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// $Id: mulAlphabet.cpp 6420 2009-06-25 11:17:08Z adist $
#include "mulAlphabet.h"
#include "distribution.h"
#include "errorMsg.h"
#include <iostream>
#include "logFile.h"
mulAlphabet::mulAlphabet(const alphabet* baseAlphabet, int mulFactor) :
_baseAlphabet(baseAlphabet->clone()),
_mulFactor(mulFactor),
_size(baseAlphabet->size() * mulFactor)
{}
mulAlphabet::mulAlphabet(const mulAlphabet& other) :
_baseAlphabet(other._baseAlphabet->clone()),
_mulFactor(other._mulFactor),
_size(other._size)
{}
mulAlphabet::~mulAlphabet()
{
if (_baseAlphabet) delete (_baseAlphabet);
}
mulAlphabet& mulAlphabet::operator=(const mulAlphabet &other)
{
if (_baseAlphabet) delete (_baseAlphabet);
_baseAlphabet = other._baseAlphabet->clone();
_mulFactor = other._mulFactor;
_size = other._size;
return (*this);
}
int mulAlphabet::unknown() const
{
return (convertFromBasedAlphaInt(_baseAlphabet->unknown()));
}
int mulAlphabet::gap() const
{
return (convertFromBasedAlphaInt(_baseAlphabet->gap()));
}
int mulAlphabet::stringSize() const
{
return _baseAlphabet->stringSize();
}
bool mulAlphabet::isSpecific(const int id) const
{
if (id >= _size)
return false;
else
return _baseAlphabet->isSpecific(convertToBasedAlphaInt(id));
}
/* The first _size characters should be first. The rest of the characters aren't multiplied.
For example, when using nucleotides as the based alphabet and _mulFactor = 2 :
0 A0
1 C0
2 G0
3 T0
4 A1
5 C1
6 G1
7 T1
8 A
9 C
10 G
11 T
12 U
13 R
14 Y
15 K
16 M
17 S
18 W
19 B
20 D
21 H
22 V
23 N
-1 -
*/
string mulAlphabet::fromInt(const int id) const
{
// category and categoryName are for debug purpose
int category(_mulFactor);
if (id>=0)
category = min(id / _baseAlphabet->size() , _mulFactor) ;
string categoryName("");
categoryName = int2string(category);
int inCategoryId = convertToBasedAlphaInt(id);
return (_baseAlphabet->fromInt(inCategoryId) + categoryName);
}
int mulAlphabet::convertFromBasedAlphaInt(int id) const
{
if (id < 0)
return (id);
return (id + _size);
}
int mulAlphabet::fromChar(const string& str, const int pos) const
{
int id = _baseAlphabet->fromChar(str,pos);
return (convertFromBasedAlphaInt(id));
}
vector<int> mulAlphabet::fromString(const string &str) const
{
vector<int> result = _baseAlphabet->fromString(str);
vector<int>::iterator itr = result.begin();
for (; itr != result.end(); ++itr)
*itr = convertFromBasedAlphaInt(*itr);
return (result);
}
int mulAlphabet::convertToBasedAlphaInt(int id) const
{
if (id<0)
return (id);
if (id >= _size)
return (id - _size);
return (id % _baseAlphabet->size());
}
int mulAlphabet::relations(const int charInSeq, const int charToCheck) const
{
int baseAlphabetSize = _baseAlphabet->size();
int categoryInSeq(_mulFactor);
if (charInSeq>=0)
categoryInSeq = min(charInSeq/baseAlphabetSize , _mulFactor);
int categoryToCheck(_mulFactor);
if (charToCheck>=0)
categoryToCheck = min(charToCheck/baseAlphabetSize , _mulFactor);
if (categoryToCheck == _mulFactor)
LOG(4,<<"mulAlphabet::relations charToCheck should belong to category < _mulFactor = " << _mulFactor << endl);
if ((categoryInSeq == categoryToCheck) || (categoryInSeq == _mulFactor))
return _baseAlphabet->relations(convertToBasedAlphaInt(charInSeq),convertToBasedAlphaInt(charToCheck));
return 0;
}
int mulAlphabet::compareCategories(int charA, int charB) const
{
// TO DO should combine code by calling mulAlphabet::rateShiftType mulAlphabet::compareCategories
int baseAlphabetSize = _baseAlphabet->size();
int categoryA(_mulFactor);
if (categoryA>=0)
categoryA = min(charA/baseAlphabetSize,_mulFactor);
int categoryB(_mulFactor);
if (categoryB>=0)
categoryB = min(charB/baseAlphabetSize,_mulFactor);
if (categoryA<categoryB)
return 1;
else if (categoryB<categoryA)
return -1;
return (0);
}
mulAlphabet::rateShiftType mulAlphabet::compareCategories(int charA, int charB, int baseAlphabetSize, int multiplicationFactor)
{
int categoryA(multiplicationFactor);
if (categoryA>=0)
categoryA = min(charA/baseAlphabetSize,multiplicationFactor);
int categoryB(multiplicationFactor);
if (categoryB>=0)
categoryB = min(charB/baseAlphabetSize,multiplicationFactor);
if (categoryA<categoryB)
return acceleration;
else if (categoryB<categoryA)
return deceleration;
return noRateShift;
}
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