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// $Id: evaluateCharacterFreq.cpp 10474 2012-03-18 07:54:07Z itaymay $
#include "evaluateCharacterFreq.h"
#include "someUtil.h"
#include <cassert>
vector<MDOUBLE> sumAlphabetCounts(const sequenceContainer & sc) {
vector<MDOUBLE> charFreq(sc.alphabetSize(),0.0);
sequenceContainer::constTaxaIterator tIt;
sequenceContainer::constTaxaIterator tItEnd;
tIt.begin(sc);
tItEnd.end(sc);
while (tIt!= tItEnd) {
sequence::constIterator sIt;
sequence::constIterator sItEnd;
sIt.begin(*tIt);
sItEnd.end(*tIt);
while (sIt != sItEnd) {
if ((*sIt >= 0) && (*sIt <charFreq.size())) ++charFreq[(*sIt)];
++sIt;
}
++tIt;
}
return charFreq;
}
void changeCountsToFreqs(vector<MDOUBLE>& charFreq){
MDOUBLE sumA = 0;
int i=0;
for (i=0; i < charFreq.size(); ++i) {
sumA+=charFreq[i] ;
}
for (i=0; i < charFreq.size(); ++i) {
charFreq[i] /= sumA;
}
}
void makeSureNoZeroFreqs(vector<MDOUBLE> & charFreq){
// CORRECT SO THAT THERE ARE NO ZERO FREQUENCIES.
// ALL FREQS THAT WERE ZERO ARE CHANGED
MDOUBLE ZERO_FREQ = 0.0000000001;
MDOUBLE sumB=0;
int charWithZeroFreq = 0;
int i=0;
for (i=0; i < charFreq.size(); ++i) {
if (DSMALL_EQUAL(charFreq[i], ZERO_FREQ)) {
charFreq[i] = ZERO_FREQ;
++charWithZeroFreq;
}
else sumB +=charFreq[i];
}
if (!DEQUAL(sumB, 1.0, 0.01))
{
cerr.precision(10);
cerr<<"sumFreq = "<<sumB<<endl;
//errorMsg::reportError("error in makeSureNoZeroFreqs(). Input frequencies must sum to 1.0");
}
scaleVec(charFreq, 1.0/charFreq.size());
//MDOUBLE scaleFactor = sumB - (charWithZeroFreq * ZERO_FREQ);
//for (i=0; i < charFreq.size(); ++i) {
// if (charFreq[i] != ZERO_FREQ)
// charFreq[i] *= scaleFactor;
//}
}
vector<MDOUBLE> evaluateCharacterFreq(const sequenceContainer & sc) {
vector<MDOUBLE> charFreq=sumAlphabetCounts(sc);
changeCountsToFreqs(charFreq);
makeSureNoZeroFreqs(charFreq);
return charFreq;
}
VVdouble evaluateCharacterFreqOneForEachGene(const vector<sequenceContainer> & scVec){
VVdouble charFreq;
for (int k=0; k < scVec.size(); ++k) {
charFreq.push_back(evaluateCharacterFreq(scVec[k]));
}
return charFreq;
}
vector<MDOUBLE> evaluateCharacterFreqBasedOnManyGenes(const vector<sequenceContainer> & scVec) {
// note: all alphabets have to be the same!
vector<MDOUBLE> charFreq(scVec[0].alphabetSize(),0.0);
for (int i=0; i < scVec.size();++i) {
assert(scVec[0].getAlphabet()->size()==scVec[i].getAlphabet()->size());
vector<MDOUBLE> charFreqTmp=sumAlphabetCounts(scVec[i]);
for (int z=0; z < charFreq.size();++z) charFreq[z]+=charFreqTmp[z];
}
changeCountsToFreqs(charFreq);
makeSureNoZeroFreqs(charFreq);
return charFreq;
}
//returns the number of each character in each position.
//NOTE: returns also the number of unknown charecters in the last place in each vector, so that the actual vector size for each position is alphabetSize()+1
void getCharacterCounts(const sequenceContainer & sc, VVint& counts4pos)
{
const alphabet* pAlph = sc.getAlphabet();
int alphSize = sc.alphabetSize();
int pos;
counts4pos.resize(sc.seqLen());
for (pos = 0; pos < sc.seqLen(); ++pos)
counts4pos[pos].resize(alphSize + 1, 0);
for (int seq = 0; seq < sc.numberOfSeqs();++seq)
{
int id = sc.placeToId(seq);
for (pos = 0; pos < sc.seqLen(); ++pos)
{
int charType = sc[id][pos];
if (pAlph->isSpecific(charType))
{
++counts4pos[pos][charType];
}
else
++counts4pos[pos][alphSize];
}
}
}
//returns the number of different character types in each position
void getCharacterType4pos(const sequenceContainer & sc, Vint& charactersType4pos)
{
VVint counts4Pos;
getCharacterCounts(sc, counts4Pos);
charactersType4pos.resize(sc.seqLen(), 0);
for (int pos = 0; pos < sc.seqLen(); ++pos)
{
for (int c = 0; c < counts4Pos[pos].size()-1; ++c)
{
if (counts4Pos[pos][c] > 0)
++charactersType4pos[pos];
}
}
}
//returns the distribution of the different character types in each position along the whole alignment
void getCharacterTypeDistribution(const sequenceContainer & sc, Vint& charactersTypeDist)
{
Vint charactersType4pos;
getCharacterType4pos(sc, charactersType4pos);
charactersTypeDist.resize(sc.numberOfSeqs()+1, 0);
for (int pos = 0; pos < sc.seqLen(); ++pos)
{
int count = charactersType4pos[pos];
++charactersTypeDist[count];
}
}
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