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#ifndef PROFILE_H_
#define PROFILE_H_
#include<cstdio>
#include<cstring>
#include<cassert>
#include "utils.h"
#include "RefSeq.h"
#include "simul.h"
class Profile {
public:
Profile(int = 1000);
~Profile() {
delete[] p;
}
Profile& operator=(const Profile&);
void init();
void update(const std::string&, const RefSeq&, int, int, double);
void finish();
double getProb(const std::string&, const RefSeq&, int, int);
void collect(const Profile&);
void read(FILE*);
void write(FILE*);
void startSimulation();
std::string simulate(simul*, int, int, int, const RefSeq&);
void finishSimulation();
private:
static const int NCODES = 5;
int proLen; // profile length
int size; // # of items in p;
double (*p)[NCODES][NCODES]; //profile matrices
double (*pc)[NCODES][NCODES]; // for simulation
};
Profile::Profile(int maxL) {
proLen = maxL;
size = proLen * NCODES * NCODES;
p = new double[proLen][NCODES][NCODES];
memset(p, 0, sizeof(double) * size);
//set initial parameters
int N = NCODES - 1;
double probN = 1e-5, portionC = 0.99; //portionC, among ACGT, the portion of probability mass the correct base takes
double probC, probO;
for (int i = 0; i < proLen; i++) {
for (int j = 0; j < NCODES - 1; j++) {
p[i][j][N] = probN;
probC = portionC * (1.0 - probN);
probO = (1.0 - portionC) / (NCODES - 2) * (1.0 - probN);
for (int k = 0; k < NCODES - 1; k++) {
p[i][j][k] = (j == k ? probC : probO);
}
}
p[i][N][N] = probN;
for (int k = 0; k < NCODES - 1; k++)
p[i][N][k] = (1.0 - probN) / (NCODES - 1);
}
}
Profile& Profile::operator=(const Profile& rv) {
if (this == &rv) return *this;
if (proLen != rv.proLen) {
delete[] p;
proLen = rv.proLen;
size = rv.size;
p = new double[rv.proLen][NCODES][NCODES];
}
memcpy(p, rv.p, sizeof(double) * rv.size);
return *this;
}
void Profile::init() {
memset(p, 0, sizeof(double) * size);
}
void Profile::update(const std::string& readseq, const RefSeq& refseq, int pos, int dir, double frac) {
int len = readseq.size();
for (int i = 0; i < len; i++) {
p[i][refseq.get_id(i + pos, dir)][get_base_id(readseq[i])] += frac;
}
}
void Profile::finish() {
double sum;
for (int i = 0; i < proLen; i++) {
for (int j = 0; j < NCODES; j++) {
sum = 0.0;
for (int k = 0; k < NCODES; k++) sum += p[i][j][k];
if (sum < EPSILON) {
for (int k = 0; k < NCODES; k++) p[i][j][k] = 0.0;
continue;
}
for (int k = 0; k < NCODES; k++) p[i][j][k] /= sum;
}
}
}
double Profile::getProb(const std::string& readseq, const RefSeq& refseq, int pos, int dir) {
double prob = 1.0;
int len = readseq.size();
for (int i = 0; i < len; i++) {
prob *= p[i][refseq.get_id(i + pos, dir)][get_base_id(readseq[i])];
}
return prob;
}
void Profile::collect(const Profile& o) {
for (int i = 0; i < proLen; i++)
for (int j = 0; j < NCODES; j++)
for (int k = 0; k < NCODES; k++)
p[i][j][k] += o.p[i][j][k];
}
void Profile::read(FILE *fi) {
int tmp_prolen, tmp_ncodes;
assert(fscanf(fi, "%d %d", &tmp_prolen, &tmp_ncodes) == 2);
assert(tmp_ncodes == NCODES);
if (tmp_prolen != proLen) {
delete[] p;
proLen = tmp_prolen;
size = proLen * NCODES * NCODES;
p = new double[proLen][NCODES][NCODES];
memset(p, 0, sizeof(double) * size);
}
for (int i = 0; i < proLen; i++)
for (int j = 0; j < NCODES; j++)
for (int k = 0; k < NCODES; k++)
assert(fscanf(fi, "%lf", &p[i][j][k]) == 1);
}
void Profile::write(FILE* fo) {
fprintf(fo, "%d %d\n", proLen, NCODES);
for (int i = 0; i < proLen; i++) {
for (int j = 0; j < NCODES; j++) {
for (int k = 0; k < NCODES - 1; k++)
fprintf(fo, "%.10g ", p[i][j][k]);
fprintf(fo, "%.10g\n", p[i][j][NCODES - 1]);
}
if (i < proLen - 1) { fprintf(fo, "\n"); }
}
}
void Profile::startSimulation() {
pc = new double[proLen][NCODES][NCODES];
for (int i = 0; i < proLen; i++) {
for (int j = 0; j < NCODES; j++)
for (int k = 0; k < NCODES; k++) {
pc[i][j][k] = p[i][j][k];
if (k > 0) pc[i][j][k] += pc[i][j][k - 1];
}
//avoid sampling from 0.0!!!
double cp_sum, cp_d, cp_n;
cp_sum = cp_d = cp_n = 0.0;
for (int j = 0; j < NCODES - 1; j++) {
cp_sum += pc[i][j][NCODES - 1];
cp_d += p[i][j][j];
cp_n += p[i][j][NCODES - 1];
}
if (cp_sum == 0.0) continue;
double p_d, p_o, p_n;
p_d = cp_d / cp_sum;
p_n = cp_n / cp_sum;
p_o = (1.0 - p_d - p_n) / (NCODES - 2);
for (int j = 0; j < NCODES - 1; j++) {
if (pc[i][j][NCODES - 1] > 0.0) continue;
for (int k = 0; k < NCODES; k++) {
if (k == j) pc[i][j][k] = p_d;
else if (k == NCODES - 1) pc[i][j][k] = p_n;
else pc[i][j][k] = p_o;
if (k > 0) pc[i][j][k] += pc[i][j][k - 1];
}
}
if (pc[i][NCODES - 1][NCODES - 1] == 0.0) {
p_o = (1.0 - p_n) / (NCODES - 1);
for (int k = 0; k < NCODES; k++) {
pc[i][NCODES - 1][k] = (k < NCODES - 1 ? p_o : p_n);
if (k > 0) pc[i][NCODES - 1][k] += pc[i][NCODES - 1][k - 1];
}
}
}
}
std::string Profile::simulate(simul* sampler, int len, int pos, int dir, const RefSeq& refseq) {
std::string readseq = "";
for (int i = 0; i < len; i++) {
readseq.push_back(getCharacter(sampler->sample(pc[i][refseq.get_id(i + pos, dir)], NCODES)));
}
return readseq;
}
void Profile::finishSimulation() {
delete[] pc;
}
#endif /* PROFILE_H_ */
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