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();
}
