/**
* Copy constructor. Adds all cells of the given alignment.
*
* @param alignment the alignment to copy
*/
public DefaultAlignment(Alignment alignment) {
// Since the cells came out of another alignment just pass addCell
for (Cell cell : alignment.getCells()) {
/*
* But copy the cell as it is not immutable (things like
* transformation mode and priority may change)
*/
internalAdd(new DefaultCell(cell)); // XXX is this working properly
// for BaseAlignmentCells?
}
baseAlignments.putAll(alignment.getBaseAlignments());
idToPropertyFunction.putAll(alignment.getCustomPropertyFunctions());
idToBaseFunction.putAll(alignment.getBasePropertyFunctions());
}
