bool AlphabetTools::checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
{
if (alphabet.getNumberOfChars() == 0)
return true; // Will this really happen?
size_t size = alphabet.intToChar(0).size();
for (int i = 1; i < static_cast<int>(alphabet.getNumberOfTypes()); ++i)
{
if (alphabet.intToChar(i).size() != size)
return false;
}
return true;
}
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
{
if (!checkAlphabetCodingSize(alphabet))
throw AlphabetException("Bad alphabet in function Alphabet::getAlphabetCodingSize().");
return static_cast<unsigned int>(alphabet.intToChar(0).size());
}
int RNY::getRNY(int i, int j, int k, const Alphabet& alph) const throw (BadCharException)
{
if (alph.getAlphabetType() != "DNA alphabet")
{
throw AlphabetException ("RNY::getRNY : Sequence must be DNA",
&alph);
}
char li = alph.intToChar(i)[0];
char lj = alph.intToChar(j)[0];
char lk = alph.intToChar(k)[0];
int r = 0;
int s = 0;
switch (li)
{
case 'A':
case 'G':
r += 0;
break;
case 'C':
r += 1;
break;
case 'T':
r += 2;
break;
case '-':
case 'N':
s += 1;
break;
default:
throw BadCharException(&li, "RNY::getRNY(int,int;int,alph): Specified base unknown.");
}
r *= 4;
s *= 2;
switch (lj)
{
case 'A':
r += 0;
break;
case 'G':
r += 1;
break;
case 'C':
r += 2;
break;
case 'T':
r += 3;
break;
case '-':
case 'N':
s += 1;
break;
default:
throw BadCharException(&lj, "RNY::getRNY(int,int;int,alph): Specified base unknown.");
}
r *= 3;
s *= 2;
switch (lk)
{
case 'A':
r += 0;
break;
case 'G':
r += 1;
break;
case 'C':
case 'T':
r += 2;
break;
case '-':
case 'N':
s += 1;
break;
default:
throw BadCharException(&lk, "RNY::getRNY(int,int;int,alph): Specified base unknown.");
}
return 50 * s + r;
}