void UnivCharsetDesc::addBaseRange(const UnivCharsetDesc &baseSet,
WideChar descMin,
WideChar descMax,
WideChar baseMin,
ISet<WideChar> &baseMissing)
{
UnivCharsetDescIter iter(baseSet);
WideChar baseMax = baseMin + (descMax - descMin);
WideChar iDescMin, iDescMax;
UnivChar iBaseMin;
WideChar missingBaseMin = baseMin;
Boolean usedAll = 0;
while (iter.next(iDescMin, iDescMax, iBaseMin) && iDescMin <= baseMax) {
// baseMin baseMax
// iDescMin iDescMax
if (iDescMax >= baseMin) {
WideChar min = baseMin > iDescMin ? baseMin : iDescMin;
if (min > missingBaseMin)
baseMissing.addRange(missingBaseMin, min - 1);
WideChar max = baseMax < iDescMax ? baseMax : iDescMax;
missingBaseMin = max + 1;
if (missingBaseMin == 0)
usedAll = 1;
ASSERT(min <= max);
descToUniv_.addRange(descMin + (min - baseMin),
descMin + (max - baseMin),
iBaseMin + (min - iDescMin));
}
}
if (!usedAll && baseMax >= missingBaseMin)
baseMissing.addRange(missingBaseMin, baseMax);
}
unsigned RangeMap<From, To>::inverseMap(To to, From &from,
ISet<WideChar> &fromSet,
WideChar &count) const
{
// FIXME use binary search
unsigned ret = 0;
count = wideCharMax;
for (size_t i = 0; i < ranges_.size(); i++) {
const RangeMapRange<From,To> &r = ranges_[i];
if (r.toMin <= to && to <= r.toMin + (r.fromMax - r.fromMin)) {
From n = r.fromMin + (to - r.toMin);
WideChar thisCount = r.fromMax - n + 1;
if (ret > 1) {
fromSet.add(n);
if (thisCount < count)
count = thisCount;
}
else if (ret == 1) {
fromSet.add(from);
fromSet.add(n);
ret = 2;
if (thisCount < count)
count = thisCount;
}
else {
count = thisCount;
from = n;
ret = 1;
}
}
else if (ret == 0 && r.toMin > to && (r.toMin - to < count))
count = r.toMin - to;
}
return ret;
}
void ClientTxnSetTest::testAddRemove() {
ISet<std::string> s = client->getSet<std::string>("testAddRemove");
s.add("item1");
TransactionContext context = client->newTransactionContext();
context.beginTransaction();
TransactionalSet<std::string> set = context.getSet<std::string>("testAddRemove");
assertTrue(set.add("item2"));
assertEqual(2, set.size());
assertEqual(1, s.size());
assertFalse(set.remove("item3"));
assertTrue(set.remove("item1"));
context.commitTransaction();
assertEqual(1, s.size());
}
void CharsetInfo::getDescSet(ISet<Char> &set) const
{
UnivCharsetDescIter iter(desc_);
WideChar descMin, descMax;
UnivChar univMin;
while (iter.next(descMin, descMax, univMin)) {
if (descMin > charMax)
break;
if (descMax > charMax)
descMax = charMax;
set.addRange(Char(descMin), Char(descMax));
}
}
void SparseGenome::init_mutations(ISet &is) {
int p = 2*is.size(); // number of "strands" = 2 * #individuals
int i, j, k, l; // counters and temp indices
int n; // number of individuals in set
mutation_t si; // mutation effect of a single gene
fitness_t xw; // change in fitness due to this gene
double qi; // frequency of gene
double gu; // genic mutation rate
int x, nx; // id of individual, #individuals
int nl = 0; // for debugging, keep track of #loci and
int nm = 0; // #mutations affected by this step
int *bin; // also keep track of distribution of mutation values
IP *v;
SparseGenome *sgp;
n = is.size();
v = new IP[n];
for (i=0; i<n; i++) // copy individuals to local vector for faster access
v[i] = is.remove(0);
bin = new int[p+1];
// cout << "Placing initial mutations in " << p << " strands...." << endl;
for (i=0; i<=p; i++)
bin[i] = 0;
gu = u/(2*gl); // genic rate = individual rate / number of genes
// cout << "Genic mutation rate (U/2N) = " << gu << endl;
// Iterate over all loci; pick a mutation effect for that locus, figure
// out the expected frequency of a gene with that effect, and then add it
// to selected individuals. In this loop 'i' is the locus index, 'j'
// is the chromosome number for that locus, and 'k' is the index of the locus
// within the chromosome.
// optimization: knowing that get_gene() and set_gene() in Strand scan
// from "left to right", start with the higher locus indices and count
// down to 0 -- this way the lookups and insertions will all be done
// in one step....
for (i = gl-1; i >= 0; i--) {
j = i / chrlength;
k = i % chrlength;
si = new_mutation_value(s,rs); // get mutation effect
qi = gu/hs(si); // frequency of allele with effect si
if (qi > 1.0)
qi = 1.0;
nx = int(rbinomial(qi,p)); // number of genes expected to have this mutation
if (nx > p)
nx = p;
// if (qi) {
// cout << "locus " << i << ": ";
// cout << ", si = " << si;
// cout << ", hs = " << hs(si,0.0);
// cout << ", qi = " << qi;
// cout << ", nx = " << nx << endl;
// }
nm += nx; // record info on this mutation
bin[nx] += 1;
if (nx)
nl += 1;
while (nx) {
x = rword(n);
l = rword(2);
sgp = (SparseGenome *)v[x]->genes;
if (sgp->sa[j].get_gene(k,l) == 0.0) {
xw = sgp->sa[j].set_gene(k,l,si);
sgp->w *= xw;
nx--;
}
}
}
// cout << "Distributed " << nm << " mutations across " << nl << " loci" << endl;
// for (i=0; i<=p; i++)
// cout << i << ": " << bin[i] << endl;
}
