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// $Id: sequence.cpp 7627 2010-03-06 21:56:30Z cohenofi $
#include "sequence.h"
#include <algorithm>
using namespace std;
sequence::sequence(const string& str,
const string& name,
const string& remark,
const int id,
const alphabet* inAlph)
: _alphabet(inAlph->clone()), _remark(remark), _name(name),_id(id)
{
for (int k=0; k < str.size() ;k += _alphabet->stringSize()) {
int charId = inAlph->fromChar(str, k);
if (charId == -99) {
string textToPrint = "unable to read sequence: " + name;
errorMsg::reportError(textToPrint);
}
_vec.push_back(charId);
}
}
sequence::sequence(const sequence& other)
: _vec(other._vec), _alphabet(other._alphabet->clone()),
_remark(other._remark), _name(other._name),_id(other._id)
{
}
// 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);
}
}
// for gainLoss project - {0,1} in both, hence no conversion needed.
// it should be the same for all cases with same alphabet
else if ( inAlph->size() == other._alphabet->size() )
{
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(mulCharId);
}
}
// 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);
}
}
sequence::~sequence()
{
if (_alphabet)
delete _alphabet;
}
void sequence::resize(const int k, const int* val) {
if (val == NULL) {
_vec.resize(k,_alphabet->unknown());
}
else {
_vec.resize(k,*val);
}
}
string sequence::toString() const{
string tmp;
for (int k=0; k < _vec.size() ; ++k ){
tmp+= _alphabet->fromInt(_vec[k]);
}
return tmp;
}
string sequence::toString(const int pos) const{
return _alphabet->fromInt(_vec[pos]);
}
void sequence::addFromString(const string& str) {
for (int k=0; k < str.size() ; k+=_alphabet->stringSize()) {
_vec.push_back(_alphabet->fromChar(str,k));
}
}
class particip {
public:
explicit particip() {}
bool operator()(int i) {
return (i==-1000);
}
};
//removePositions: the poitions to be removed are marked as '1' in posToRemoveVec
//all othehr positions are '0'
void sequence::removePositions(const vector<int> & posToRemoveVec)
{
if(posToRemoveVec.size() != seqLen())
errorMsg::reportError("the input vector must be same size as sequence length. in sequence::removePositions");
for (int k=0; k < posToRemoveVec.size(); ++k) {
if (posToRemoveVec[k] == 1)
_vec[k] = -1000;
}
vector<int>::iterator vec_iter;
vec_iter = remove_if(_vec.begin(),_vec.end(),particip());
_vec.erase(vec_iter,_vec.end()); // pg 1170, primer.
}
//return the number of sites that are specific = not unknown, nor ambiguity, nor gap (for example, for nucleotides it will true for A,C,G, or T).
int sequence::seqLenSpecific() const
{
int res = 0;
for (int pos = 0; pos < seqLen(); ++pos)
{
if (isSpecific(pos))
++res;
}
return res;
}
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