private void runSicer() {
sicerControl = new SicerControl();
sicerControl.setKoBedFile(txtKobedFileSICER.getText(), txtKoPrefixSICER.getText());
sicerControl.setWtBedFile(txtWtBedFileSICER.getText(), txtWtPrefixSICER.getText());
sicerControl.setKoControlFile(txtKoColFileSICER.getText());
sicerControl.setWtControlFile(txtWtcolFileSICER.getText());
sicerControl.setEvalue(100);
sicerControl.setFDR(0.01);
sicerControl.setSpecies(guiLayeredPanSpeciesVersion.getSelectSpecies());
sicerControl.setSicerType(cmbSICERtype.getSelectedValue());
sicerControl.setOutputDir(txtSavePath.getText());
methylationType = cmbMethyTypeSicer.getSelectedValue();
sicerControl.setMethylationType(methylationType);
if (methylationType == SicerControl.METHY_UNKNOWN) {
if (dialog.getWindowSize() == 0 && dialog.getGapSize() == 0) {
dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
dialog.setVisible(true);
sicerControl.setMethylationType(dialog.getWindowSize(), dialog.getGapSize());
} else {
sicerControl.setMethylationType(dialog.getWindowSize(), dialog.getGapSize());
}
}
sicerControl.peakCalling();
}
private void runMacs() {
macs14control = new Macs14control();
Species species = guiLayeredPanSpeciesVersion.getSelectSpecies();
Double pvalue = Double.parseDouble(txtPvalue.getText());
int mfoldMax = (Integer) mfoldMaxspinner.getValue();
int mfoldMin = (Integer) mfoldminspinner.getValue();
macs14control.setmfoldMax(mfoldMax);
macs14control.setMfoldMin(mfoldMin);
macs14control.setPathinput(txtInFileMacs.getText());
macs14control.setpathinputColl(txtControlFileMacs.getText());
macs14control.setPathoutput(txtSavePath.getText());
macs14control.setPvalue(pvalue);
macs14control.setSpecies(species);
macs14control.peakCalling();
}
/** Create the panel. */
public GuiPeakCalling() {
setLayout(null);
macs14RadioButton = new JRadioButton("macs14");
macs14RadioButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
if (macs14RadioButton.isSelected()) {
macs14Panel.setVisible(true);
Sicerpanel.setVisible(false);
}
}
});
macs14RadioButton.setFont(new Font("Dialog", Font.BOLD, 15));
macs14RadioButton.setHorizontalAlignment(SwingConstants.CENTER);
macs14RadioButton.setBounds(19, 116, 122, 31);
add(macs14RadioButton);
buttonGroup.add(macs14RadioButton);
sicerRadioButton = new JRadioButton("Sicer");
sicerRadioButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
if (sicerRadioButton.isSelected()) {
Sicerpanel.setVisible(true);
macs14Panel.setVisible(false);
}
}
});
sicerRadioButton.setFont(new Font("Dialog", Font.BOLD, 15));
sicerRadioButton.setBounds(27, 261, 103, 23);
add(sicerRadioButton);
buttonGroup.add(sicerRadioButton);
guiLayeredPanSpeciesVersion = new GuiLayeredPanSpeciesVersion();
guiLayeredPanSpeciesVersion.setBounds(27, 12, 237, 96);
add(guiLayeredPanSpeciesVersion);
JButton saveButton = new JButton("SAVE");
saveButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
String outPath = guiFileOpen.saveFileNameAndPath("", "");
txtSavePath.setText(outPath);
}
});
saveButton.setBounds(276, 25, 118, 25);
add(saveButton);
txtSavePath = new JTextField();
txtSavePath.setBounds(429, 25, 292, 25);
add(txtSavePath);
txtSavePath.setColumns(10);
macs14Panel = new JPanel();
macs14Panel.setLayout(null);
macs14Panel.setBounds(37, 157, 684, 96);
add(macs14Panel);
txtControlFileMacs = new JTextField();
txtControlFileMacs.setColumns(10);
txtControlFileMacs.setBounds(149, 49, 114, 25);
macs14Panel.add(txtControlFileMacs);
txtInFileMacs = new JTextField();
txtInFileMacs.setColumns(10);
txtInFileMacs.setBounds(149, 12, 114, 25);
macs14Panel.add(txtInFileMacs);
JButton controlFilebutton = new JButton("ControlFile");
controlFilebutton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
txtControlFileMacs.setText(guiFileOpen.openFileName("", ""));
}
});
controlFilebutton.setBounds(12, 49, 93, 25);
macs14Panel.add(controlFilebutton);
JButton inFilebutton = new JButton("InFile");
inFilebutton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
txtInFileMacs.setText(guiFileOpen.openFileName("", ""));
}
});
inFilebutton.setBounds(12, 12, 93, 25);
macs14Panel.add(inFilebutton);
mfoldminspinner = new JSpinner();
mfoldminspinner.setModel(new SpinnerNumberModel(new Integer(2), null, null, new Integer(1)));
mfoldminspinner.setBounds(403, 13, 69, 23);
macs14Panel.add(mfoldminspinner);
mfoldMaxspinner = new JSpinner();
mfoldMaxspinner.setModel(new SpinnerNumberModel(new Integer(300), null, null, new Integer(1)));
mfoldMaxspinner.setBounds(584, 13, 69, 23);
macs14Panel.add(mfoldMaxspinner);
JLabel pvalueLabel = new JLabel("pvalue");
pvalueLabel.setBounds(304, 49, 69, 25);
macs14Panel.add(pvalueLabel);
JLabel mfoldMaxLabel = new JLabel("mfoldMax");
mfoldMaxLabel.setBounds(495, 12, 81, 25);
macs14Panel.add(mfoldMaxLabel);
JLabel mfoldminLabel = new JLabel("mfoldMin");
mfoldminLabel.setBounds(304, 12, 81, 25);
macs14Panel.add(mfoldminLabel);
JButton mac14startbutton = new JButton("macs14Start");
mac14startbutton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
runMacs();
}
});
mac14startbutton.setBounds(521, 42, 132, 38);
macs14Panel.add(mac14startbutton);
txtPvalue = new JTextField();
txtPvalue.setText("0.01");
txtPvalue.setColumns(10);
txtPvalue.setBounds(403, 49, 69, 25);
macs14Panel.add(txtPvalue);
Sicerpanel = new JPanel();
Sicerpanel.setBounds(37, 294, 691, 296);
Sicerpanel.setVisible(false);
add(Sicerpanel);
Sicerpanel.setLayout(null);
cmbSICERtype = new JComboBoxData<PeakCallingSicerType>();
cmbSICERtype.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
setComponentVisibleSICER(cmbSICERtype.getSelectedValue());
}
});
cmbSICERtype.setBounds(18, 10, 323, 32);
Sicerpanel.add(cmbSICERtype);
cmbSICERtype.setMapItem(PeakCallingSicerType.getMapType());
sicer_df_rbPanel = new JPanel();
sicer_df_rbPanel.setBounds(18, 80, 517, 81);
Sicerpanel.add(sicer_df_rbPanel);
sicer_df_rbPanel.setLayout(null);
kobedFilebutton = new JButton("koBedFile");
kobedFilebutton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
String koBedPathAndFile = guiFileOpen.openFileName("", "");
txtKobedFileSICER.setText(koBedPathAndFile);
txtKoPrefixSICER.setText(FileOperate.getFileName(koBedPathAndFile).split("_")[0]);
}
});
kobedFilebutton.setBounds(16, 12, 106, 25);
sicer_df_rbPanel.add(kobedFilebutton);
txtKobedFileSICER = new JTextField();
txtKobedFileSICER.setColumns(10);
txtKobedFileSICER.setBounds(134, 11, 177, 27);
sicer_df_rbPanel.add(txtKobedFileSICER);
KoColFilebutton = new JButton("koColFile");
KoColFilebutton.setBounds(16, 49, 106, 25);
sicer_df_rbPanel.add(KoColFilebutton);
KoColFilebutton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
String koColPathAndFile = guiFileOpen.openFileName("", "");
txtKoColFileSICER.setText(koColPathAndFile);
}
});
KoColFilebutton.setEnabled(false);
txtKoColFileSICER = new JTextField();
txtKoColFileSICER.setBounds(134, 50, 175, 25);
sicer_df_rbPanel.add(txtKoColFileSICER);
txtKoColFileSICER.setColumns(10);
txtKoColFileSICER.setEnabled(false);
sicer_dfPanel = new JPanel();
sicer_dfPanel.setLayout(null);
sicer_dfPanel.setBounds(18, 173, 517, 81);
Sicerpanel.add(sicer_dfPanel);
wtBedFilebutton = new JButton("wtBedFile");
wtBedFilebutton.setBounds(12, 12, 106, 25);
sicer_dfPanel.add(wtBedFilebutton);
wtBedFilebutton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
String wtBedPathAndFile = guiFileOpen.openFileName("", "");
txtWtBedFileSICER.setText(wtBedPathAndFile);
txtWtPrefixSICER.setText(FileOperate.getFileName(wtBedPathAndFile).split("_")[0]);
}
});
wtBedFilebutton.setEnabled(false);
txtWtBedFileSICER = new JTextField();
txtWtBedFileSICER.setBounds(136, 12, 175, 25);
sicer_dfPanel.add(txtWtBedFileSICER);
txtWtBedFileSICER.setColumns(10);
txtWtBedFileSICER.setEditable(false);
wtcolFilebutton = new JButton("wtColFile");
wtcolFilebutton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
String wtColPathAndFile = guiFileOpen.openFileName("", "");
txtWtcolFileSICER.setText(wtColPathAndFile);
}
});
wtcolFilebutton.setBounds(12, 49, 106, 25);
sicer_dfPanel.add(wtcolFilebutton);
txtWtcolFileSICER = new JTextField();
txtWtcolFileSICER.setColumns(10);
txtWtcolFileSICER.setBounds(136, 49, 175, 25);
sicer_dfPanel.add(txtWtcolFileSICER);
JButton sicerStartbutton = new JButton("sicerSTART");
sicerStartbutton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
runSicer();
}
});
sicerStartbutton.setBounds(547, 80, 129, 174);
Sicerpanel.add(sicerStartbutton);
cmbMethyTypeSicer = new JComboBoxData<Integer>();
cmbMethyTypeSicer.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
methylationType = cmbMethyTypeSicer.getSelectedValue();
if (methylationType == 40) {
dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
dialog.setVisible(true);
System.out.println(dialog.getWindowSize());
System.out.println(dialog.getGapSize());
}
}
});
cmbMethyTypeSicer.setMapItem(SicerControl.getMapMethyStr2Int());
cmbMethyTypeSicer.setBounds(18, 54, 323, 24);
Sicerpanel.add(cmbMethyTypeSicer);
kobedFilebutton.setEnabled(true);
txtKobedFileSICER.setEnabled(true);
txtKoPrefixSICER = new JTextField();
txtKoPrefixSICER.setBounds(382, 15, 123, 19);
sicer_df_rbPanel.add(txtKoPrefixSICER);
txtKoPrefixSICER.setColumns(10);
JLabel koPrelabel = new JLabel("koPrefix");
koPrelabel.setBounds(315, 17, 68, 15);
sicer_df_rbPanel.add(koPrelabel);
wtcolFilebutton.setEnabled(false);
txtWtcolFileSICER.setEnabled(false);
txtWtPrefixSICER = new JTextField();
txtWtPrefixSICER.setBounds(386, 15, 119, 19);
sicer_dfPanel.add(txtWtPrefixSICER);
txtWtPrefixSICER.setColumns(10);
txtWtPrefixSICER.setEditable(false);
wtPrefix = new JLabel("wtPrefix");
wtPrefix.setBounds(317, 17, 68, 15);
sicer_dfPanel.add(wtPrefix);
wtPrefix.setEnabled(false);
}
