ShapeFunctionTable::ShapeFunctionTable(int ngauss, int nsf)
: f_table(ngauss, DoubleVec(nsf)),
df_table(ngauss, std::vector<DoubleVec>(nsf, DoubleVec(DIM)))
{
}
//Function to initialize the Felsenstein Pruning Tables on the Inner Nodes of the Tree
//This is not done simulataneously with the tree creation because the Substitution Matrices are needed for the
//Felsenstein Probablilities estimation, and for these, the corresponding branch lengths are required (i.e. the tree has to be fully created first)
void PairInitializer::InitTreeFPTables() {
//Nodes A, B, C and D
{
for (int k=0;k<4;k++){
FTree->Get_TreeNodes()[k].N1.FPTable.resize(4, DoubleVec(Seqs->Get_BareSeqs()[k].size(),0));
for (int i=0; i<Seqs->Get_BareSeqs()[k].size(); i++) {
FTree->Get_TreeNodes()[k].N1.FPTable[GetAlphabet(Seqs->Get_BareSeqs()[k][i])][i]= 1.0;
}
FTree->Get_TreeNodes()[k].N2.FPTable.resize(4, DoubleVec(Seqs->Get_BareSeqs()[k].size(),0));
FTree->Get_TreeNodes()[k].N3.FPTable.resize(4, DoubleVec(Seqs->Get_BareSeqs()[k].size(),0));
}
}
//Node E
{
//InnerNode N1 conditioned on Nodes A and B
double len1 = FTree->Get_TreeNodes()[4].N2.Length;
int idx1 = GetPosOfElement(OverallSubMatsLengths, len1, 0);
double len2 = FTree->Get_TreeNodes()[4].N3.Length;
int idx2 = GetPosOfElement(OverallSubMatsLengths, len2, 0);
FTree->Get_TreeNodes()[4].N1.FPTable.resize(4, DoubleVec(0,0));
for (int j=0; j<AlignmentHomologies[4].size(); j++) {
if (AlignmentHomologies[4][j]==-1) {
continue;
}
for (int i=0; i<4; i++) { //For each possibility, meaning A,C,G or T
double prob = 1;
if (AlignmentHomologies[0][j]!=-1) {
prob *= OverallSubMats[idx1][GetAlphabetPair(i, Seqs->Get_BareSeqs()[0][AlignmentHomologies[0][j]-1])];
}
if (AlignmentHomologies[1][j]!=-1) {
prob *= OverallSubMats[idx2][GetAlphabetPair(i, Seqs->Get_BareSeqs()[1][AlignmentHomologies[1][j]-1])];
}
FTree->Get_TreeNodes()[4].N1.FPTable[i].push_back(prob);
}
}
}
//Node 6
{
//InnerNode N1 conditioned on Nodes C and D
double len1 = FTree->Get_TreeNodes()[5].N2.Length;
int idx1 = GetPosOfElement(OverallSubMatsLengths, len1, 0);
double len2 = FTree->Get_TreeNodes()[5].N3.Length;
int idx2 = GetPosOfElement(OverallSubMatsLengths, len2, 0);
FTree->Get_TreeNodes()[5].N1.FPTable.resize(4, DoubleVec(0,0));
for (int j=0; j<AlignmentHomologies[5].size(); j++) {
if (AlignmentHomologies[5][j]==-1) {
continue;
}
for (int i=0; i<4; i++) { //For each possibility, meaning A,C,G or T
double prob = 1;
if (AlignmentHomologies[2][j]!=-1) {
prob *= OverallSubMats[idx1][GetAlphabetPair(i, Seqs->Get_BareSeqs()[2][AlignmentHomologies[2][j]-1])];
}
if (AlignmentHomologies[3][j]!=-1) {
prob *= OverallSubMats[idx2][GetAlphabetPair(i, Seqs->Get_BareSeqs()[3][AlignmentHomologies[3][j]-1])];
}
FTree->Get_TreeNodes()[5].N1.FPTable[i].push_back(prob);
}
}
}
//Node 5 - InnerNodes N2 and N3
{
//InnerNode N2 conditioned on Nodes B, C and D
{
double len1 = FTree->Get_TreeNodes()[4].N3.Length;
int idx1 = GetPosOfElement(OverallSubMatsLengths, len1, 0);
double len2 = FTree->Get_TreeNodes()[4].N1.Length;
int idx2 = GetPosOfElement(OverallSubMatsLengths, len2, 0);
FTree->Get_TreeNodes()[4].N2.FPTable.resize(4, DoubleVec(0,0));
for (int j=0; j<AlignmentHomologies[4].size(); j++) {
if (AlignmentHomologies[4][j]==-1) {
continue;
}
for (int i=0; i<4; i++) { //For each possibility, meaning A,C,G or T
double prob = 1;
if (AlignmentHomologies[1][j]!=-1) {
prob *= OverallSubMats[idx1][GetAlphabetPair(i, Seqs->Get_BareSeqs()[1][AlignmentHomologies[1][j]-1])];
}
//if (FTree->Get_TreeNodes()[4]->Get_Homologies()[5][j]!=-1) {
if (AlignmentHomologies[5][j]!=-1) {
double sum = 0;
for (int k=0; k<4; k++) {
sum += OverallSubMats[idx2][GetAlphabetPair(i, k)]* (FTree->Get_TreeNodes()[5].N1.FPTable[k][AlignmentHomologies[5][j]-1]);
}
prob *= sum;
}
FTree->Get_TreeNodes()[4].N2.FPTable[i].push_back(prob);
}
}
}
//InnerNode N3 conditioned on Nodes A, C and D
{
double len1 = FTree->Get_TreeNodes()[4].N2.Length;
int idx1 = GetPosOfElement(OverallSubMatsLengths, len1, 0);
double len2 = FTree->Get_TreeNodes()[4].N1.Length;
int idx2 = GetPosOfElement(OverallSubMatsLengths, len2, 0);
FTree->Get_TreeNodes()[4].N3.FPTable.resize(4, DoubleVec(0,0));
for (int j=0; j<AlignmentHomologies[4].size(); j++) {
if (AlignmentHomologies[4][j]==-1) {
continue;
}
for (int i=0; i<4; i++) { //For each possibility, meaning A,C,G or T
double prob = 1;
if (AlignmentHomologies[0][j]!=-1) {
prob *= OverallSubMats[idx1][GetAlphabetPair(i, Seqs->Get_BareSeqs()[0][AlignmentHomologies[0][j]-1])];
}
if (AlignmentHomologies[5][j]!=-1) {
double sum = 0;
for (int k=0; k<4; k++) {
sum += OverallSubMats[idx2][GetAlphabetPair(i, k)]* (FTree->Get_TreeNodes()[5].N1.FPTable[k][AlignmentHomologies[5][j]-1]);
}
prob *= sum;
}
FTree->Get_TreeNodes()[4].N3.FPTable[i].push_back(prob);
}
}
}
}
//Node 6 - InnerNodes N2 and N3
{
//InnerNode N2 conditioned on Nodes A, B and D
{
double len1 = FTree->Get_TreeNodes()[5].N3.Length;
int idx1 = GetPosOfElement(OverallSubMatsLengths, len1, 0);
double len2 = FTree->Get_TreeNodes()[5].N1.Length;
int idx2 = GetPosOfElement(OverallSubMatsLengths, len2, 0);
FTree->Get_TreeNodes()[5].N2.FPTable.resize(4, DoubleVec(0,0));
for (int j=0; j<AlignmentHomologies[5].size(); j++) {
if (AlignmentHomologies[5][j]==-1) {
continue;
}
for (int i=0; i<4; i++) { //For each possibility, meaning A,C,G or T
double prob = 1;
if (AlignmentHomologies[3][j]!=-1) {
prob *= OverallSubMats[idx1][GetAlphabetPair(i, Seqs->Get_BareSeqs()[3][AlignmentHomologies[3][j]-1])];
}
if (AlignmentHomologies[4][j]!=-1) {
double sum = 0;
for (int k=0; k<4; k++) {
sum += OverallSubMats[idx2][GetAlphabetPair(i, k)]* (FTree->Get_TreeNodes()[4].N1.FPTable[k][AlignmentHomologies[4][j]-1]);
}
prob *= sum;
}
FTree->Get_TreeNodes()[5].N2.FPTable[i].push_back(prob);
}
}
}
//InnerNode N3 conditioned on Nodes A, B and C
{
double len1 = FTree->Get_TreeNodes()[5].N2.Length;
int idx1 = GetPosOfElement(OverallSubMatsLengths, len1, 0);
double len2 = FTree->Get_TreeNodes()[5].N1.Length;
int idx2 = GetPosOfElement(OverallSubMatsLengths, len2, 0);
FTree->Get_TreeNodes()[5].N3.FPTable.resize(4, DoubleVec(0,0));
for (int j=0; j<AlignmentHomologies[5].size(); j++) {
if (AlignmentHomologies[5][j]==-1) {
continue;
}
for (int i=0; i<4; i++) { //For each possibility, meaning A,C,G or T
double prob = 1;
if (AlignmentHomologies[2][j]!=-1) {
prob *= OverallSubMats[idx1][GetAlphabetPair(i, Seqs->Get_BareSeqs()[2][AlignmentHomologies[2][j]-1])];
}
if (AlignmentHomologies[4][j]!=-1) {
double sum = 0;
for (int k=0; k<4; k++) {
sum += OverallSubMats[idx2][GetAlphabetPair(i, k)]* (FTree->Get_TreeNodes()[4].N1.FPTable[k][AlignmentHomologies[4][j]-1]);
}
prob *= sum;
}
FTree->Get_TreeNodes()[5].N3.FPTable[i].push_back(prob);
}
}
}
}
}
