// create the final list of trimmed haplotypes
final List<Haplotype> trimmedHaplotypes = new ArrayList<>(originalByTrimmedHaplotypes.keySet());
// resort the trimmed haplotypes.
Collections.sort(trimmedHaplotypes,new HaplotypeSizeAndBaseComparator());
final Map<Haplotype,Haplotype> sortedOriginalByTrimmedHaplotypes = new LinkedHashMap<>(trimmedHaplotypes.size());
for (final Haplotype trimmed : trimmedHaplotypes)
sortedOriginalByTrimmedHaplotypes.put(trimmed,originalByTrimmedHaplotypes.get(trimmed));