/** * 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()); }