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Public Member Functions | Data Fields
ScoringScheme Class Referenceabstract

Base class for scoring schemes. More...

+ Inheritance diagram for ScoringScheme:
+ Collaboration diagram for ScoringScheme:

Public Member Functions

 ScoringScheme (SubMatrix *sub, AlignmentData *ad, Structure *str)
 Default constructor. More...
 
 ScoringScheme (const ScoringScheme &orig)
 Copy constructor.
 
virtual ~ScoringScheme ()
 Destructor.
 
virtual bool checkSequence (const string &s) const
 Check if s consists only of characters defined in sub.getResidues. More...
 
virtual void copy (const ScoringScheme &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual ScoringScheme * newCopy ()=0
 Construct a new "deep copy" of this object.
 
ScoringScheme & operator= (const ScoringScheme &orig)
 Assignment operator. More...
 
virtual void reverse ()
 Reverse template components (sequence and/or profile).
 
virtual double scoring (int i, int j)=0
 Calculate scores to create matrix values.
 

Data Fields

AlignmentData * ad
 Pointer to AlignmentData.
 
Structure * str
 Pointer to Structure.
 
SubMatrix * sub
 Substitution matrix.
 

Detailed Description

Base class for scoring schemes.

Constructor & Destructor Documentation

ScoringScheme ( SubMatrix *  sub,
AlignmentData *  ad,
Structure *  str 
)

Default constructor.

Parameters
sub
ad
str

Member Function Documentation

bool checkSequence ( const string &  s) const
virtual

Check if s consists only of characters defined in sub.getResidues.

Parameters
s
Returns
void copy ( const ScoringScheme &  orig)
virtual

Copy orig object to this object ("deep copy").

Parameters
orig
ScoringScheme & operator= ( const ScoringScheme &  orig)

Assignment operator.

Parameters
orig
Returns
The documentation for this class was generated from the following files: