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Public Member Functions | Data Fields
ScoringS2S Class Reference

Calculate scores for sequence to sequence alignment. More...

+ Inheritance diagram for ScoringS2S:
+ Collaboration diagram for ScoringS2S:

Public Member Functions

 ScoringS2S (SubMatrix *sub, AlignmentData *ad, Structure *str, double cSeq)
 Default constructor. More...
 
 ScoringS2S (const ScoringS2S &orig)
 Copy constructor. More...
 
virtual ~ScoringS2S ()
 Destructor.
 
virtual bool checkSequence (const string &s) const
 Check if s consists only of characters defined in sub.getResidues. More...
 
virtual void copy (const ScoringS2S &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual void copy (const ScoringScheme &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual ScoringS2S * newCopy ()
 Construct a new "deep copy" of this object.
 
ScoringS2S & operator= (const ScoringS2S &orig)
 Assignment operator.
 
virtual void reverse ()
 Reverse template sequence.
 
virtual double scoring (int i, int j)
 Calculate scores to create matrix values. More...
 

Data Fields

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

Detailed Description

Calculate scores for sequence to sequence alignment.

Constructor & Destructor Documentation

ScoringS2S ( SubMatrix *  sub,
AlignmentData *  ad,
Structure *  str,
double  cSeq 
)

Default constructor.

Parameters
sub
ad
str
cSeq
ScoringS2S ( const ScoringS2S &  orig)

Copy constructor.

Parameters
orig

Member Function Documentation

bool checkSequence ( const string &  s) const
virtualinherited

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

Parameters
s
Returns
void copy ( const ScoringS2S &  orig)
virtual

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

Parameters
orig
void copy ( const ScoringScheme &  orig)
virtualinherited

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

Parameters
orig
double scoring ( int  i,
int  j 
)
virtual

Calculate scores to create matrix values.

Parameters
i
j
Returns

Implements ScoringScheme.

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