Make XML Parameters

Script

List split = new ArrayList();
if (!string.equals("")) {
	String regexString = ",";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = string.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

Value

Script

List split = new ArrayList();
if (!string.equals("")) {
	String regexString = ",";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = string.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

Script

import org.dom4j.Document;
import org.dom4j.Element;
import org.dom4j.dom.DOMDocument;

// Create Document.
Document paramDoc = new DOMDocument();

// Add root element.
Element rootElement = paramDoc.addElement("Parameters");
Element paramElement = rootElement.addElement("Parameter")
	.addAttribute("name", "associatedSNPs");
Element assocElement = paramElement.addElement("AssociatedSNPs");

//ArrayList xmlElements = new ArrayList();
// Loop through SNPs, split into ID & pValue.
for (int i = 0; i < associatedSNPs.size(); i++) {
	String line = (String) associatedSNPs.get(i);
	if (line == null || line.equals(""))
		continue;
	String [] lineArray = line.split("\t");
	Element snpElement = assocElement.addElement("AssociatedSNP")
		.addAttribute("rsId", lineArray[0]);
	if (lineArray.length > 1)
		snpElement.addAttribute("pValue", lineArray[1]);
}

paramXML = paramDoc.asXML();

Script

import org.dom4j.Element;
import org.dom4j.Document;
import org.dom4j.io.SAXReader;

List errors = new ArrayList();

if (additionalParams == void || additionalParams.size() == 0) {
	paramXmlOut = paramXmlIn;
} else {

	// Initialise Reader for parameter XML.
	SAXReader reader = new SAXReader(false);
	reader.setIncludeInternalDTDDeclarations(false);
	reader.setIncludeExternalDTDDeclarations(false);

	Document paramDoc = reader.read(new StringReader(paramXmlIn));
	Element rootElement = paramDoc.getRootElement();
	for (int i = 0; i < additionalParams.size(); i++) {
		String paramInfo = (String) additionalParams.get(i);
		if (paramInfo == null || paramInfo.equals(""))
			continue;
		String [] paramArray = paramInfo.split("\t");
		if (paramArray.length != 2) {
			errors.add("Invalid parameter '" + paramInfo + "' on line " + (i + 1) + ".");
			continue;
		}
		// Add Parameter.
		Element paramElement = rootElement.addElement("Parameter")
			.addAttribute("name", paramArray[0]);
		paramElement.addText(paramArray[1]);
	}
	paramXmlOut = paramDoc.asXML();
}