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ScoringP2S Class Reference

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

+ Inheritance diagram for ScoringP2S:
+ Collaboration diagram for ScoringP2S:

Public Member Functions

 ScoringP2S (SubMatrix *sub, AlignmentData *ad, Structure *str, Profile *pro, double cSeq)
 Default constructor. More...
 
 ScoringP2S (const ScoringP2S &orig)
 Copy constructor.
 
virtual ~ScoringP2S ()
 Destructor.
 
virtual bool checkSequence (const string &s) const
 Check if s consists only of characters defined in sub.getResidues. More...
 
virtual void copy (const ScoringP2S &orig)
 Copy orig object to this object ("deep copy").
 
virtual void copy (const ScoringScheme &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual ScoringP2SnewCopy ()
 Construct a new "deep copy" of this object.
 
ScoringP2Soperator= (const ScoringP2S &orig)
 Assignment operator.
 
virtual void reverse ()
 Reverse template sequence.
 
virtual double scoring (int i, int j)
 Calculate scores to create matrix values.
 

Data Fields

AlignmentDataad
 Pointer to AlignmentData.
 
Structurestr
 Pointer to Structure.
 
SubMatrixsub
 Substitution matrix.
 

Detailed Description

Calculate scores for profile to sequence alignment.

Constructor & Destructor Documentation

ScoringP2S ( SubMatrix sub,
AlignmentData ad,
Structure str,
Profile pro,
double  cSeq 
)

Default constructor.

Parameters
sub
ad
str
pro
cSeq

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 ScoringScheme orig)
virtualinherited

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

Parameters
orig

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