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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef GLBALIGN__HPP
#define GLBALIGN__HPP
#include <utility>
#include <string>
#include <list>
#include <vector>
#include <cmath>
using namespace std;
namespace DeBruijn {
typedef pair<string,string> TCharAlign;
typedef pair<int,int> TRange;
class CCigar {
public:
CCigar(int qto = -1, int sto = -1) : m_qfrom(qto+1), m_qto(qto), m_sfrom(sto+1), m_sto(sto) {}
struct SElement {
SElement(int l, char t) : m_len(l), m_type(t) {}
int m_len;
char m_type; // 'M' 'D' 'I'
};
void PushFront(const SElement& el);
void PushBack(const SElement& el);
void PushFront(const CCigar other_cigar);
string CigarString(int qstart, int qlen) const; // qstart, qlen identify notaligned 5'/3' parts
string DetailedCigarString(int qstart, int qlen, const char* query, const char* subject, bool include_soft_clip = true) const;
string BtopString(int qstart, int qlen, const char* query, const char* subject) const;
TRange QueryRange() const { return TRange(m_qfrom, m_qto); }
TRange SubjectRange() const { return TRange(m_sfrom, m_sto); }
TCharAlign ToAlign(const char* query, const char* subject) const;
int Matches(const char* query, const char* subject) const;
int Distance(const char* query, const char* subject) const;
int Score(const char* query, const char* subject, int gopen, int gapextend, const char delta[256][256]) const;
private:
list<SElement> m_elements;
int m_qfrom, m_qto, m_sfrom, m_sto;
};
//Needleman-Wunsch
CCigar GlbAlign(const char* query, int querylen, const char* subject, int subjectlen, int gopen, int gapextend, const char delta[256][256]);
//Smith-Waterman
CCigar LclAlign(const char* query, int querylen, const char* subject, int subjectlen, int gopen, int gapextend, const char delta[256][256]);
//Smith-Waterman with optional NW ends
CCigar LclAlign(const char* query, int querylen, const char* subject, int subjectlen, int gopen, int gapextend, bool pinleft, bool pinright, const char delta[256][256]);
//variable band Smith-Waterman (traceback matrix full)
CCigar VariBandAlign(const char* query, int querylen, const char* subject, int subjectlen, int gopen, int gapextend, const char delta[256][256], const TRange* subject_limits);
//band Smith-Waterman (traceback matrix banded)
CCigar BandAlign(const char* query, int querylen, const char* subject, int subjectlen, int gopen, int gapextend, const char delta[256][256], int band);
struct SMatrix
{
SMatrix(int match, int mismatch); // matrix for DNA
SMatrix(); // matrix for proteins blosum62
char matrix[256][256];
};
template<class T>
int EditDistance(const T &s1, const T & s2) {
const int len1 = s1.size(), len2 = s2.size();
vector<int> col(len2+1), prevCol(len2+1);
for (int i = 0; i < (int)prevCol.size(); i++)
prevCol[i] = i;
for (int i = 0; i < len1; i++) {
col[0] = i+1;
for (int j = 0; j < len2; j++)
col[j+1] = min( min( 1 + col[j], 1 + prevCol[1 + j]),
prevCol[j] + (s1[i]==s2[j] ? 0 : 1) );
col.swap(prevCol);
}
return prevCol[len2];
}
template<class RandomIterator>
double Entropy(RandomIterator start, size_t length) {
if(length == 0)
return 0;
double tA = 1.e-8;
double tC = 1.e-8;
double tG = 1.e-8;
double tT = 1.e-8;
for(auto it = start; it != start+length; ++it) {
switch(*it) {
case 'A': tA += 1; break;
case 'C': tC += 1; break;
case 'G': tG += 1; break;
case 'T': tT += 1; break;
default: break;
}
}
double entropy = -(tA*log(tA/length)+tC*log(tC/length)+tG*log(tG/length)+tT*log(tT/length))/(length*log(4.));
return entropy;
}
}; // namespace
#endif // GLBALIGN__HPP
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