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#include "samplingSequences.h"
#include "logFile.h"
#include "talRandom.h"
sampleSequences::sampleSequences(sequenceContainer &sc){
_sc = sc;
}
sequenceContainer sampleSequences::removeSequences(sequenceContainer &sc){
int noOfSeq = sc.numberOfSeqs();
int gap = sc.getAlphabet()->gap();
int unknown = sc.getAlphabet()->unknown();
bool seqToAdd;
int n =0;
sequenceContainer newSc;
for (int i=0;i<noOfSeq;i++){
seqToAdd = true;
for (int j=0;j<sc[i].seqLen();j++){
if ((sc[i][j]== gap) || (sc[i][j]== unknown ) || (sc[i].seqLen() != 297)){
seqToAdd = false;
}
}
if (seqToAdd == true) {
sequence add = sc[i];
sequence sc(add);
sc.setID(n);
n++;
newSc.add(sc);
}
}
return newSc;
}
void sampleSequences::printDistances(){
for (int i=0;i< _distances.size();i++){
for (int j=0;j<_distances[i].size();j++){
cout<<_distances[i][j]<<" ";
}
cout<<endl;
}
}
void sampleSequences::setDistance(int i,int j,MDOUBLE dist){
(i<j ? _distances[i][j-i] :_distances[j][i-j]) = dist;
}
MDOUBLE sampleSequences::getDistance(int i,int j){
return (i<j ? _distances[i][j-i] :_distances[j][i-j]);
}
sequenceContainer sampleSequences::sampleFarthestSequences(int n, distanceMethod *dm){
_sc.removeIdenticalSequences();
if (n >= _sc.numberOfSeqs()){
cerr<<"Number of sequences to sample is bigger than the origin number of sequences so the all sequences were chosen in sampleSequences::sampleFarthestSequences"<<endl;
return _sc;
}
int numberOfSeq = _sc.numberOfSeqs();
_distances.resize(numberOfSeq);
int i;
for (i=0;i<numberOfSeq;i++)
_distances[i].resize(numberOfSeq-i);
for (i=0;i<numberOfSeq;i++){
for(int j=i;j<numberOfSeq;j++){
int id1 = _sc.placeToId(i);
int id2 = _sc.placeToId(j);
setDistance(i,j,dm->giveDistance(_sc[id1],_sc[id2],NULL));
}
}
sequenceContainer newSc;
vector<int> sampled;
sampled.push_back(0);//to change
int id = 0;
int p = _sc.placeToId(0);
sequence sc(_sc[p]);
sc.setID(id++);
newSc.add(sc);
while (newSc.numberOfSeqs()<n){
int i = findNextSeq(sampled);
p = _sc.placeToId(i);
sequence sc(_sc[p]);
sc.setID(id);
newSc.add(sc);
id++;
sampled.push_back(i);
}
return newSc;
}
int sampleSequences::findNextSeq(vector<int> &sampled){
MDOUBLE max = 0,min;
int seqi = -1;
for(int i=0;i< _sc.numberOfSeqs();i++){
min=10000;//to update
for (int j=0;j<sampled.size();j++){
if (getDistance(i,sampled[j])<min)
min = getDistance(i,sampled[j]);
}
if (max<min){
max=min;
seqi = i;
}
}
if (seqi>_sc.numberOfSeqs() ||seqi<0){
errorMsg::reportError("Error in sampleSequences::findNextSeq");
}
return seqi;
}
//sequenceContainer sampleSequences::sampleRandomSequences(int seqNum)
//{
// if (seqNum > _sc.numberOfSeqs())
// errorMsg::reportError("sampleSequences::sampleRandomSequences(): the number of requested seqeuences is larger than the number of sequences in the MSA");
// sequenceContainer newSc(_sc);
// while (newSc.numberOfSeqs() > seqNum)
// {
// int seqPlaceToRemove = talRandom::giveIntRandomNumberBetweenZeroAndEntry(newSc.numberOfSeqs());
// newSc.remove(newSc.placeToId(seqPlaceToRemove));
// }
// return newSc;
//}
sequenceContainer sampleSequences::sampleRandomSequences(int seqNum)
{
if (seqNum > _sc.numberOfSeqs())
errorMsg::reportError("sampleSequences::sampleRandomSequences(): the number of requested seqeuences is larger than the number of sequences in the MSA");
sequenceContainer newSc;
Vint vec2Add(_sc.numberOfSeqs(),0);
int n = 0;
while (n < seqNum)
{
int seqPlaceToAdd = talRandom::giveIntRandomNumberBetweenZeroAndEntry(_sc.numberOfSeqs());
if (vec2Add[seqPlaceToAdd] == 0){
vec2Add[seqPlaceToAdd] = 1;
n++;
}
}
for (int i = 0; i<vec2Add.size();i++){
if (vec2Add[i] == 1)
newSc.add(_sc[i]);
}
return newSc;
}
//sequenceContainer sampleSequences::sampleRandomCharacters(int seqLen)
//{
// if (seqLen > _sc.seqLen())
// errorMsg::reportError("sampleSequences::sampleRandomCharacters(): the requested sequence length is larger than the number of characters in the MSA");
// Vint posToRemove(_sc.seqLen(),1);
// //first create a vector with seqLen positions to be sampled in the begining of the vector
// for (int i = 0; i < seqLen; ++i)
// posToRemove[i] = 0;
// //then randomly swap the positions in posToRemove.
// //The end result is a random vector with the positions to remove marked with '1'
// int swapNum = _sc.seqLen() * 10;
// for (int x = 0; x < swapNum; ++x)
// {
// int pos1 = talRandom::giveIntRandomNumberBetweenZeroAndEntry(_sc.seqLen());
// int pos2 = talRandom::giveIntRandomNumberBetweenZeroAndEntry(_sc.seqLen());
// int tmp = posToRemove[pos1];
// posToRemove[pos1] = posToRemove[pos2];
// posToRemove[pos2] = tmp;
// }
//
// sequenceContainer newSc(_sc);
// newSc.removePositions(posToRemove);
// return newSc;
//}
sequenceContainer sampleSequences::sampleRandomCharacters(int seqLen)
{
if (seqLen > _sc.seqLen())
errorMsg::reportError("sampleSequences::sampleRandomCharacters(): the requested sequence length is larger than the number of characters in the MSA");
sequenceContainer newSc(_sc);
while (newSc.seqLen() > seqLen)
{
Vint posToRemove(newSc.seqLen(),0);
int seqPlaceToRemove = talRandom::giveIntRandomNumberBetweenZeroAndEntry(newSc.seqLen());
posToRemove[seqPlaceToRemove] = 1;
newSc.removePositions(posToRemove);
}
return newSc;
}
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