void peel_n_mutations(const alphabet& a, const vector<int>& letters, const SequenceTree& T,
const ublas::matrix<B>& cost,ublas::matrix<B>& n_muts,
const vector<const_branchview>& branches)
{
const int A = a.size();
assert(letters.size() == T.n_leaves());
assert(cost.size1() == A);
assert(cost.size2() == A);
// we need a scratch row in the matrix
assert(n_muts.size1() == T.n_nodes());
assert(n_muts.size2() == A);
// compute the max cost -- is this approach a good idea?
// Well... this apparently doesn't work.
B max_cost = 0;
for(int i=0;i<A;i++)
for(int j=0;j<A;j++)
max_cost = std::max(cost(i,j)+1, max_cost);
// clear the length matrix.
for(int i=0;i<n_muts.size1();i++)
for(int j=0;j<n_muts.size2();j++)
n_muts(i,j)=0;
// set the leaf costs
for(int s=0;s<T.n_leaves();s++)
{
int L = letters[s];
if (a.is_letter_class(L))
for(int l=0;l<A;l++)
if (a.matches(l,L))
n_muts(s,l) = 0;
else
n_muts(s,l) = max_cost;
}
// compute the costs for letters at each node
for(int i=0;i<branches.size();i++)
{
int s = branches[i].source();
int t = branches[i].target();
// for each letter l of node target...
for(int l=0;l<A;l++)
{
// compute minimum treelength for data behind source.
B temp = n_muts(s,0)+cost(0,l);
for(int k=1;k<A;k++)
temp = min(temp, n_muts(s,k)+cost(k,l) );
// add it to treelengths for data behind target
n_muts(t,l) += temp;
}
}
}
vector<vector<int> > get_all_parsimony_letters(const alphabet& a, const vector<int>& letters, const SequenceTree& T,
const ublas::matrix<int>& cost)
{
int root = T.directed_branch(0).target();
ublas::matrix<int> n_muts(T.n_nodes(), a.size());
peel_n_mutations(a,letters,T,cost,n_muts, branches_toward_node(T,root) );
// get an order list of branches point away from the root;
vector<const_branchview> branches = branches_from_node(T,root);
std::reverse(branches.begin(),branches.end());
// Allocate space to store the letters for each node
vector<vector<int> > node_letters(T.n_nodes());
const unsigned A = a.size();
// choose the cheapest letters at the root
{
double m = row_min(n_muts,root);
for(int l=0;l<A;l++)
if (n_muts(root,l) <= m)
node_letters[root].push_back(l);
}
vector<double> temp(A);
for(int i=0;i<branches.size();i++)
{
int s = branches[i].source();
int t = branches[i].target();
vector<double> best(node_letters[s].size());
for(int j=0;j<node_letters[s].size();j++)
{
for(int l=0;l<A;l++)
temp[l] = n_muts(t,l)+cost(l,node_letters[s][j]);
best[j] = min(temp);
}
for(int l=0;l<A;l++)
{
bool is_best = false;
for(int j=0;j<node_letters[s].size() and not is_best;j++)
if (n_muts(t,l)+cost(l,node_letters[s][j]) <= best[j])
is_best=true;
if (is_best)
node_letters[t].push_back(l);
}
}
return node_letters;
}
inline double sum(const Matrix Q,const vector<unsigned>& smap,
int s1, int l2, const alphabet& a)
{
double total=0;
int n_letters = a.n_letters();
#ifdef DEBUG_SMAP
for(int s=0;s<smap.size();s++)
if (a.matches(smap[s],l2))
total += Q(s1,s);
#else
for(int L=0;L<n_letters;L++)
if (a.matches(L,l2))
total += sum(Q,smap,n_letters,s1,L);
#endif
return total;
}
B n_mutations(const alphabet& a, const vector<int>& letters, const SequenceTree& T,const ublas::matrix<B>& cost)
{
int root = T.directed_branch(0).target();
vector<const_branchview> branches = branches_toward_node(T,root);
ublas::matrix<B> n_muts(T.n_nodes(), a.size());
return n_mutations(a,letters,T,cost,n_muts,branches);
}
vector<int> get_parsimony_letters(const alphabet& a, const vector<int>& letters, const SequenceTree& T,
const ublas::matrix<int>& cost)
{
int root = T.directed_branch(0).target();
ublas::matrix<int> n_muts(T.n_nodes(),a.size());
peel_n_mutations(a,letters,T,cost,n_muts, branches_toward_node(T,root) );
// get an order list of branches point away from the root;
vector<const_branchview> branches = branches_from_node(T,root);
std::reverse(branches.begin(),branches.end());
// Allocate space to store the letter for each node
vector<int> node_letters(T.n_nodes(),-1);
// choose the cheapest letter at the root
node_letters[root] = row_min(n_muts,root);
const unsigned A = a.size();
vector<double> temp(A);
for(int i=0;i<branches.size();i++)
{
int s = branches[i].source();
int t = branches[i].target();
int k = node_letters[s];
assert(k != -1);
for(int l=0;l<A;l++)
temp[l] = n_muts(t,l)+cost(l,k);
node_letters[t] = argmin(temp);
}
return node_letters;
}
std::vector<lstring> convert_split_words_allow_alphabet(const lstring <, const alphabet &allow) {
lstring copy;
lstring *ptr = (lstring *)<
bool changed = false;
static letter space(' ');
for (size_t i = 0; i < lt.size(); ++i) {
if (!allow.ok(lt[i])) {
if (!changed) {
copy = lt;
ptr = ©
changed = true;
}
copy[i] = space;
}
}
return convert_split_words(*ptr);
}
alignment load_next_alignment(istream& ifile, const alphabet& a, const vector<string>& names)
{
shared_ptr<const alphabet> aa ( a.clone() );
alignment A = load_next_alignment(ifile,aa);
return reorder_sequences(A,names);
}
alignment load_next_alignment(istream& ifile, const alphabet& a)
{
shared_ptr<const alphabet> aa ( a.clone() );
return load_next_alignment(ifile,aa);
}
ublas::matrix<int> unit_cost_matrix(const alphabet& a)
{
return unit_cost_matrix(a.size());
}
void show_frequencies(std::ostream& o,const alphabet& a,const std::valarray<double>& f) {
for(int i=0;i<a.size();i++)
o<<"f"<<a.lookup(i)<<" = "<<f[i]<<"\n";
}
alignment::alignment(const alphabet& a1,const string& filename)
:a(a1.clone())
{
load(filename);
}
alignment::alignment(const alphabet& a1, const vector<sequence>& S)
:sequences(S),array(0,S.size()),a(a1.clone())
{}
alignment::alignment(const alphabet& a1,int n)
:sequences(vector<sequence>(n)),array(0,n),a(a1.clone())
{
}
alignment::alignment(const alphabet& a1)
:a(a1.clone())
{}
alignment::alignment(const alphabet& a1, const vector<sequence>& S)
:array(0,S.size()),sequences(S),a(a1.clone())
{
// Do NOT load the sequences here -- this is used for constructing
// new alignment matrices during MCMC for some reason.
}
alignment::alignment(const alphabet& a1,int n,int L)
:array(L,n),sequences(vector<sequence>(n)),a(a1.clone())
{
}