void count_pair_distances::operator()(const SequenceTree& T)
{
if (not initialized) {
N = T.n_leaves();
names = T.get_leaf_labels();
m1.resize(N*(N-1)/2);
m2.resize(N*(N-1)/2);
m1 = 0;
m2 = 0;
initialized = true;
}
n_samples++;
// Theoretically, we could do this much faster, I think.
// vector<vector<int> > leaf_sets = partition_sets(T);
int k=0;
for(int i=0;i<N;i++)
for(int j=0;j<i;j++,k++)
{
double D = 0;
if (RF)
D = T.edges_distance(i,j);
else
D = T.distance(i,j);
m1[k] += D;
m2[k] += D*D;
}
}
Partition partition_from_branch(const SequenceTree& T,int b)
{
dynamic_bitset<> group(T.n_leaves());
const dynamic_bitset<>& with_internal = T.partition(b);
for(int i=0;i<group.size();i++)
group[i] = with_internal[i];
return Partition(T.get_leaf_labels(), group);
}
/// \brief Re-index the leaves of tree \a T so that the labels have the same ordering as in \a names.
///
/// \param T The leaf-labelled tree.
/// \param names The ordered leaf labels.
///
void remap_T_leaf_indices(SequenceTree& T,const vector<string>& names)
{
assert(names.size() == T.n_leaves());
//----- Remap leaf indices for T onto A's leaf sequence indices -----//
try {
vector<int> mapping = compute_mapping(T.get_leaf_labels(), names);
T.standardize(mapping);
}
catch(const bad_mapping<string>& b)
{
bad_mapping<string> b2 = b;
b2.clear();
if (b2.from == 0)
b2<<"Couldn't find leaf sequence \""<<b2.missing<<"\" in names.";
else
b2<<"Sequence '"<<b2.missing<<"' not found in the tree.";
throw b2;
}
}
int main(int argc,char* argv[])
{
try {
cerr.precision(10);
cout.precision(10);
//---------- Parse command line -------//
variables_map args = parse_cmd_line(argc,argv);
//---------- Initialize random seed -----------//
unsigned long seed = 0;
if (args.count("seed")) {
seed = args["seed"].as<unsigned long>();
myrand_init(seed);
}
else
seed = myrand_init();
cout<<"random seed = "<<seed<<endl<<endl;
alignment A;
SequenceTree T;
load_A_and_T(args,A,T);
cout<<"Using alphabet: "<<A.get_alphabet().name<<endl<<endl;
//------------- Show Similarity/Distances between sequences ---------//
cout.precision(3);
cout<<"conserved = \n";
print_entire(cout,T.get_leaf_labels(),getConserved(A))<<"\n";
Matrix S = getSimilarity(A);
cout<<"%similarity = \n";
print_lower(cout,T.get_leaf_labels(),S)<<"\n";
owned_ptr<substitution::MultiModel> smodel_in = get_smodel(args,A);
set_parameters(*smodel_in,args);
cout<<"Using substitution model: "<<smodel_in->name()<<endl;
smodel_in->set_rate(1);
show_parameters(cout,*smodel_in);
cout<<endl;
cout<<"input T = "<<T<<endl;
cout<<endl;
//----- Prior & Posterior Rate Distributions (rate-bin probabilities) -------- //
analyze_rates(A,T,*smodel_in);
//------- Estimate branch lengths -------------//
owned_ptr<substitution::MultiModel> smodel_est = smodel_in;
SequenceTree T2 = T;
if (args.count("search")) {
vector<int> parameters;
if (args["search"].as<string>() == "smodel")
for(int i=0;i<smodel_est->n_parameters();i++)
if (not smodel_est->is_fixed(i))
parameters.push_back(i);
estimate_tree(A,T2,*smodel_est,parameters);
cout<<"E T = "<<T2<<endl;
show_parameters(cout,*smodel_est);
cout<<endl<<endl;
analyze_rates(A,T2,*smodel_est);
}
//------- Set up function to maximize --------//
Matrix S1 = getSimilarity(T,*smodel_in);
Matrix S2 = getSimilarity(T2,*smodel_est);
Matrix D = C(S);
cout<<"%difference (actual) = \n";
print_lower(cout,T.get_leaf_labels(),D)<<"\n";
cout<<"%difference (input) = \n";
print_lower(cout,T.get_leaf_labels(),C(S1))<<"\n";
if (args.count("search")){
cout<<"%difference (estimated) = \n";
print_lower(cout,T.get_leaf_labels(),C(S2))<<"\n\n";
}
cout<<"tree distances (input) = \n";
print_lower(cout,T.get_leaf_labels(),DistanceMatrix(T))<<"\n";
if (args.count("search")){
cout<<"tree distances (estimated) = \n";
print_lower(cout,T.get_leaf_labels(),DistanceMatrix(T2))<<"\n\n";
}
}
catch (std::exception& e) {
cerr<<"analyze_distances: Error! "<<e.what()<<endl;
exit(1);
}
return 0;
}