/**
* Get names of read elements expected in each read
*
* @return Ordered list of read element names
*/
public final ArrayList<String> getElementNames() {
ArrayList<String> rtrn = new ArrayList<String>();
for (ReadSequenceElement elt : elements) {
rtrn.add(elt.elementName());
}
return rtrn;
}
/**
* @param elementSequence Sequence of elements expected in each read
* @param readLength Read length
*/
public ReadLayout(ArrayList<ReadSequenceElement> elementSequence, int readLength) {
int totalLen = 0;
for (ReadSequenceElement elt : elementSequence) {
totalLen += elt.getLength();
}
if (totalLen > readLength) {
throw new IllegalArgumentException(
"Total length of read sequence elements ("
+ totalLen
+ ") must be at most declared read length ("
+ readLength
+ ").");
}
elements = elementSequence;
readLen = readLength;
initializeElementsByRepresentative();
}
private void initializeElementsByRepresentative() {
elementsByRepresentative = new HashMap<ReadSequenceElement, Map<String, ReadSequenceElement>>();
for (ReadSequenceElement element : elements) {
elementsByRepresentative.put(element, element.sequenceToElement());
}
}