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(); }