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Public Member Functions
DotPFreq Class Reference

Calculate scores for profile to profile alignment using dot product method. More...

+ Inheritance diagram for DotPFreq:
+ Collaboration diagram for DotPFreq:

Public Member Functions

 DotPFreq (Profile *pro1, Profile *pro2)
 Default constructor. More...
 
 DotPFreq (const DotPFreq &orig)
 Copy constructor. More...
 
virtual ~DotPFreq ()
 Destructor.
 
virtual void copy (const ScoringFunction &orig)
 Copy orig object to this object ("deep copy").
 
virtual void copy (const DotPFreq &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual DotPFreq * newCopy ()
 Construct a new "deep copy" of this object. More...
 
DotPFreq & operator= (const DotPFreq &orig)
 Assignment operator. More...
 
virtual double scoringSeq (int i, int j)
 Calculate scores to create matrix values. More...
 

Detailed Description

Calculate scores for profile to profile alignment using dot product method.

Some explanations can be found in: 

           Mittelman D., Sadreyev R., Grishin N.
           Probabilistic scoring measures for profile-profile
           comparison yield more accurate short seed alignments.
           Bioinformatics. 2003 Aug 12;19(12):1531-9.
           PMID: 12912834 [PubMed - indexed for MEDLINE]

           Marti-Renom MA., Madhusudhan MS., Sali A.
           Alignment of protein sequences by their profiles.
           Protein Sci. 2004 Apr;13(4):1071-87.
           PMID: 15044736 [PubMed - indexed for MEDLINE]

Constructor & Destructor Documentation

DotPFreq ( Profile *  pro1,
Profile *  pro2 
)

Default constructor.

Parameters
pro1
pro2
DotPFreq ( const DotPFreq &  orig)

Copy constructor.

Parameters
orig

Member Function Documentation

void copy ( const DotPFreq &  orig)
virtual

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

Parameters
orig
DotPFreq * newCopy ( )
virtual

Construct a new "deep copy" of this object.

Returns

Implements ScoringFunction.

DotPFreq & operator= ( const DotPFreq &  orig)

Assignment operator.

Parameters
orig
Returns
double scoringSeq ( int  i,
int  j 
)
virtual

Calculate scores to create matrix values.

Parameters
i
j
Returns

Implements ScoringFunction.

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