@Override
@SuppressWarnings(value = "unchecked")
public RunImportData constructRunImportData() {
// Instanciate the DOM document
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
docFactory.setIgnoringComments(true);
docFactory.setIgnoringElementContentWhitespace(true);
docFactory.setValidating(false);
DocumentBuilder docBuilder;
Document xmlDoc = null;
try {
docBuilder = docFactory.newDocumentBuilder();
xmlDoc = docBuilder.parse(new InputSource("./LC480.xml"));
} catch (Exception ex) {
Exceptions.printStackTrace(ex);
}
// Setup the objects need for the import
// Setup the Run object
// Run run = new RunImpl();
// Set the run name and date
Run run = new RunImpl();
// Retrieve the xml file
// For development purposes, just use an example xml file
// File lcRdmlFile = IOUtilities.openXmlFile("Lightcycler XML Data Import");
// if (lcRdmlFile == null) {
// return null;
// }
// Setup the profile arraylists
ArrayList<SampleProfile> sampleProfileList = Lists.newArrayList();
ArrayList<CalibrationProfile> calbnProfileList = Lists.newArrayList();
// Determine the strandedness of the majority of the Targets...too bad that this is not provided
// by the instrument
TargetStrandedness targetStrandedness = RunImportUtilities.isTheTargetSingleStranded();
// Get the all of the profile nodes
NodeList profileNodeList = xmlDoc.getElementsByTagName("series");
// Cycle through all of the profile nodes
for (int i = 0; i < profileNodeList.getLength(); i++) {
// TODO determine whether this profile is sample or calibration
Profile profile = createProfileType(run);
Element profileElement = (Element) profileNodeList.item(i);
String wellLabel = profileElement.getAttribute("title");
// TODO parse the well label, sample and amplicon name from the wellLabel
NodeList cycleList = profileElement.getElementsByTagName("point");
// Collect and set the Fc reading
profile.setFcReadings(retrieveFcReadings(cycleList));
if (CalibrationProfile.class.isAssignableFrom(profile.getClass())) {
CalibrationProfile calProfile = (CalibrationProfile) profile;
calbnProfileList.add(calProfile);
} else {
SampleProfile sampleProfile = (SampleProfile) profile;
sampleProfileList.add(sampleProfile);
}
}
return null;
}
/**
* This conducts both nonlinear regression-derived Fb subtraction and baseline slope correction.
*
* @param profile
*/
private void conductBaselineCorrection() {
// Start with correcting for the NR-derived Fb slope
double[] rawFcReadings = profile.getRawFcReadings();
double[] processedFcDataset = new double[rawFcReadings.length]; // The new optimized Fc dataset
// This assumes that nonlinear regression has been conducted AND it was successfully completed
double nrFb = profile.getNrFb(); // The regression derived Fb
double nrFbSlope = profile.getNrFbSlope(); // The regression-derived Fb slope
for (int i = 0; i < processedFcDataset.length; i++) {
processedFcDataset[i] = rawFcReadings[i] - nrFb - (nrFbSlope * (i + 1));
}
profile.setFcReadings(processedFcDataset);
}