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MainWindow.java
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MainWindow.java
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package uk.ac.liv.iib.pgb.neo;
import javax.swing.*;
import javax.swing.UIManager.LookAndFeelInfo;
import javax.swing.border.*;
import java.awt.*;
import java.awt.event.*;
import java.io.*;
import java.util.*;
// A Formatted JFileChooser
class NewFileChooser extends JFileChooser
{
private static final long serialVersionUID = -6120691117434635908L;
public NewFileChooser( )
{
super();
JTextArea help = new JTextArea(6,14);
help.setLineWrap(true);
help.setWrapStyleWord(true);
help.setText("You should load a Fasta file format database");
// setAccessory(help);
}
}
public class MainWindow extends JFrame
{
final boolean TRYPTIC_OUTPUT = false;
private static final long serialVersionUID = 7722552335555737726L;
static File settingsFile = new File(".settings.txt");
private void writePair(String key, String value, BufferedWriter wr ) throws IOException
{
// String output ="\""+key+"\",\""+value+"\"\n";
// wr.write(output);
}
//Saves all settings to properties file
// These are automatically reloaded when program restarts
public void saveSettings()
{
try {
Properties prop = new Properties();
// set the properties value
prop.setProperty("database", databaseName.getText());
BufferedWriter wr = new BufferedWriter(new FileWriter(settingsFile));
wr.write(databaseName.getText()+"\n");
String column = ""+setColumn+"\n";
if (setColumn == 0)
column = autoDetect+"\n";
writePair("column",column,wr);
wr.write(column);
wr.write(setDelim+"\n");
writePair("delimiter",column,wr);
writePair("inputFile",inputName.getText(),wr);
writePair("outputFile",outputName.getText(),wr);
writePair("processedOutputFile",outputTrypticName.getText(),wr);
writePair("searchoption",""+Options.DBSearch,wr);
wr.write(inputName.getText()+"\n");
wr.write(outputName.getText()+"\n");
wr.write(outputTrypticName.getText()+"\n");
wr.write(""+Options.DBSearch+"\n");
wr.write(""+Options.removeUnused+"\n");
wr.write(Options.getSearch()+"\n");
wr.write(""+Options.sameFolder+"\n");
wr.write(""+Options.sameDriveLetter+"\n");
wr.write(""+Options.matchingPeptides+"\n");
wr.write(""+Options.getMIN()+"\n");
wr.write(""+Options.getFDR()+"\n");
wr.write(""+Options.useLogRatio+"\n");
wr.close();
} catch (IOException e)
{
e.printStackTrace();
}
}
public void loadSettings()
{
if (hide)
System.err.println("Loading "+settingsFile);
Scanner s;
try {
s = new Scanner(settingsFile);
if (s.hasNext())
{
String fileName = s.nextLine();
databaseFile = new File(fileName);
databaseName.setText(fileName);
if (hide)
System.err.println("Database = "+fileName);
fcDB.setCurrentDirectory(databaseFile);
}
if (s.hasNext())
{
String popColumn = s.nextLine();
setColumnCB.setSelectedItem(popColumn);
//for command-line mode
if (popColumn.equals(autoDetect))
{
setColumn = 0;
}
else
setColumn = Integer.parseInt(popColumn);
}
if (s.hasNext())
{
String popColumn = s.nextLine();
setDelimCB.setSelectedItem(popColumn);
setDelim = popColumn;
}
if (s.hasNext())
{
String fileName = s.nextLine();
inputFile = new File(fileName);
inputName.setText(fileName);
fcInput.setCurrentDirectory(inputFile);
if (hide)
System.err.println("Input = "+fileName);
}
if (s.hasNext())
{
String fileName = s.nextLine();
outputFile = new File(fileName);
outputName.setText(fileName);
fcOutput.setCurrentDirectory(outputFile);
if (hide)
System.err.println("Output = "+fileName);
}
if (s.hasNext())
{
String fileName = s.nextLine();
outputTrypticFile = new File(fileName);
outputTrypticName.setText(fileName);
fcOutputTryptic.setCurrentDirectory(outputFile);
if (hide)
System.err.println("Tryptic Output = "+fileName);
}
if (s.hasNext())
{
String searchDisabled = s.nextLine();
if (searchDisabled.trim().toLowerCase().equals("true"))
{
optionPanel.setSearch(true);
}
}
if (s.hasNext())
{
String searchDisabled = s.nextLine();
if (searchDisabled.trim().toLowerCase().equals("true"))
{
optionPanel.setUnused(true);
}
}
if (s.hasNext())
{
String setSearchString = s.nextLine();
Options.setSearchString(setSearchString);
}
if (s.hasNext())
{
String searchSame = s.nextLine();
if (searchSame.trim().toLowerCase().equals("true"))
{
optionPanel.setSameFolder(true);
}
else
optionPanel.setSameFolder(false);
}
if (s.hasNext())
{
String searchSame = s.nextLine();
if (searchSame.trim().toLowerCase().equals("true"))
{
optionPanel.setSameDriveLetter(true);
}
else
optionPanel.setSameDriveLetter(false);
}
if (s.hasNext())
{
String searchSame = s.nextLine();
if (searchSame.trim().toLowerCase().equals("true"))
{
optionPanel.setMatching(true);
}
else
optionPanel.setMatching(false);
}
if (s.hasNext())
{
String value = s.nextLine();
Options.setMIN(value);
}
if (s.hasNext())
{
String value = s.nextLine();
Options.setFDR(value);
}
if (s.hasNext())
{
String searchSame = s.nextLine();
if (searchSame.trim().toLowerCase().equals("true"))
{
optionPanel.setLogRatio(true);
}
else
optionPanel.setLogRatio(false);
}
if (Options.sameDriveLetter)
{
remapFiles();
}
appendStatus("Settings loaded\n");
s.close();
} catch (FileNotFoundException e) {
appendStatus("Settings file not found, a new file will be created.\n");
}
}
// Drive letters may change between uses
// common when using portable hard disks
void remapFiles()
{
File f= new File(".");
String path = f.getAbsolutePath();
if (path.length() < 2)
return;
if (path.charAt(1) != ':')
return;
String input = inputName.getText();
if ( (input.length() > 1) && (input.charAt(1) == ':') )
{
String newpath = path.substring(0,1) + input.substring(1);
inputFile = new File(newpath);
inputName.setText(newpath);
fcInput.setCurrentDirectory(inputFile);
}
input = databaseName.getText();
if ( (input.length() > 1) && (input.charAt(1) == ':') )
{
String newpath = path.substring(0,1) + input.substring(1);
databaseFile = new File(newpath);
databaseName.setText(newpath);
fcDB.setCurrentDirectory(databaseFile);
}
input = outputTrypticName.getText();
if ( (input.length() > 1) && (input.charAt(1) == ':') )
{
String newpath = path.substring(0,1) + input.substring(1);
outputTrypticFile = new File(newpath);
outputTrypticName.setText(newpath);
fcOutputTryptic.setCurrentDirectory(outputFile);
}
input = outputName.getText();
if ( (input.length() > 1) && (input.charAt(1) == ':') )
{
String newpath = path.substring(0,1) + input.substring(1);
outputFile = new File(newpath);
outputName.setText(newpath);
fcOutput.setCurrentDirectory(outputFile);
}
}
public MainWindow()
{
fcDB = new NewFileChooser();
fcInput = new NewFileChooser();
fcOutput = new NewFileChooser();
fcOutputTryptic = new NewFileChooser();
buildGUI();
pack();
if (hide)
{
startProcess();
System.exit(0);
}
else
{
setVisible(true);
}
setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
}
static JFileChooser fcDB ; //= new NewFileChooser();
static JFileChooser fcInput ; //= new NewFileChooser();
static JFileChooser fcOutput ; //= new NewFileChooser();
static JFileChooser fcOutputTryptic ; //= new NewFileChooser();
public void changeDatabase()
{
databaseFile = changeFile(fcDB,databaseName);
}
public void changeInput()
{
inputFile = changeFile(fcInput,inputName);
if (inputFile == null)
return;
String fname = inputFile.getPath().replaceAll(".csv","");
if ((outputFile == null) || (Options.sameFolder) )
{
outputFile = new File(fname+"_with_filter.csv");
outputName.setText(outputFile.getPath());
}
if ((outputTrypticFile == null) || (Options.sameFolder) )
{
outputTrypticFile = new File(fname+"_processed.csv");
outputTrypticName.setText(outputTrypticFile.getPath());
}
}
public void changeOutput()
{
fcOutput.setPreferredSize(new Dimension(getWidth()*7/8,getHeight()*4/5) );
if (fcOutput.showSaveDialog(this) == JFileChooser.APPROVE_OPTION)
{
outputFile = fcOutput.getSelectedFile();
if (inputFile != null)
if (inputFile.getPath().toLowerCase().endsWith(".csv"))
if (!outputFile.getPath().toLowerCase().endsWith(".csv"))
{
outputFile = new File(outputFile.getPath()+".csv");
}
outputName.setText(outputFile.getPath());
}
}
public void changeOutputTryptic()
{
fcOutputTryptic.setPreferredSize(new Dimension(getWidth()*7/8,getHeight()*4/5) );
if (fcOutputTryptic.showSaveDialog(this) == JFileChooser.APPROVE_OPTION)
{
outputTrypticFile = fcOutputTryptic.getSelectedFile();
if (inputFile != null)
if (inputFile.getPath().toLowerCase().endsWith(".csv"))
if (!outputTrypticFile.getPath().toLowerCase().endsWith(".csv"))
{
outputTrypticFile = new File(outputTrypticFile.getPath()+".csv");
}
outputTrypticName.setText(outputTrypticFile.getPath());
}
}
public File changeFile(JFileChooser fc, JTextField fname)
{
fc.setPreferredSize(new Dimension(getWidth()*7/8,getHeight()*4/5) );
int returnVal = fc.showOpenDialog(this);
File newFile = null;
if (returnVal == JFileChooser.APPROVE_OPTION)
{
newFile = fc.getSelectedFile();
}
if (newFile == null)
return null;
fname.setText(newFile.getPath());
return newFile;
}
String autoDetect = "Auto-Detect";
static int setColumn = 0;
File databaseFile;
JTextField databaseName = new JTextField();
File inputFile;
JTextField inputName = new JTextField();
File outputFile;
JTextField outputName = new JTextField();
File outputTrypticFile;
JTextField outputTrypticName = new JTextField();
JComboBox<String> setColumnCB;
JComboBox<String> setDelimCB;
String setDelim="";
String[] headingsDelim = {autoDetect, "Tab", "Comma"};
private JPanel makeTopPanel()
{
JPanel top = new JPanel();
top.setBorder(new TitledBorder("Settings"));
GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.HORIZONTAL ;
c.gridx = 0;
c.gridy = 0;
c.weightx = 1;
c.ipady = 10;
top.setLayout(new GridBagLayout());
top.add(new JLabel("Database File"),c);
c.gridx = 1;
c.weightx = 4;
databaseName.setToolTipText("<html>A fasta file to search against for tryptic peptides.</html>");
databaseName.setEditable(false);
top.add(databaseName,c);
c.weightx = 1;
c.gridx=2;
JButton changeDB = new JButton("Change Database");
changeDB.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
changeDatabase();
checkReady();
}
}
);
top.add(changeDB,c);
c.gridy++;
c.gridx = 0;
top.add(new JLabel("Peptide Column"),c);
c.gridx++;
int maxColumn = 99;
String[] headings = new String[maxColumn+1];
headings[0]=autoDetect;
for (int i=1; i <= maxColumn; i++)
headings[i] =""+i;
setColumnCB = new JComboBox<String>(headings);
top.add(setColumnCB,c);
setColumnCB.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
JComboBox<String> cb = (JComboBox<String>)e.getSource();
String name = (String)cb.getSelectedItem();
if (name.equals(autoDetect))
{
setColumn = 0;
}
else
setColumn = Integer.parseInt(name);
}
}
);
c.gridy++;
c.gridx = 0;
top.add(new JLabel("Delimiter"),c);
c.gridx++;
setDelimCB = new JComboBox<String>(headingsDelim);
top.add(setDelimCB,c);
setDelimCB.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
@SuppressWarnings("unchecked")
JComboBox<String> cb = (JComboBox<String>)e.getSource();
String name = (String)cb.getSelectedItem();
setDelim = name;
}
}
);
return top;
}
private JPanel makeFilesPanel()
{
JPanel top = new JPanel();
top.setBorder(new TitledBorder("Files"));
GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.HORIZONTAL ;
c.gridx = 0;
c.gridy = 0;
c.weightx = 1;
c.ipady = 10;
top.setLayout(new GridBagLayout());
top.add(new JLabel("Input File"),c);
c.gridx = 1;
c.weightx = 6;
inputName.setToolTipText("<html>This file contains the Progenesis peptides output csv.</html>");
inputName.setEditable(false);
top.add(inputName,c);
c.weightx = 1;
c.gridx=4;
JButton changeDB = new JButton("Change File");
changeDB.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
changeInput();
checkReady();
}
}
);
top.add(changeDB,c);
c.gridx++;
JButton viewInput = new JButton("Open");
viewInput.setToolTipText("<html>Opens with external program</html>");
top.add(viewInput,c);
viewInput.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (Desktop.isDesktopSupported())
{
Desktop desktop = Desktop.getDesktop();
try
{
desktop.open(inputFile);
}catch(Exception xe) {xe.printStackTrace();}
}
}
}
);
c.gridy++;
c.gridx = 0;
top.add(new JLabel("Output File"),c);
c.gridx = 1;
c.weightx = 6;
outputName.setEditable(false);
outputName.setToolTipText("<html>This file will be written to with the Progenesis peptides output csv including additional columns.</html>");
top.add(outputName,c);
c.weightx = 1;
c.gridx=4;
JButton changeOutputB = new JButton("Change File");
changeOutputB.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
changeOutput();
checkReady();
}
}
);
top.add(changeOutputB,c);
c.gridx++;
JButton viewOutputB = new JButton("Open");
viewOutputB.setToolTipText("<html>Opens with external program</html>");
top.add(viewOutputB,c);
viewOutputB.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (Desktop.isDesktopSupported())
{
Desktop desktop = Desktop.getDesktop();
try
{
desktop.open(outputFile);
}catch(Exception xe) {xe.printStackTrace();}
}
}
}
);
c.gridy++;
c.gridx = 0;
if (true)
{
top.add(new JLabel("Processed Output"),c);
c.gridx = 1;
c.weightx = 6;
outputTrypticName.setEditable(false);
outputTrypticName.setToolTipText("<html>This file will be written to with the 'normalised' neopeptide values.</html>");
top.add(outputTrypticName,c);
c.weightx = 1;
c.gridx=4;
JButton changeTrypticOutputB = new JButton("Change File");
changeTrypticOutputB.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
changeOutputTryptic();
checkReady();
}
}
);
top.add(changeTrypticOutputB,c);
c.gridx++;
JButton viewTrypticeOutputB = new JButton("Open");
viewTrypticeOutputB.setToolTipText("<html>Opens with external program</html>");
top.add(viewTrypticeOutputB,c);
viewTrypticeOutputB.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (Desktop.isDesktopSupported())
{
Desktop desktop = Desktop.getDesktop();
try
{
desktop.open(outputTrypticFile);
}catch(Exception xe) {xe.printStackTrace();}
}
}
}
);
}
return top;
}
JTextArea statusArea = new JTextArea();
private JPanel makeStatusPanel()
{
JPanel statusPanel = new JPanel();
statusPanel.setLayout(new BorderLayout());
statusPanel.setBorder(new TitledBorder("Status"));
statusArea.setEditable(false);
JScrollPane scroller = new JScrollPane(statusArea);
statusPanel.add(scroller);
return statusPanel;
}
JButton startButton = new JButton("Process neopeptides");
JButton cancelButton = new JButton("Stop process");
JButton quitButton = new JButton("Exit");
void checkReady()
{
boolean ready = false;
if (inputFile != null)
if (outputFile != null)
if (databaseFile != null)
{
ready = true;
}
startButton.setEnabled(ready);
}
private JPanel makeButtonPanel()
{
JPanel top = new JPanel();
top.setLayout(new BorderLayout());
top.setBorder(new TitledBorder("Actions"));
cancelButton.setEnabled(false);
cancelButton.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
doCancel();
}
}
);
quitButton.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
doExit();
}
}
);
startButton.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
startButton.setEnabled(false);
cancelButton.setEnabled(true);
startProcess();
}
}
);
top.add(startButton,BorderLayout.NORTH);
// top.add(cancelButton,BorderLayout.SOUTH);
JPanel subPanel = new JPanel();
subPanel.setLayout(new BorderLayout());
subPanel.add(quitButton,BorderLayout.EAST);
subPanel.add(cancelButton,BorderLayout.WEST);
subPanel.add(startButton,BorderLayout.CENTER);
//
top.add(subPanel,BorderLayout.SOUTH);
return top;
}
void buildMenus()
{
JMenuBar mb = new JMenuBar();
JMenu root = new JMenu("Tools");
JMenuItem check = new JMenuItem("Check peptides against database");
root.add(check);
mb.add(root);
check.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
startCheckProcess();
}
}
);
JMenuItem showOptions = new JMenuItem("Show / Hide Options");
root.add(showOptions);
showOptions.addActionListener(
new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
optionPanel.setVisible(!optionPanel.isVisible());
}
}
);
setJMenuBar(mb);
}
void appendStatus(String text)
{
statusArea.append(text);
statusArea.setCaretPosition(statusArea.getText().length());
}
void updateStatus(String text)
{
String allText = statusArea.getText();
if(allText.lastIndexOf("\n")>0) {
allText = allText.substring(0, allText.lastIndexOf("\n"));
}
statusArea.setText(allText+"\n");
statusArea.append(text);
}
Options optionPanel = new Options();
private void buildGUI()
{
JPanel containerPanel = new JPanel();
JPanel mainPanel = new JPanel();
JPanel topPanel = makeTopPanel();
JPanel inputPanel = makeFilesPanel();
JPanel statusPanel = makeStatusPanel();
JPanel buttonPanel = makeButtonPanel();
mainPanel.setLayout(new BorderLayout());
JPanel topSub = new JPanel();
topSub.setLayout(new GridLayout(2,1));
topSub.add(topPanel);
topSub.add(inputPanel);
mainPanel.add(topSub, BorderLayout.NORTH);
JPanel botSub = new JPanel();
botSub.setLayout(new BorderLayout());
botSub.add(statusPanel,BorderLayout.CENTER);
botSub.add(buttonPanel,BorderLayout.SOUTH);
mainPanel.add(botSub, BorderLayout.CENTER);
int h = (int) java.awt.Toolkit.getDefaultToolkit().getScreenSize().getHeight();
int w = (int) java.awt.Toolkit.getDefaultToolkit().getScreenSize().getWidth();
w = Math.max(1100, w*1/2);
h = Math.min(800, h*7/8);
setPreferredSize(new Dimension(w,h));
containerPanel.setLayout(new BorderLayout());
containerPanel.add(mainPanel,BorderLayout.CENTER);
containerPanel.add(optionPanel,BorderLayout.NORTH);