public void save(XMLElement element) {
XMLElement child = new XMLElement();
child.setName(NAME);
super.saveAttributes(child);
child.setAttribute(ATTRIBUTE, attribute);
element.addChild(child);
}
/** Overrides the toString method to show how the rule was parsed. */
public String toString() {
if (node != null) {
return node.toString();
} else {
return "null";
}
}
public static Node rndNode() {
Node n = new Node();
n.setCondition((NodeCondition) rndChoice(NodeCondition.values()));
n.setId(rndInt(0, 10000));
n.setAddress(rndIp());
n.setPort(rndInt(1, 32000));
n.setStatus((NodeStatus) rndChoice(NodeStatus.values()));
return n;
}
/**
* It parses the rule logical description to create the corresponding node conditions. i.e. ((A
* and B ) or C) -> is parsed as: node_1 represents condition "A", node_2 represents condition
* "B", node_3 represents expression "(node_1 and node_2)", node_4 represents condition "C" and
* node_5 represents expression "(node_3 or node_4)". For example,a condition could be "has some
* BRCA1_1"
*
* @param nodeExpression The logical description of the rule o a subsection of the rule
*/
private NodeCondition getTypeNode(String nodeExpression) throws BadRuleDefinitionException {
nodeExpression = nodeExpression.trim();
String mainType = "";
String mainNumber = "";
String mainElement = "";
String mainQuality = "";
ArrayList<NodeCondition> mainListNodes = null;
while (nodeExpression.length() > 0) {
if (nodeExpression.startsWith("has")) {
String hasType = "";
String hasNumber = "";
String hasElement = "";
String hasQuality = "";
ArrayList<NodeCondition> hasListNodes = null;
nodeExpression = nodeExpression.substring(nodeExpression.indexOf("has") + 3).trim();
if (nodeExpression.startsWith("some")) {
hasType = "some";
nodeExpression = nodeExpression.substring(nodeExpression.indexOf("some") + 4).trim();
}
if (nodeExpression.startsWith("min")) {
hasType = "min";
nodeExpression = nodeExpression.substring(nodeExpression.indexOf("min") + 3).trim();
hasNumber = nodeExpression.substring(0, nodeExpression.indexOf(" "));
nodeExpression = nodeExpression.substring(nodeExpression.indexOf(" ") + 1).trim();
}
if (nodeExpression.startsWith("exactly")) {
hasType = "exactly";
nodeExpression = nodeExpression.substring(nodeExpression.indexOf("exactly") + 7).trim();
hasNumber = nodeExpression.substring(0, nodeExpression.indexOf(" "));
nodeExpression = nodeExpression.substring(nodeExpression.indexOf(" ") + 1).trim();
}
if (nodeExpression.startsWith("(")) {
hasListNodes = new ArrayList<NodeCondition>();
String listElements = nodeExpression.substring(1, nodeExpression.indexOf(")")).trim();
nodeExpression = nodeExpression.substring(nodeExpression.indexOf(")") + 1).trim();
while (listElements.length() > 0) {
if ((listElements.startsWith("and") && hasQuality.equals("or"))
|| (listElements.startsWith("and") && hasQuality.equals("or"))) {
throw new BadRuleDefinitionException(
"and/or inconsistency in has expression condition: " + nodeExpression);
// System.out.println("ERROR: and/or inconsistency in has expression condition");
// return null;
}
if (listElements.startsWith("and")) {
hasQuality = "and";
listElements = listElements.substring(listElements.indexOf("and") + 3).trim();
continue;
}
if (listElements.startsWith("or")) {
hasQuality = "or";
listElements = listElements.substring(listElements.indexOf("or") + 2).trim();
continue;
}
String nodeElement = "";
if (listElements.indexOf(" ") >= 0) {
nodeElement = listElements.substring(0, listElements.indexOf(" ")).trim();
listElements = listElements.substring(listElements.indexOf(" ") + 1).trim();
} else {
nodeElement = listElements;
listElements = "";
}
NodeCondition subNode = new NodeCondition();
subNode.setElement(nodeElement);
hasListNodes.add(subNode);
}
} else {
if (nodeExpression.indexOf(" ") >= 0) {
hasElement = nodeExpression.substring(0, nodeExpression.indexOf(" ")).trim();
nodeExpression = nodeExpression.substring(nodeExpression.indexOf(" ") + 1).trim();
} else {
hasElement = nodeExpression;
nodeExpression = "";
}
}
NodeCondition node = new NodeCondition();
node.setElement(hasElement);
node.setQuality(hasQuality);
node.setType(hasType);
node.setNumber(hasNumber);
if (hasListNodes != null) {
for (NodeCondition subNode : hasListNodes) {
node.addNode(subNode);
}
}
if (mainListNodes == null) mainListNodes = new ArrayList<NodeCondition>();
mainListNodes.add(node);
} else {
if (nodeExpression.startsWith("and") || nodeExpression.startsWith("or")) {
if ((nodeExpression.startsWith("or") && mainQuality.equals("and"))
|| (nodeExpression.startsWith("and") && mainQuality.equals("or"))) {
throw new BadRuleDefinitionException(
"and/or inconsistency in has expression condition: " + nodeExpression);
// System.out.println("ERROR: and/or inconsistency");
// return null;
} else {
if (nodeExpression.startsWith("or")) {
mainQuality = "or";
nodeExpression = nodeExpression.substring(nodeExpression.indexOf("or") + 2).trim();
}
if (nodeExpression.startsWith("and")) {
mainQuality = "and";
nodeExpression = nodeExpression.substring(nodeExpression.indexOf("and") + 3).trim();
}
}
} else {
if (nodeExpression.startsWith("(")) {
int nCondition = 1;
String subNodeString = nodeExpression.substring(1).trim();
String completeNode = "";
while (nCondition > 0) {
if (subNodeString.indexOf("(") < subNodeString.indexOf(")")
&& subNodeString.indexOf("(") >= 0) {
nCondition++;
if (subNodeString.startsWith("(")) {
completeNode += "(";
subNodeString = subNodeString.substring(1).trim();
} else {
completeNode +=
" " + subNodeString.substring(0, subNodeString.indexOf("(") + 1).trim();
subNodeString = subNodeString.substring(subNodeString.indexOf("(") + 1).trim();
}
} else {
nCondition--;
if (nCondition > 0) {
completeNode +=
" " + subNodeString.substring(0, subNodeString.indexOf(")") + 1).trim();
} else {
completeNode +=
" " + subNodeString.substring(0, subNodeString.indexOf(")")).trim();
}
subNodeString = subNodeString.substring(subNodeString.indexOf(")") + 1).trim();
}
}
NodeCondition nodeCondition = getTypeNode(completeNode);
if (mainListNodes == null) mainListNodes = new ArrayList<NodeCondition>();
mainListNodes.add(nodeCondition);
nodeExpression = subNodeString;
} else {
if (nodeExpression.indexOf(" ") >= 0) {
String element = nodeExpression.substring(0, nodeExpression.indexOf(" ")).trim();
nodeExpression = nodeExpression.substring(nodeExpression.indexOf(" ") + 1).trim();
NodeCondition node = new NodeCondition();
node.setElement(element);
if (mainListNodes == null) mainListNodes = new ArrayList<NodeCondition>();
mainListNodes.add(node);
} else {
mainElement = nodeExpression;
nodeExpression = "";
}
}
}
}
}
NodeCondition mainNode = new NodeCondition();
mainNode.setElement(mainElement);
mainNode.setNumber(mainNumber);
mainNode.setQuality(mainQuality);
mainNode.setType(mainType);
if (mainListNodes != null) {
for (NodeCondition subnodes : mainListNodes) {
mainNode.addNode(subnodes);
}
}
return mainNode;
}
/**
* Check if the rule matches the provided patient's genotype.
*
* @param A patient's genotype.
* @return Whether the genotype matches the rule logical description or not.
*/
public boolean matchPatientProfile(Genotype genotype) {
ArrayList<GenotypeElement> listGenotypeElements = genotype.getListGenotypeElements();
return node.test(listGenotypeElements);
}