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/**
* Title: ProAlign<p>
* Description: <p>
* Copyright: Copyright (c) Ari Loytynoja<p>
* License: GNU GENERAL PUBLIC LICENSE<p>
* @see http://www.gnu.org/copyleft/gpl.html
* Company: ULB<p>
* @author Ari Loytynoja
* @version 1.0
*/
package proalign;
class Viterbi {
AlignmentLoop al;
double[] charFreqs;
String alphabet;
double delta;
double epsilon;
double logDelta;
double logEpsilon;
double logMinus2Delta;
double logMinusEpsilon;
double constantM;
double constantX;
double constantY;
TransformLog tl;
int aSize;
Viterbi(AlignmentLoop al) {
this.al = al;
this.charFreqs = al.pa.sm.charFreqs;
this.alphabet = al.pa.sm.alphabet;
delta = al.pa.sm.delta;
epsilon = al.pa.sm.epsilon;
logDelta = Math.log(al.pa.sm.delta);
logEpsilon = Math.log(al.pa.sm.epsilon);
logMinus2Delta = Math.log(1-2*al.pa.sm.delta);
logMinusEpsilon = Math.log(1-al.pa.sm.epsilon);
aSize = al.seq1[0].length; // aSize = alphabet size;
tl = new TransformLog();
}
// get viterbi value for M-state; set probability of each path to this cell;
// pathM[i][j][0] = P(match to M)
// pathM[i][j][1] = P(match to X)
// 1 - pathM[i][j][0] - pathM[i][j][1] = P(match to Y)
double getViterbiM(int i, int j) {
constantM = Math.log(sumOverChars(i,j));
double max = maxOfThree(logMinus2Delta+al.vitM[i-1][j],
logMinusEpsilon+al.vitX[i-1][j],
logMinusEpsilon+al.vitY[i-1][j]);
double pm = logMinus2Delta+al.vitM[i-1][j];
double px = logMinusEpsilon+al.vitX[i-1][j];
double py = logMinusEpsilon+al.vitY[i-1][j];
double sum = tl.sumLogs(pm,tl.sumLogs(px,py));
al.pathM[i][j][0] = (double) Math.exp(pm-sum);
al.pathM[i][j][1] = (double) Math.exp(px-sum);
return (constantM+max);
}
// get viterbi value for X-state; set probability of each path to this cell;
// pathX[i][j] = P(match to M)
// 1 - pathX[i][j] = P(match to X)
double getViterbiX(int i, int j) {
if(j==al.BWIDTH-1) { // lower border of band, an X-gap impossible
return Double.NEGATIVE_INFINITY;
}
constantX = Math.log(sumOverCharsX(i,j));
double max = maxOfTwoX(logDelta+al.vitM[i-1][j+1],
logEpsilon+al.vitX[i-1][j+1]);
double pm = logDelta+al.vitM[i-1][j+1];
double px = logEpsilon+al.vitX[i-1][j+1];
double sum = tl.sumLogs(px,pm);
al.pathX[i][j] = (double) Math.exp(pm-sum);
return constantX+max;
}
// get viterbi value for X-state; set probability of each path to this cell;
// pathY[i][j] = P(match to M)
// 1 - pathY[i][j] = P(match to Y)
double getViterbiY(int i, int j) {
if(j==0) { // upper border of band, a Y-gap impossible
return Double.NEGATIVE_INFINITY;
}
constantY = Math.log(sumOverCharsY(i,j));
double max = maxOfTwoY(logDelta+al.vitM[i][j-1],
logEpsilon+al.vitY[i][j-1]);
double pm = logDelta+al.vitM[i][j-1];
double py = logEpsilon+al.vitY[i][j-1];
double sum = tl.sumLogs(py,pm);
al.pathY[i][j] = (double) Math.exp(pm-sum);
return constantY+max;
}
// set vierbi end, set forward end,
// set probability of each path ending.
// pathEnd[0] = P(match to M), pathEnd[1] = P(gap to x)
// 1 - pathEnd[0] - pathEnd[1] = P(gap to y)
// endPoint is not necessarily MIDDLE!
double getViterbiEnd(int endPoint) {
if(al.an.hasTrailers) {
double pm = al.vitM[al.vitM.length-1][endPoint];
double px = al.vitX[al.vitX.length-1][endPoint];
double py = al.vitY[al.vitY.length-1][endPoint];
double sum;
if(al.an.end0>al.an.end1) {
sum = tl.sumLogs(pm,px);
al.pathEnd[0] = (double) Math.exp(pm-sum);
al.pathEnd[1] = (double) Math.exp(px-sum);
al.fwdEnd = (double) tl.sumLogs(al.fwdM[al.fwdM.length-1][endPoint],
al.fwdX[al.fwdX.length-1][endPoint]);
} else {
sum = tl.sumLogs(pm,py);
al.pathEnd[0] = (double) Math.exp(pm-sum);
al.pathEnd[1] = Double.NEGATIVE_INFINITY;
al.fwdEnd = (double) tl.sumLogs(al.fwdM[al.fwdM.length-1][endPoint],
al.fwdY[al.fwdY.length-1][endPoint]);
}
} else {
double pm = al.vitM[al.vitM.length-1][endPoint];
double px = al.vitX[al.vitX.length-1][endPoint];
double py = al.vitY[al.vitY.length-1][endPoint];
double sum = tl.sumLogs(pm,tl.sumLogs(px,py));
al.pathEnd[0] = (double) Math.exp(pm-sum);
al.pathEnd[1] = (double) Math.exp(px-sum);
al.fwdEnd = (double) tl.sumLogs(al.fwdM[al.fwdM.length-1][endPoint],
tl.sumLogs(al.fwdX[al.fwdX.length-1][endPoint],
al.fwdY[al.fwdY.length-1][endPoint]));
}
return (double) maxOfThree(al.vitM[al.vitM.length-1][endPoint],
al.vitX[al.vitX.length-1][endPoint],
al.vitY[al.vitY.length-1][endPoint]);
}
double getForwardM(int i, int j) {
return constantM+tl.sumLogs(logMinus2Delta+al.fwdM[i-1][j],
logMinusEpsilon+tl.sumLogs(al.fwdX[i-1][j],al.fwdY[i-1][j]));
}
double getForwardX(int i, int j) {
if(j==al.BWIDTH-1) { // lower border of band, an X-gap impossible
return Double.NEGATIVE_INFINITY;
}
if(j-al.MIDDLE+i==1) { // only X-gaps possible, constant's not set
constantX = Math.log(sumOverCharsX(i,j));
}
return constantX+tl.sumLogs(logDelta+al.fwdM[i-1][j+1],logEpsilon+al.fwdX[i-1][j+1]);
}
double getForwardY(int i, int j) {
if(j==0) { // upper border of band, a Y-gap impossible
return Double.NEGATIVE_INFINITY;
}
if(i==1) { // only Y-gaps possible, constant's not set
constantY = Math.log(sumOverCharsY(i,j));
}
return constantY+tl.sumLogs(logDelta+al.fwdM[i][j-1],logEpsilon+al.fwdY[i][j-1]);
}
double getBackwardM(int i, int j) {
if(i==al.vitM.length-1) { // left border of matrix
constantM = Double.NEGATIVE_INFINITY;
constantX = Double.NEGATIVE_INFINITY;
constantY = Math.log(sumOverCharsY(i,j+1));
}else if(j-al.MIDDLE+i==al.seq2.length+1) { // lower border of real matrix
constantM = Double.NEGATIVE_INFINITY;
constantX = Math.log(sumOverCharsX(i+1,j-1));
constantY = Double.NEGATIVE_INFINITY;
}else if(j==0) {
constantM = Math.log(sumOverChars(i+1,j));
constantX = Double.NEGATIVE_INFINITY;
constantY = Math.log(sumOverCharsY(i,j+1));
}else if(j==al.BWIDTH-1) {
constantM = Math.log(sumOverChars(i+1,j));
constantX = Math.log(sumOverCharsX(i+1,j-1));
constantY = Double.NEGATIVE_INFINITY;
} else {
constantM = Math.log(sumOverChars(i+1,j));
constantX = Math.log(sumOverCharsX(i+1,j-1));
constantY = Math.log(sumOverCharsY(i,j+1));
}
if(j==0) { // upper border of the band; an X-gap impossible
return tl.sumLogs(logMinus2Delta+constantM+al.bwdM[i+1][j],
logDelta+constantY+al.bwdY[i][j+1]);
}
if(j==al.BWIDTH-1) { // lower border of the band; a Y-gap impossible
return tl.sumLogs(logMinus2Delta+constantM+al.bwdM[i+1][j],
logDelta+constantX+al.bwdX[i+1][j-1]);
}
return tl.sumLogs(logMinus2Delta+constantM+al.bwdM[i+1][j],
logDelta+tl.sumLogs(constantX+al.bwdX[i+1][j-1],
constantY+al.bwdY[i][j+1]));
}
double getBackwardX(int i, int j) {
if(j==0) { // upper border of the band; an X-gap impossible
return logMinusEpsilon+constantM+al.bwdM[i+1][j];
}
return tl.sumLogs(logMinusEpsilon+constantM+al.bwdM[i+1][j],
logEpsilon+constantX+al.bwdX[i+1][j-1]);
}
double getBackwardY(int i, int j) {
if(j==al.BWIDTH-1) { // lower border of the band; a Y-gap impossible
return logMinusEpsilon+constantM+al.bwdM[i+1][j];
}
return tl.sumLogs(logMinusEpsilon+constantM+al.bwdM[i+1][j],
logEpsilon+constantY+al.bwdY[i][j+1]);
}
// sum over all possible characters [k] at the node [i][j]
double sumOverChars(int i, int j){
double sum = 0d;
for(int k = 0; k<aSize; k++) {
sum += al.price[i][j][k];
}
return sum;
}
double sumOverCharsX(int i, int j){
double sum = 0d;
for(int k = 0; k<aSize; k++) {
sum += al.priceX[i][j][k];
}
return sum;
}
double sumOverCharsY(int i, int j){
double sum = 0d;
for(int k = 0; k<aSize; k++) {
sum += al.priceY[i][j][k];
}
return sum;
}
double maxOfTwoX(double m, double x) {
double max = 0d;
if(m > x) {
max = m;
} else {
max = x;
}
return max;
}
double maxOfTwoY(double m, double y) {
double max = 0d;
if(m > y) {
max = m;
} else {
max = y;
}
return max;
}
double maxOfThree(double m, double x, double y) {
double max = 0d;
if(m > x && m > y) {
max = m;
} else if(x > y){
max = x;
} else {
max = y;
}
return max;
}
}
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