18 #ifndef __ScoringScheme_H__
19 #define __ScoringScheme_H__
21 #include <AlignmentData.h>
22 #include <Structure.h>
23 #include <SubMatrix.h>
27 namespace Victor {
namespace Align2{
58 virtual double scoring(
int i,
int j) = 0;
ScoringScheme & operator=(const ScoringScheme &orig)
Assignment operator.
Definition: ScoringScheme.cc:61
Implement a standard substitution matrix.
Definition: SubMatrix.h:30
Structure * str
Pointer to Structure.
Definition: ScoringScheme.h:80
virtual ~ScoringScheme()
Destructor.
Definition: ScoringScheme.cc:50
Base class for printing alignments.
Definition: AlignmentData.h:35
virtual void reverse()
Reverse template components (sequence and/or profile).
Definition: ScoringScheme.cc:112
virtual ScoringScheme * newCopy()=0
Construct a new "deep copy" of this object.
SubMatrix * sub
Substitution matrix.
Definition: ScoringScheme.h:78
Base class for structural scores.
Definition: Structure.h:32
virtual double scoring(int i, int j)=0
Calculate scores to create matrix values.
AlignmentData * ad
Pointer to AlignmentData.
Definition: ScoringScheme.h:79
virtual bool checkSequence(const string &s) const
Check if s consists only of characters defined in sub.getResidues.
Definition: ScoringScheme.cc:76
ScoringScheme(SubMatrix *sub, AlignmentData *ad, Structure *str)
Default constructor.
Definition: ScoringScheme.cc:34
Base class for scoring schemes.
Definition: ScoringScheme.h:34
virtual void copy(const ScoringScheme &orig)
Copy orig object to this object ("deep copy").
Definition: ScoringScheme.cc:105