getReporterGui().getLastSelectedFolder().getLastSelectedFolder(),
null,
true);
if (selectedFile != null) {
try {
methodsFactory.importMethods(selectedFile);
newDialog.setSelectedMethod(newDialog.getMethod(newDialog.getSelectedMethod().getName()));
newDialog.setReagents(newDialog.getSelectedMethod().getReagentsSortedByMass());
refresh();
txtConfigurationFileLocation.setText(selectedFile.getAbsolutePath());
newDialog.setMethodsFile(selectedFile);
newDialog
.getReporterGui()
.getLastSelectedFolder()
.setLastSelectedFolder(selectedFile.getPath());
} catch (IOException e) {
JOptionPane.showMessageDialog(
null,
"File " + selectedFile.getAbsolutePath() + " not found.",
"File Not Found",
JOptionPane.WARNING_MESSAGE);
} catch (XmlPullParserException e) {
JOptionPane.showMessageDialog(
null,
"An error occurred while parsing "
+ selectedFile.getAbsolutePath()
+ " at line "
+ e.getLineNumber()
+ ".",
"Parsing Error",
JOptionPane.WARNING_MESSAGE);
e.printStackTrace();
}
}
} // GEN-LAST:event_browseConfigButtonActionPerformed
/**
* Save the method settings.
*
* @param evt
*/
private void saveConfigButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_saveConfigButtonActionPerformed
String tempFileName = null;
if (txtConfigurationFileLocation.getText().length() > 0) {
newDialog
.getReporterGui()
.getLastSelectedFolder()
.setLastSelectedFolder(txtConfigurationFileLocation.getText());
tempFileName = new File(txtConfigurationFileLocation.getText()).getName();
}
File selectedFile =
Util.getUserSelectedFile(
this,
".xml",
"Reporter Method File (*.xml)",
"Save Settings File",
newDialog.getReporterGui().getLastSelectedFolder().getLastSelectedFolder(),
tempFileName,
false);
if (selectedFile != null) {
try {
methodsFactory.saveFile(selectedFile);
newDialog.setMethodsFile(selectedFile);
txtConfigurationFileLocation.setText(selectedFile.getAbsolutePath());
valuesChanged = false;
JOptionPane.showMessageDialog(
null,
"Settings saved to " + selectedFile.getAbsolutePath() + ".",
"Settings Saved",
JOptionPane.INFORMATION_MESSAGE);
} catch (IOException ex) {
JOptionPane.showMessageDialog(
null,
"An error occured when saving the file.",
"File Error",
JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
} // GEN-LAST:event_saveConfigButtonActionPerformed
/**
* Dialog for setting the reporter method details.
*
* @author Harald Barsnes
*/
public class MethodSettingsDialog extends javax.swing.JDialog {
/** The parent dialog. */
private NewDialog newDialog;
/** The compomics reporter methods factory. */
private ReporterMethodFactory methodsFactory = ReporterMethodFactory.getInstance();
/** Boolean indicating of the user has made changes to the table. */
private boolean valuesChanged = false;
/**
* Creates a new MethodSettingsDialog.
*
* @param newDialog the parent dialog
* @param modal if the dialog is to be modal or not
*/
public MethodSettingsDialog(NewDialog newDialog, boolean modal) {
super(newDialog, modal);
this.newDialog = newDialog;
initComponents();
setUpGui();
setLocationRelativeTo(newDialog);
setVisible(true);
}
/** Set up the GUI. */
private void setUpGui() {
reagentsTableJScrollPane.getViewport().setOpaque(false);
reagentsTable.getTableHeader().setReorderingAllowed(false);
if (newDialog.getMethodsFile() != null) {
txtConfigurationFileLocation.setText(newDialog.getMethodsFile().getAbsolutePath());
} else {
txtConfigurationFileLocation.setText("(not saved to file)");
}
reagentsTable.getColumnModel().getColumn(0).setMaxWidth(30);
reagentsTable.getColumnModel().getColumn(1).setMaxWidth(100);
}
/**
* 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();
isotopeCorrectionPanel = new javax.swing.JPanel();
reagentsTableJScrollPane = new javax.swing.JScrollPane();
reagentsTable = new javax.swing.JTable();
configFilePanel = new javax.swing.JPanel();
txtConfigurationFileLocation = new javax.swing.JTextField();
browseConfigButton = new javax.swing.JButton();
saveConfigButton = new javax.swing.JButton();
okButton = new javax.swing.JButton();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
setTitle("Reporter Method Settings");
backgroundPanel.setBackground(new java.awt.Color(230, 230, 230));
isotopeCorrectionPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Reagents"));
isotopeCorrectionPanel.setOpaque(false);
reagentsTable.setModel(new CorrectionTableModel());
reagentsTable.setOpaque(false);
reagentsTableJScrollPane.setViewportView(reagentsTable);
javax.swing.GroupLayout isotopeCorrectionPanelLayout =
new javax.swing.GroupLayout(isotopeCorrectionPanel);
isotopeCorrectionPanel.setLayout(isotopeCorrectionPanelLayout);
isotopeCorrectionPanelLayout.setHorizontalGroup(
isotopeCorrectionPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
isotopeCorrectionPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
reagentsTableJScrollPane,
javax.swing.GroupLayout.DEFAULT_SIZE,
804,
Short.MAX_VALUE)
.addContainerGap()));
isotopeCorrectionPanelLayout.setVerticalGroup(
isotopeCorrectionPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
isotopeCorrectionPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
reagentsTableJScrollPane,
javax.swing.GroupLayout.DEFAULT_SIZE,
308,
Short.MAX_VALUE)
.addContainerGap()));
configFilePanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Settings File"));
configFilePanel.setOpaque(false);
txtConfigurationFileLocation.setEditable(false);
browseConfigButton.setText("Browse");
browseConfigButton.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
browseConfigButtonActionPerformed(evt);
}
});
saveConfigButton.setText("Save As");
saveConfigButton.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
saveConfigButtonActionPerformed(evt);
}
});
javax.swing.GroupLayout configFilePanelLayout = new javax.swing.GroupLayout(configFilePanel);
configFilePanel.setLayout(configFilePanelLayout);
configFilePanelLayout.setHorizontalGroup(
configFilePanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
configFilePanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(txtConfigurationFileLocation)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(browseConfigButton)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(saveConfigButton)
.addContainerGap()));
configFilePanelLayout.setVerticalGroup(
configFilePanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
configFilePanelLayout
.createSequentialGroup()
.addContainerGap()
.addGroup(
configFilePanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(
txtConfigurationFileLocation,
javax.swing.GroupLayout.PREFERRED_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(saveConfigButton)
.addComponent(browseConfigButton))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)));
okButton.setText("OK");
okButton.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
okButtonActionPerformed(evt);
}
});
javax.swing.GroupLayout backgroundPanelLayout = new javax.swing.GroupLayout(backgroundPanel);
backgroundPanel.setLayout(backgroundPanelLayout);
backgroundPanelLayout.setHorizontalGroup(
backgroundPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
backgroundPanelLayout
.createSequentialGroup()
.addContainerGap()
.addGroup(
backgroundPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(
configFilePanel,
javax.swing.GroupLayout.Alignment.TRAILING,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE)
.addComponent(
isotopeCorrectionPanel,
javax.swing.GroupLayout.Alignment.TRAILING,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE)
.addGroup(
javax.swing.GroupLayout.Alignment.TRAILING,
backgroundPanelLayout
.createSequentialGroup()
.addGap(0, 0, Short.MAX_VALUE)
.addComponent(
okButton,
javax.swing.GroupLayout.PREFERRED_SIZE,
66,
javax.swing.GroupLayout.PREFERRED_SIZE)))
.addContainerGap()));
backgroundPanelLayout.setVerticalGroup(
backgroundPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
backgroundPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
configFilePanel,
javax.swing.GroupLayout.PREFERRED_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(
isotopeCorrectionPanel,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(okButton)
.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
/**
* Opens a file chooser for importing method settings.
*
* @param evt
*/
private void browseConfigButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_browseConfigButtonActionPerformed
if (txtConfigurationFileLocation.getText().length() > 0) {
newDialog
.getReporterGui()
.getLastSelectedFolder()
.setLastSelectedFolder(txtConfigurationFileLocation.getText());
}
File selectedFile =
Util.getUserSelectedFile(
this,
".xml",
"Reporter Method File (*.xml)",
"Select Settings File",
newDialog.getReporterGui().getLastSelectedFolder().getLastSelectedFolder(),
null,
true);
if (selectedFile != null) {
try {
methodsFactory.importMethods(selectedFile);
newDialog.setSelectedMethod(newDialog.getMethod(newDialog.getSelectedMethod().getName()));
newDialog.setReagents(newDialog.getSelectedMethod().getReagentsSortedByMass());
refresh();
txtConfigurationFileLocation.setText(selectedFile.getAbsolutePath());
newDialog.setMethodsFile(selectedFile);
newDialog
.getReporterGui()
.getLastSelectedFolder()
.setLastSelectedFolder(selectedFile.getPath());
} catch (IOException e) {
JOptionPane.showMessageDialog(
null,
"File " + selectedFile.getAbsolutePath() + " not found.",
"File Not Found",
JOptionPane.WARNING_MESSAGE);
} catch (XmlPullParserException e) {
JOptionPane.showMessageDialog(
null,
"An error occurred while parsing "
+ selectedFile.getAbsolutePath()
+ " at line "
+ e.getLineNumber()
+ ".",
"Parsing Error",
JOptionPane.WARNING_MESSAGE);
e.printStackTrace();
}
}
} // GEN-LAST:event_browseConfigButtonActionPerformed
/**
* Save the method settings.
*
* @param evt
*/
private void saveConfigButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_saveConfigButtonActionPerformed
String tempFileName = null;
if (txtConfigurationFileLocation.getText().length() > 0) {
newDialog
.getReporterGui()
.getLastSelectedFolder()
.setLastSelectedFolder(txtConfigurationFileLocation.getText());
tempFileName = new File(txtConfigurationFileLocation.getText()).getName();
}
File selectedFile =
Util.getUserSelectedFile(
this,
".xml",
"Reporter Method File (*.xml)",
"Save Settings File",
newDialog.getReporterGui().getLastSelectedFolder().getLastSelectedFolder(),
tempFileName,
false);
if (selectedFile != null) {
try {
methodsFactory.saveFile(selectedFile);
newDialog.setMethodsFile(selectedFile);
txtConfigurationFileLocation.setText(selectedFile.getAbsolutePath());
valuesChanged = false;
JOptionPane.showMessageDialog(
null,
"Settings saved to " + selectedFile.getAbsolutePath() + ".",
"Settings Saved",
JOptionPane.INFORMATION_MESSAGE);
} catch (IOException ex) {
JOptionPane.showMessageDialog(
null,
"An error occured when saving the file.",
"File Error",
JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
} // GEN-LAST:event_saveConfigButtonActionPerformed
/**
* Close the dialog.
*
* @param evt
*/
private void okButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_okButtonActionPerformed
if (valuesChanged) {
int selection =
JOptionPane.showConfirmDialog(
this,
"Do you want to save the new settings to a file?",
"Save File?",
JOptionPane.YES_NO_CANCEL_OPTION);
if (selection == JOptionPane.YES_OPTION) {
saveConfigButtonActionPerformed(null);
} else if (selection == JOptionPane.CANCEL_OPTION) {
return;
} else if (selection == JOptionPane.NO_OPTION) {
newDialog.setMethodsFile(null);
}
}
newDialog.updateReagentNames();
dispose();
} // GEN-LAST:event_okButtonActionPerformed
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JPanel backgroundPanel;
private javax.swing.JButton browseConfigButton;
private javax.swing.JPanel configFilePanel;
private javax.swing.JPanel isotopeCorrectionPanel;
private javax.swing.JButton okButton;
private javax.swing.JTable reagentsTable;
private javax.swing.JScrollPane reagentsTableJScrollPane;
private javax.swing.JButton saveConfigButton;
private javax.swing.JTextField txtConfigurationFileLocation;
// End of variables declaration//GEN-END:variables
/**
* Updates the combo box and table values based on the currently selected quantification method.
*/
private void refresh() {
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
reagentsTable.revalidate();
reagentsTable.repaint();
}
});
}
/** Table model for the correction factors table. */
private class CorrectionTableModel extends DefaultTableModel {
@Override
public int getRowCount() {
return newDialog.getReagents().size();
}
@Override
public int getColumnCount() {
return 8;
}
@Override
public String getColumnName(int column) {
switch (column) {
case 0:
return " ";
case 1:
return "Name";
case 2:
return "Mass";
case 3:
return "-2 C13 [%]";
case 4:
return "-1 C13 [%]";
case 5:
return "Monoisotopic [%]";
case 6:
return "+1 C13 [%]";
case 7:
return "+2 C13 [%]";
default:
return "";
}
}
@Override
public Object getValueAt(int row, int column) {
String reagentName = newDialog.getReagents().get(row);
switch (column) {
case 0:
return row + 1;
case 1:
return newDialog.getSelectedMethod().getReagent(reagentName).getReporterIon().getName();
case 2:
return newDialog
.getSelectedMethod()
.getReagent(reagentName)
.getReporterIon()
.getTheoreticMass()
+ ElementaryIon.proton.getTheoreticMass();
case 3:
return newDialog.getSelectedMethod().getReagent(reagentName).getMinus2();
case 4:
return newDialog.getSelectedMethod().getReagent(reagentName).getMinus1();
case 5:
return newDialog.getSelectedMethod().getReagent(reagentName).getRef();
case 6:
return newDialog.getSelectedMethod().getReagent(reagentName).getPlus1();
case 7:
return newDialog.getSelectedMethod().getReagent(reagentName).getPlus2();
default:
return "";
}
}
@Override
public void setValueAt(Object aValue, int row, int column) {
String reagentName = newDialog.getReagents().get(row);
switch (column) {
case 1:
newDialog
.getSelectedMethod()
.getReagent(reagentName)
.getReporterIon()
.setName((String) aValue);
valuesChanged = true;
break;
case 2:
newDialog
.getSelectedMethod()
.getReagent(reagentName)
.getReporterIon()
.setTheoreticMass((Double) aValue);
valuesChanged = true;
break;
case 3:
newDialog.getSelectedMethod().getReagent(reagentName).setMinus2((Double) aValue);
valuesChanged = true;
break;
case 4:
newDialog.getSelectedMethod().getReagent(reagentName).setMinus1((Double) aValue);
valuesChanged = true;
break;
case 5:
newDialog.getSelectedMethod().getReagent(reagentName).setRef((Double) aValue);
valuesChanged = true;
break;
case 6:
newDialog.getSelectedMethod().getReagent(reagentName).setPlus1((Double) aValue);
valuesChanged = true;
break;
case 7:
newDialog.getSelectedMethod().getReagent(reagentName).setPlus2((Double) aValue);
valuesChanged = true;
break;
default:
break;
}
}
@Override
public Class getColumnClass(int columnIndex) {
return getValueAt(0, columnIndex).getClass();
}
@Override
public boolean isCellEditable(int row, int column) {
return column != 0;
}
}
}