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malign.cpp
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malign.cpp
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#include "malign.h"
MAlignment::MAlignment(float a,float b,float c){
gap=a;
mismatch=b;
similar=c;
}
void MAlignment::AddSeq(vector<string>& a){
names.push_back(a[0]);
vector<string> temp;
for(unsigned int i=1;i < a.size();i++){
temp.push_back(a[i]);
}
seqs.push_back(temp);
return;
}
void MAlignment::AddSeq(vector<vector<string> > & a){
for(unsigned int i=0; i < a.size();i++){
AddSeq(a[i]);
}
return;
}
float MAlignment::align(){
profile.push_back(seqs[0]);
float FinalScore;
int total_length=seqs[0].size();
for(unsigned int i=1;i < seqs.size();i++){
total_length+=seqs[i].size();
/*******Calculate the TABLE********/
int ydim=profile[0].size()+1;
int xdim=seqs[i].size()+1;
float score[xdim*ydim];
int trace[xdim*ydim]; // to record traces for finding the aligned sequences 1 for gap in x,2 for match,3 for gap in y
for(int l=0; l < ydim;l++){
score[l*xdim]=(float)l*gap;
trace[l*xdim]=3;
}
for(int l=0; l < xdim;l++){
score[l]=(float)l*gap;
trace[l]=1;
}
for(int j=1; j <xdim;j++){
for(int k=1; k <ydim;k++){
float temp=0.0;
score[k*xdim+j]=score[(k-1)*xdim+j]+gap;//initialize min with adding gap in y direction
trace[k*xdim+j]=3;
for(unsigned int m=0;m < profile.size();m++){
float Percentage=Similarity(profile[m][k-1],seqs[i][j-1]);
if(FloatEqual(Percentage,1.0) == true){
temp=temp+score[(k-1)*xdim+j-1]+identical;
//cout<<"Identical "<<profile[m][k-1]<<","<<seqs[i][j-1]<<" Score:"<<temp<<endl;
}else if(FloatEqual(Percentage,0.9) == true){
temp=temp+score[(k-1)*xdim+j-1]+verysimilar;
//cout<<"Almost "<<profile[m][k-1]<<","<<seqs[i][j-1]<<" Score:"<<temp<<endl;
}else if(Percentage >= 0.66 ){
//cout<<"Temp now is "<<temp<<endl;
temp=temp+score[(k-1)*xdim+j-1]+similar;
//cout<<"Similar "<<profile[m][k-1]<<","<<seqs[i][j-1]<<" Score:"<<temp<<endl;
}else if(Percentage < 0.0 ){
temp=temp+score[(k-1)*xdim+j-1]+gap;
//cout<<"MatchToGap "<<profile[m][k-1]<<","<<seqs[i][j-1]<<" Score:"<<temp<<endl;
}else{
temp=temp+score[(k-1)*xdim+j-1]+mismatch;
//cout<<"Mismatch "<<profile[m][k-1]<<","<<seqs[i][j-1]<<" Score:"<<temp<<endl;
}
}
temp=temp/float(profile.size());
//cout<<"Finally the score is "<<temp<<endl;
if(temp < score[k*xdim+j]){
//cout<<temp << " is smaller than "<< score[k*xdim+j] <<endl;
score[k*xdim+j]=temp;
trace[k*xdim+j]=2;
}
temp=score[k*xdim+j-1]+gap; //adding gap in x direction
if(temp < score[k*xdim+j]){
//cout<<temp << " is smaller than "<< score[k*xdim+j] <<endl;
score[k*xdim+j]=temp;
trace[k*xdim+j]=1;
}
}
}
//cout<<"Finish Scoring?"<<endl;
/************** Output score matrix*************
for(int k=ydim-1; k >=0;k--){
if( k >= 1){
cout<<profile[0][k-1];
}else{
cout<<"-";
}
for(int j=0; j <xdim;j++){
cout<<"\t"<<score[k*xdim+j];
}
cout<<endl;
}
cout<<"\t"<<"-";
for(unsigned int j=0; j < seqs[i].size();j++){
cout<<"\t"<<seqs[i][j];
}
cout<<endl;
cout<<"Final Score :"<<score[xdim*ydim-1]<<endl;
*************************************************/
/************** Out put matrix
for(int l=ydim-1; l >=0;l--){
for(int m=0; m <xdim;m++){
cout<<"\t"<<trace[l*xdim+m];
}
cout<<endl;
}
*/
/**Trace back find the alignment*/
int xInd=xdim-1;
int yInd=ydim-1;
while(xInd > 0 || yInd > 0 ){
//cout <<"Checking "<<xInd<<","<<yInd<<endl;
if(xInd-1 >=0 && trace[yInd*xdim+xInd] == 1){
for(unsigned int m=0;m < profile.size();m++){
if(alignment.size() > m){
alignment[m].insert(alignment[m].begin(),"-");
}else{
vector<string> temp;
temp.push_back("-");
alignment.push_back(temp);
}
}
if(alignment.size() > profile.size() ){
alignment[int(profile.size())].insert(alignment[int(profile.size())].begin(),seqs[i][xInd-1]);
}else{
vector<string> temp;
temp.push_back(seqs[i][xInd-1]);
alignment.push_back(temp);
}
xInd=xInd-1;
continue;
}
if(yInd-1 >=0 && trace[yInd*xdim+xInd] == 3){
for(unsigned int m=0;m < profile.size();m++){
if(alignment.size() > m){
alignment[m].insert(alignment[m].begin(),profile[m][yInd-1]);
}else{
vector<string> temp;
temp.push_back(profile[m][yInd-1]);
alignment.push_back(temp);
}
}
if(alignment.size() > profile.size()){
alignment[int(profile.size())].insert(alignment[int(profile.size())].begin(),"-");
}else{
vector<string> temp;
temp.push_back("-");
alignment.push_back(temp);
}
yInd=yInd-1;
continue;
}
if(trace[yInd*xdim+xInd] == 2){
for(unsigned int m=0;m < profile.size();m++){
if(alignment.size() > m){
alignment[m].insert(alignment[m].begin(),profile[m][yInd-1]);
}else{
vector<string> temp;
temp.push_back(profile[m][yInd-1]);
alignment.push_back(temp);
}
}
if(alignment.size() > profile.size()){
alignment[int(profile.size())].insert(alignment[int(profile.size())].begin(),seqs[i][xInd-1]);
}else{
vector<string> temp;
temp.push_back(seqs[i][xInd-1]);
alignment.push_back(temp);
}
xInd=xInd-1;
yInd=yInd-1;
}
}
//~ while (i > 0)
//~ {
//~ AlignmentA <- Ai + AlignmentA
//~ AlignmentB <- "-" + AlignmentB
//~ i <- i - 1
//~ }
//~ while (j > 0)
//~ {
//~ AlignmentA <- "-" + AlignmentA
//~ AlignmentB <- Bj + AlignmentB
//~ j <- j - 1
//~ }
UpdateProfile();
FinalScore=score[xdim*ydim-1];
}
return (FinalScore)/(int)(profile[0].size())+2;
}
void MAlignment::UpdateProfile(){
for(unsigned int i=0; i< profile.size();i++){
profile[i].clear();
for(unsigned int j=0;j < alignment[i].size();j++){
string temp = alignment[i][j];
profile[i].push_back(temp);
}
}
profile.push_back(alignment[int(profile.size())]);
for(unsigned int j=0;j < alignment.size();j++){
alignment[j].clear();
}
return;
}
void MAlignment::outputalign(){
for(unsigned int i=0; i< profile.size();i++){
cout<<names[i];
for(unsigned int j=0;j < profile[i].size();j++){
cout<<"\t"<<profile[i][j];
}
cout<<endl;
}
return;
}
//Helper function to compare two float numbers to 0.01 precision
bool MAlignment::FloatEqual(float A, float B){
if (A == B)
return true;
float Error = fabs((A - B));
if (Error <= 0.01)
return true;
return false;
}
float MAlignment::Similarity(string a,string b){
string tempa,tempb;
float sim=0.0;
if(a.size() != b.size() || a.compare("-") == 0 || b.compare("-") == 0){
return -1.0;
}
if(a.compare(b) == 0)
return 1;
for(unsigned int i=0;i < a.size();i++){
tempa=a.substr(i,1);
tempb=b.substr(i,1);
if(tempa.compare(tempb)== 0 && tempa.compare("x") != 0 ){
sim=sim+1.0;
}else{
if(a.length() == 4 && i == 1){
sim=sim+0.5;
}
}
}
if( sim == ((float)a.size()-0.5) ){
return 0.9;
}
if( sim == (float)a.size() ){
return 1;
}
return ((float)((int)sim))/(float)a.size();
}