18 #ifndef __ScoringP2P_H__
19 #define __ScoringP2P_H__
22 #include <ScoringFunction.h>
23 #include <ScoringScheme.h>
25 namespace Victor {
namespace Align2{
57 virtual double scoring(
int i,
int j);
virtual ~ScoringP2P()
Destructor.
Definition: ScoringP2P.cc:48
virtual double scoring(int i, int j)
Calculate scores to create matrix values.
Definition: ScoringP2P.cc:75
virtual void reverse()
Reverse template sequence and profile.
Definition: ScoringP2P.cc:109
virtual void copy(const ScoringP2P &orig)
Copy orig object to this object ("deep copy").
Definition: ScoringP2P.cc:89
Calculate scores for profile to profile alignment.
Definition: ScoringP2P.h:32
Calculate a frequency profile or PSSM.
Definition: Profile.h:35
Implement a standard substitution matrix.
Definition: SubMatrix.h:30
Structure * str
Pointer to Structure.
Definition: ScoringScheme.h:80
ScoringP2P & operator=(const ScoringP2P &orig)
Assignment operator.
Definition: ScoringP2P.cc:59
Base class for printing alignments.
Definition: AlignmentData.h:35
SubMatrix * sub
Substitution matrix.
Definition: ScoringScheme.h:78
Base class for structural scores.
Definition: Structure.h:32
ScoringP2P(SubMatrix *sub, AlignmentData *ad, Structure *str, Profile *pro1, Profile *pro2, ScoringFunction *fun, double cSeq)
Default constructor.
Definition: ScoringP2P.cc:37
AlignmentData * ad
Pointer to AlignmentData.
Definition: ScoringScheme.h:79
Base class for scoring functions.
Definition: ScoringFunction.h:31
Base class for scoring schemes.
Definition: ScoringScheme.h:34
virtual ScoringP2P * newCopy()
Construct a new "deep copy" of this object.
Definition: ScoringP2P.cc:103