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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* The reason why we have 2 different types of profiles is because one of them
* (ProfileWithSub) has the substitution matrix information already in it. This
* increases the performance when aligning 2 profile columns.
*/
#ifndef PROFILEBASE_H
#define PROFILEBASE_H
#include "../alignment/Alignment.h"
namespace clustalw
{
class ProfileBase
{
public:
/* Functions */
ProfileBase(int prfLen, int firstS, int lastS);
void calcGapCoeff(SeqArray* seqArray, vector<int>* gaps, bool useStructPenalties,
vector<char>* gapPenaltyMask, int gapCoef, int lenCoef);
const SeqArray* getProfilePtr(){return &profile;};
void resetProfile(){for(int i = 0; i < (int)profile.size();i++)
{
profile[i].clear();
}
profile.clear();
};
/* Attributes */
protected:
/* Functions */
void calcVPenalties(SeqArray* aln, vector<int>* weight);
void calcResidueSpecificPen(SeqArray* aln, vector<int>* weight);
void calcHydrophilicPen(SeqArray* aln, vector<int>* weight);
int localPenalty(int penalty, int n, vector<int>* resWeight, vector<int>* hydWeight,
vector<int>* vWeight);
float percentId(vector<int>* s1, vector<int>* s2);
/* Attributes */
vector<vector<int> > profile;
/* number of residues used for a window for the variable zone
penalties */
int vwindow;
/* vll is the lower limit for the variable zone penalties
(vll < pen < 1.0) */
int vll;
/* "Pascarella and Argos" residue specific gap modification
factors. See Table 1 in the ClustalW 1994 NAR paper
http://www.ncbi.nlm.nih.gov/pubmed/7984417
*/
string pascarellaRes;
vector<int> pascarellaProb;
vector<vector<int> > vlut;
static const int numLetters = 26;
float reducedGap;
bool nVarPen;
bool nHydPen;
bool nPrefPen;
int gdist;
int prfLength;
int firstSeq, lastSeq;
private:
/* Functions */
/* Attributes */
};
}
#endif
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