// a file with color-coding from Ka/Ks values to color-bins
void kaks2Color(const Vdouble & kaksVec, const Vdouble &lowerBoundV,
const sequence & refSeq, string fileName,codon *co) {
vector<int> colors;
int numOfSitesinAln = kaksVec.size();
Vdouble negativesKaksVec,negativesSite;
negativesKaksVec.clear();
negativesSite.clear();
int i,gapsInRefSeq=0;
for (i=0;i<numOfSitesinAln;i++){
if (codonUtility::aaOf(refSeq[i],*co) == -1) gapsInRefSeq++;
}
// first dealing with positive selection
colors.resize(numOfSitesinAln-gapsInRefSeq);
int gap=0;
for (i=0;i<numOfSitesinAln;i++){
if (codonUtility::aaOf(refSeq[i],*co) == -1){
gap++;
continue;
}
if (lowerBoundV[i]>1) // color 1 (positive selection) : if confidence interval lower bound > 1
colors[i-gap]=1;
else if (kaksVec[i]>1) // color 2(positive selection) : "non-significant"
colors[i-gap]=2;
else {
negativesKaksVec.push_back(kaksVec[i]); //add the value of kaks < 1
negativesSite.push_back(i-gap); //add the number of site of the kaks
}
}
// now dealing with purifying selection
Vdouble orderVec = negativesKaksVec;
if (orderVec.size()>0) // this is since once the whole protein was positive selection... (anomaly)
sort(orderVec.begin(), orderVec.end()); //sort the kaks values to be divided to 5 groups
MDOUBLE percentileNum = 5.0;
int percentileNumInt = 5;
Vdouble maxScoreForPercentile(percentileNumInt);
if (orderVec.size()>0) {
maxScoreForPercentile[0] = orderVec[0];
for (int c = 1; c < percentileNumInt; ++c){
int place = (int)((c / percentileNum) * negativesKaksVec.size());
MDOUBLE maxScore = orderVec[place];
maxScoreForPercentile[c] = maxScore;
}
}
//loop over all the Ka/Ks < 1
for (int j=0; j < negativesKaksVec.size(); ++j){
MDOUBLE r = negativesKaksVec[j]; //the kaks of the site.
int s = (int)negativesSite[j]; //the site.
if (r > maxScoreForPercentile[4])
colors[s] = 3;
else if (r > maxScoreForPercentile[3])
colors[s] = 4;
else if (r> maxScoreForPercentile[2])
colors[s] = 5;
else if (r > maxScoreForPercentile[1])
colors[s] = 6;
else if (r >= maxScoreForPercentile[0])
colors[s] = 7;
}
//print to file
ofstream out(fileName.c_str());
gap=0;
amino aminoAcid;
LOG(5,<<"Printing selection color bins to file"<<endl);
for (i=0;i<refSeq.seqLen();i++){
int aa = codonUtility::aaOf(refSeq[i], *co);
if (aa==-1){
gap++;
continue;
}
string aaStr = aminoAcid.fromInt(aa);
out<<i+1-gap <<"\t"<<aaStr<<"\t"<<colors[i-gap];
out<<endl;
}
out.close();
}
// convert the other sequence to the alphabet inAlph.
sequence::sequence(const sequence& other,const alphabet* inAlph)
: _alphabet(inAlph->clone()), _remark(other._remark), _name(other._name), _id(other._id)
{
const mulAlphabet* pMulAlphabet;
// if the other.alphabet is amino or nucleotide and the inAlph is indel
if ( (other._alphabet->size() == 20 && inAlph->size() == 2)
|| (other._alphabet->size() == 4 && inAlph->size() == 2) )
{
for (int k=0; k < other.seqLen() ;k += other._alphabet->stringSize())
{
int charId = other._vec[k];
if (charId == other._alphabet->gap())
_vec.push_back(inAlph->fromChar("-",0));
else
_vec.push_back(inAlph->fromChar("X",0)); //also converts "." (charId==-3) to "X"
// unknown amino/nucleotide is converted to "X" and not to "?"
}
}
// if the other.alphabet is amino or nucleotide and the inAlph is mulAlphabet
else if ( (other._alphabet->size() == 20 && inAlph->size()%20 == 0)
|| (other._alphabet->size() == 4 && inAlph->size()%4 == 0) )
{
for (int k=0; k < other.seqLen() ;++k)
{
int charId = other._vec[k];
string ch = other._alphabet->fromInt(charId);
int mulCharId = _alphabet->fromChar(ch,0);
_vec.push_back(mulCharId);
}
// debug OZ
//cout << "other sequence: " << other << endl;
//cout << "mul sequence " << (*this) << endl;
// end of debug
}
// if the other.alphabet is mulAlphabet and the inAlph is it's baseAlphabet
// (for example, if other.alphabet is a multiplied-amino and inAlph is amino, then the converted sequence
// will have alphabet amino)
else if ( ((inAlph->size() == 20) && (other._alphabet->size()%20 == 0))
|| (inAlph->size() == 4) && (other._alphabet->size()%4 == 0))
{
pMulAlphabet=(mulAlphabet*)(other._alphabet);
for (int k=0; k < other.seqLen() ;++k)
{
int mulCharId = other._vec[k];
int baseId = pMulAlphabet->convertToBasedAlphaInt(mulCharId);
_vec.push_back(baseId);
}
}
// I tried to implement it using dynamic_cast but it doesn't work...
/*else if
(
(pMulAlphabet = dynamic_cast<const mulAlphabet*>(other._alphabet)) != NULL
)
{
if (pMulAlphabet->getBaseAlphabet()->size() == inAlph->size())
{
for (int k=0; k < other.seqLen() ;++k)
{
int mulCharId = other._vec[k];
int baseId = pMulAlphabet->convertToBasedAlphaInt(mulCharId);
_vec.push_back(baseId);
}
}
}*/
// (currently, there is no implimentions for other converts)
else
{
string error = "unable to convert this kind of alphabet";
errorMsg::reportError(error);
}
}
