dDeterministicFiniteAutonata::dDeterministicFiniteAutonata(const char* const regularExpression)
:dFiniteAutomata()
,m_startState(NULL)
{
dNonDeterministicFiniteAutonata nfa (regularExpression);
CreateDeterministicFiniteAutomaton(nfa);
}
int main()
{
InputTokenizer inpTok;
inpTok.parseFile("input.txt");
NFABuilder nfa(inpTok);
nfa.test();
return 0;
}
void eskoTest() {
unsigned step = 5000;
unsigned start = 30000;
unsigned stop = 120000;
unsigned topL = 300;
unsigned minL = 5;
for(unsigned cur = start; cur <= stop; cur += step) {
takeSubstring("data/ecoli.seq", "data/tmpseq.seq", 0, cur);
//takeSubstring("data/ecoli.seq", "data/tmpseq.seq", 278000, 293000);
unsigned L = minL;
unsigned R = topL;
unsigned ans = 0U;
while (L<=R) {
unsigned mid = (L+R) / 2U;
unsigned k = mid-1U;
Genome genome;
readGenome("data/tmpseq.seq", mid, genome);
AhoCorasick * aho = new AhoCorasick(genome);
aho->filterOverlaps(k);
NFA_Automata nfa(*aho, genome, 0, genome.generatedReads.size()-1);
delete aho;
DFA_Automata dfa(nfa, genome, 1.0);
// remove reads since we do not need them anymore
genome.generatedReads.resize(0);
genome.sequence.resize(0);
bool uniqueOk = dfa.isCOAUnique();
if (uniqueOk) {
R = mid-1U;
ans = mid;
} else {
L = mid+1U;
}
}
std::string seq = readSequence("data/tmpseq.seq");
std::cout << cur << " " << ans << " " << getLongestSingleRepeat(seq) << std::endl;
}
}
int main()
{
XYZ_NBA_Generator nba_generator;
NFA_Generator<XYZ_NBA_Generator::Representation_t> nfa_generator;
CPP_Code_Generator<XYZ_NBA_Generator::Representation_t> code_generator;
//XYZ_NBA_Generator::Representation_t == Graphviz_Representation.
Nondet_Buechi_Automonton<XYZ_NBA_Generator::Representation_t> * nba(nba_generator.translate("[]<>p"));
Nondet_Finite_Automonton<XYZ_NBA_Generator::Representation_t> * nfa(nfa_generator.translate(nba));
code_generator->generate(nfa, ::std::cout);
delete nba;
delete nfa;
return 0;
}
void MaxMeaningfulClustering::build_merge_info(t_float *Z, t_float *X, int N, int dim, bool use_full_merge_rule, vector<HCluster> *merge_info, vector< vector<int> > *meaningful_clusters)
{
// walk the whole dendogram
for (int i=0; i<(N-1)*4; i=i+4)
{
HCluster cluster;
cluster.num_elem = Z[i+3]; //number of elements
int node1 = Z[i];
int node2 = Z[i+1];
float dist = Z[i+2];
if (node1<N)
{
vector<float> point;
for (int n=0; n<dim; n++)
point.push_back(X[node1*dim+n]);
cluster.points.push_back(point);
cluster.elements.push_back((int)node1);
}
else
{
for (int i=0; i<merge_info->at(node1-N).points.size(); i++)
{
cluster.points.push_back(merge_info->at(node1-N).points[i]);
cluster.elements.push_back(merge_info->at(node1-N).elements[i]);
}
//update the extended volume of node1 using the dist where this cluster merge with another
merge_info->at(node1-N).dist_ext = dist;
}
if (node2<N)
{
vector<float> point;
for (int n=0; n<dim; n++)
point.push_back(X[node2*dim+n]);
cluster.points.push_back(point);
cluster.elements.push_back((int)node2);
}
else
{
for (int i=0; i<merge_info->at(node2-N).points.size(); i++)
{
cluster.points.push_back(merge_info->at(node2-N).points[i]);
cluster.elements.push_back(merge_info->at(node2-N).elements[i]);
}
//update the extended volume of node2 using the dist where this cluster merge with another
merge_info->at(node2-N).dist_ext = dist;
}
Minibox mb;
for (int i=0; i<cluster.points.size(); i++)
{
mb.check_in(&cluster.points.at(i));
}
cluster.dist = dist;
cluster.volume = mb.volume();
if (cluster.volume >= 1)
cluster.volume = 0.999999;
if (cluster.volume == 0)
cluster.volume = 0.001; //TODO is this the minimum we can get?
cluster.volume_ext=1;
if (node1>=N)
{
merge_info->at(node1-N).volume_ext = cluster.volume;
}
if (node2>=N)
{
merge_info->at(node2-N).volume_ext = cluster.volume;
}
cluster.node1 = node1;
cluster.node2 = node2;
merge_info->push_back(cluster);
}
for (int i=0; i<merge_info->size(); i++)
{
merge_info->at(i).nfa = nfa(merge_info->at(i).volume, merge_info->at(i).volume_ext, merge_info->at(i).num_elem, N);
int node1 = merge_info->at(i).node1;
int node2 = merge_info->at(i).node2;
{
if ((node1<N)&&(node2<N))
{
//els dos nodes son single samples (nfa=1) per tant aquest cluster es maxim
merge_info->at(i).max_meaningful = true;
merge_info->at(i).max_in_branch.push_back(i);
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
} else {
if ((node1>=N)&&(node2>=N))
{
//els dos nodes son "sets" per tant hem d'avaluar el merging condition
if ( ( (use_full_merge_rule) && ((merge_info->at(i).nfa < merge_info->at(node1-N).nfa + merge_info->at(node2-N).nfa) && (merge_info->at(i).nfa<min(merge_info->at(node1-N).min_nfa_in_branch,merge_info->at(node2-N).min_nfa_in_branch))) ) || ( (!use_full_merge_rule) && ((merge_info->at(i).nfa<min(merge_info->at(node1-N).min_nfa_in_branch,merge_info->at(node2-N).min_nfa_in_branch))) ) )
{
merge_info->at(i).max_meaningful = true;
merge_info->at(i).max_in_branch.push_back(i);
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
for (int k =0; k<merge_info->at(node1-N).max_in_branch.size(); k++)
merge_info->at(merge_info->at(node1-N).max_in_branch.at(k)).max_meaningful = false;
for (int k =0; k<merge_info->at(node2-N).max_in_branch.size(); k++)
merge_info->at(merge_info->at(node2-N).max_in_branch.at(k)).max_meaningful = false;
} else {
merge_info->at(i).max_meaningful = false;
merge_info->at(i).max_in_branch.insert(merge_info->at(i).max_in_branch.end(),merge_info->at(node1-N).max_in_branch.begin(),merge_info->at(node1-N).max_in_branch.end());
merge_info->at(i).max_in_branch.insert(merge_info->at(i).max_in_branch.end(),merge_info->at(node2-N).max_in_branch.begin(),merge_info->at(node2-N).max_in_branch.end());
if (merge_info->at(i).nfa<min(merge_info->at(node1-N).min_nfa_in_branch,merge_info->at(node2-N).min_nfa_in_branch))
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
else
merge_info->at(i).min_nfa_in_branch = min(merge_info->at(node1-N).min_nfa_in_branch,merge_info->at(node2-N).min_nfa_in_branch);
}
} else {
//un dels nodes es un "set" i l'altre es un single sample, s'avalua el merging condition pero amb compte
if (node1>=N)
{
if ((merge_info->at(i).nfa < merge_info->at(node1-N).nfa + 1) && (merge_info->at(i).nfa<merge_info->at(node1-N).min_nfa_in_branch))
{
merge_info->at(i).max_meaningful = true;
merge_info->at(i).max_in_branch.push_back(i);
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
for (int k =0; k<merge_info->at(node1-N).max_in_branch.size(); k++)
merge_info->at(merge_info->at(node1-N).max_in_branch.at(k)).max_meaningful = false;
} else {
merge_info->at(i).max_meaningful = false;
merge_info->at(i).max_in_branch.insert(merge_info->at(i).max_in_branch.end(),merge_info->at(node1-N).max_in_branch.begin(),merge_info->at(node1-N).max_in_branch.end());
merge_info->at(i).min_nfa_in_branch = min(merge_info->at(i).nfa,merge_info->at(node1-N).min_nfa_in_branch);
}
} else {
if ((merge_info->at(i).nfa < merge_info->at(node2-N).nfa + 1) && (merge_info->at(i).nfa<merge_info->at(node2-N).min_nfa_in_branch))
{
merge_info->at(i).max_meaningful = true;
merge_info->at(i).max_in_branch.push_back(i);
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
for (int k =0; k<merge_info->at(node2-N).max_in_branch.size(); k++)
merge_info->at(merge_info->at(node2-N).max_in_branch.at(k)).max_meaningful = false;
} else {
merge_info->at(i).max_meaningful = false;
merge_info->at(i).max_in_branch.insert(merge_info->at(i).max_in_branch.end(),merge_info->at(node2-N).max_in_branch.begin(),merge_info->at(node2-N).max_in_branch.end());
merge_info->at(i).min_nfa_in_branch = min(merge_info->at(i).nfa,merge_info->at(node2-N).min_nfa_in_branch);
}
}
}
}
}
}
for (int i=0; i<merge_info->size(); i++)
{
if (merge_info->at(i).max_meaningful)
{
vector<int> cluster;
for (int k=0; k<merge_info->at(i).elements.size();k++)
cluster.push_back(merge_info->at(i).elements.at(k));
meaningful_clusters->push_back(cluster);
}
}
}
void MaxMeaningfulClustering::build_merge_info(t_float *Z, int N, vector<HCluster> *merge_info, vector< vector<int> > *meaningful_clusters)
{
// walk the whole dendogram
for (int i=0; i<(N-1)*4; i=i+4)
{
HCluster cluster;
cluster.num_elem = Z[i+3]; //number of elements
int node1 = Z[i];
int node2 = Z[i+1];
float dist = Z[i+2];
if (dist != dist) //this is to avoid NaN values
dist=0;
//fprintf(stderr," merging %d %d\n",node1,node2);
if (node1<N)
{
cluster.elements.push_back((int)node1);
}
else
{
for (int i=0; i<merge_info->at(node1-N).elements.size(); i++)
{
cluster.elements.push_back(merge_info->at(node1-N).elements[i]);
}
}
if (node2<N)
{
cluster.elements.push_back((int)node2);
}
else
{
for (int i=0; i<merge_info->at(node2-N).elements.size(); i++)
{
cluster.elements.push_back(merge_info->at(node2-N).elements[i]);
}
}
cluster.dist = dist;
if (cluster.dist >= 1)
cluster.dist = 0.999999;
if (cluster.dist == 0)
cluster.dist = 1.e-25; //TODO is this the minimum we can get?
cluster.dist_ext = 1;
if (node1>=N)
{
merge_info->at(node1-N).dist_ext = cluster.dist;
}
if (node2>=N)
{
merge_info->at(node2-N).dist_ext = cluster.dist;
}
cluster.node1 = node1;
cluster.node2 = node2;
merge_info->push_back(cluster);
}
//print all merge info
//cout << "---------------------------------------------------------" << endl;
//cout << "-- MERGE INFO ---- Evidence Accumulation " << endl;
//cout << "---------------------------------------------------------" << endl;
for (int i=0; i<merge_info->size(); i++)
{
merge_info->at(i).nfa = nfa(merge_info->at(i).dist, merge_info->at(i).dist_ext, merge_info->at(i).num_elem, N);
int node1 = merge_info->at(i).node1;
int node2 = merge_info->at(i).node2;
{
if ((node1<N)&&(node2<N))
{
//els dos nodes son single samples (nfa=1) per tant aquest cluster es maxim
merge_info->at(i).max_meaningful = true;
merge_info->at(i).max_in_branch.push_back(i);
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
//fprintf(stderr,"%d = (%d,%d) els dos nodes son single samples (nfa=1) per tant aquest merge_info->at(i) es maxim min_nfa_in_branch = %d \n",i,node1-N,node2-N,merge_info->at(i).min_nfa_in_branch);
} else {
if ((node1>=N)&&(node2>=N))
{
//els dos nodes son "sets" per tant hem d'avaluar el merging condition
if ((merge_info->at(i).nfa < merge_info->at(node1-N).nfa + merge_info->at(node2-N).nfa) && (merge_info->at(i).nfa<min(merge_info->at(node1-N).min_nfa_in_branch,merge_info->at(node2-N).min_nfa_in_branch)))
{
//fprintf(stderr,"%d = (%d,%d) MAX because merging condition 1 (%d < %d + %d ) && (%d<min(%d,%d)) \n",i,node1-N,node2-N,merge_info->at(i).nfa,merge_info->at(node1-N).nfa, merge_info->at(node2-N).nfa, merge_info->at(i).nfa, merge_info->at(node1-N).nfa,merge_info->at(node2-N).nfa);
merge_info->at(i).max_meaningful = true;
merge_info->at(i).max_in_branch.push_back(i);
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
for (int k =0; k<merge_info->at(node1-N).max_in_branch.size(); k++)
merge_info->at(merge_info->at(node1-N).max_in_branch.at(k)).max_meaningful = false;
for (int k =0; k<merge_info->at(node2-N).max_in_branch.size(); k++)
merge_info->at(merge_info->at(node2-N).max_in_branch.at(k)).max_meaningful = false;
//fprintf(stderr," min_nfa_in_branch = %d \n",merge_info->at(i).min_nfa_in_branch);
} else {
merge_info->at(i).max_meaningful = false;
merge_info->at(i).max_in_branch.insert(merge_info->at(i).max_in_branch.end(),merge_info->at(node1-N).max_in_branch.begin(),merge_info->at(node1-N).max_in_branch.end());
merge_info->at(i).max_in_branch.insert(merge_info->at(i).max_in_branch.end(),merge_info->at(node2-N).max_in_branch.begin(),merge_info->at(node2-N).max_in_branch.end());
if (merge_info->at(i).nfa<min(merge_info->at(node1-N).min_nfa_in_branch,merge_info->at(node2-N).min_nfa_in_branch))
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
else
merge_info->at(i).min_nfa_in_branch = min(merge_info->at(node1-N).min_nfa_in_branch,merge_info->at(node2-N).min_nfa_in_branch);
//fprintf(stderr,"%d = (%d,%d) NONmax min_nfa_in_branch = %d \n",i,node1-N,node2-N,merge_info->at(i).min_nfa_in_branch);
}
} else {
//un dels nodes es un "set" i l'altre es un single sample, s'avalua el merging condition pero amb compte
if (node1>=N)
{
if ((merge_info->at(i).nfa < merge_info->at(node1-N).nfa + 1) && (merge_info->at(i).nfa<merge_info->at(node1-N).min_nfa_in_branch))
{
//fprintf(stderr,"%d = (%d,%d) MAX because merging condition 2 (%d < %d + 1 ) && (%d<%d) \n",i,node1-N,node2-N,merge_info->at(i).nfa,merge_info->at(node1-N).nfa, merge_info->at(i).nfa, merge_info->at(node1-N).min_nfa_in_branch);
merge_info->at(i).max_meaningful = true;
merge_info->at(i).max_in_branch.push_back(i);
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
for (int k =0; k<merge_info->at(node1-N).max_in_branch.size(); k++)
merge_info->at(merge_info->at(node1-N).max_in_branch.at(k)).max_meaningful = false;
} else {
merge_info->at(i).max_meaningful = false;
merge_info->at(i).max_in_branch.insert(merge_info->at(i).max_in_branch.end(),merge_info->at(node1-N).max_in_branch.begin(),merge_info->at(node1-N).max_in_branch.end());
merge_info->at(i).min_nfa_in_branch = min(merge_info->at(i).nfa,merge_info->at(node1-N).min_nfa_in_branch);
//fprintf(stderr,"%d = (%d,%d) NONmax2 min_nfa_in_branch = %d \n",i,node1-N,node2-N,merge_info->at(i).min_nfa_in_branch);
}
} else {
if ((merge_info->at(i).nfa < merge_info->at(node2-N).nfa + 1) && (merge_info->at(i).nfa<merge_info->at(node2-N).min_nfa_in_branch))
{
//fprintf(stderr,"%d = (%d,%d) MAX because merging condition 3 (%d < %d + 1 ) && (%d<%d) \n ",i,node1-N,node2-N,merge_info->at(i).nfa,merge_info->at(node2-N).nfa, merge_info->at(i).nfa, merge_info->at(node2-N).min_nfa_in_branch);
merge_info->at(i).max_meaningful = true;
merge_info->at(i).max_in_branch.push_back(i);
merge_info->at(i).min_nfa_in_branch = merge_info->at(i).nfa;
for (int k =0; k<merge_info->at(node2-N).max_in_branch.size(); k++)
merge_info->at(merge_info->at(node2-N).max_in_branch.at(k)).max_meaningful = false;
} else {
merge_info->at(i).max_meaningful = false;
merge_info->at(i).max_in_branch.insert(merge_info->at(i).max_in_branch.end(),merge_info->at(node2-N).max_in_branch.begin(),merge_info->at(node2-N).max_in_branch.end());
merge_info->at(i).min_nfa_in_branch = min(merge_info->at(i).nfa,merge_info->at(node2-N).min_nfa_in_branch);
//fprintf(stderr,"%d = (%d,%d) NONmax3 min_nfa_in_branch = %d \n",i,node1-N,node2-N,merge_info->at(i).min_nfa_in_branch);
}
}
}
}
}
}
for (int i=0; i<merge_info->size(); i++)
{
if (merge_info->at(i).max_meaningful)
{
vector<int> cluster;
for (int k=0; k<merge_info->at(i).elements.size();k++)
cluster.push_back(merge_info->at(i).elements.at(k));
meaningful_clusters->push_back(cluster);
}
}
}
