public Double eval(Double lmbda) {
double c1 = 0.0;
double c3 = -1.0 / (double) Math.sqrt(2.0 * variance);
double sum = 0.0;
double cpart = -0.5 * Math.log(Math.sqrt(2.0 * Math.PI * variance));
for (int i = 0; i < data.size(); i++) {
for (int k = 0; k < channels.length; k++) {
c1 += cpart;
double pi = 0.0;
for (Integer t : transcripts.keySet()) {
if (transcripts.get(t).contains(i)) {
double dit = delta(i, t);
double gammai = gammas[t][k];
double pit = gammai * Math.exp(-lmbda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = data.values(i)[channels[k]] - zi;
sum += (err * err);
}
}
return c1 + c3 * sum;
}
public Double eval(Double gamma) {
double c1 = 0.0;
double c3 = -1.0 / (double) Math.sqrt(2.0 * variance);
double sum = 0.0;
double cpart = -0.5 * Math.log(Math.sqrt(2.0 * Math.PI * variance));
for (Integer i : transcripts.get(gammat)) {
c1 += cpart;
double pi = 0.0;
for (int t = 0; t < fiveprime.length; t++) {
if (transcripts.get(t).contains(i)) {
double gammai = gammat == t ? gamma : gammas[t][gammak];
double dit = delta(i, t);
double pit = gammai * Math.exp(-lambda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = data.values(i)[channels[gammak]] - zi;
sum += (err * err);
}
return c1 + c3 * sum;
}
public Double eval(Double lmbda) {
double c = 1.0 / (double) Math.sqrt(variance);
double sum = 0.0;
for (int i = 0; i < data.size(); i++) {
for (int k = 0; k < channels.length; k++) {
double pi = 0.0;
double pdi = 0.0;
for (Integer t : transcripts.keySet()) {
if (transcripts.get(t).contains(i)) {
double gammai = gammas[t][k];
double dit = delta(i, t);
double falloff = Math.exp(-lmbda * dit);
double pit = gammai * falloff;
double pdit = pit * dit;
pi += pit;
pdi += pdit;
}
}
double zi = Math.log(pi);
double err = data.values(i)[channels[k]] - zi;
double ratio = pdi / pi;
double termi = (err * ratio);
sum += termi;
}
}
return c * sum;
}
public Double eval(Double gamma) {
double c = 1.0 / (double) Math.sqrt(variance);
double sum = 0.0;
for (Integer i : transcripts.get(gammat)) {
double pi = 0.0;
for (int t = 0; t < fiveprime.length; t++) {
if (transcripts.get(t).contains(i)) {
double gammai = gammat == t ? gamma : gammas[t][gammak];
double dit = delta(i, t);
double pit = gammai * Math.exp(-lambda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = data.values(i)[channels[gammak]] - zi;
double ratio = (Math.exp(-lambda * delta(i, gammat))) / pi;
double termi = (err * ratio);
sum += termi;
}
return c * sum;
}
public double error() {
double sum = 0.0;
for (int i = 0; i < data.size(); i++) {
for (int k = 0; k < channels.length; k++) {
double pi = 0.0;
for (Integer t : transcripts.keySet()) {
if (transcripts.get(t).contains(i)) {
double gammai = gammas[t][k];
double dit = delta(i, t);
double pit = gammai * Math.exp(-lambda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = Math.abs(data.values(i)[channels[k]] - zi);
sum += err;
}
}
return sum;
}