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Public Member Functions
DotPOdds Class Reference

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

+ Inheritance diagram for DotPOdds:
+ Collaboration diagram for DotPOdds:

Public Member Functions

 DotPOdds (Profile *pro1, Profile *pro2)
 Default constructor. More...
 
 DotPOdds (const DotPOdds &orig)
 Copy constructor. More...
 
virtual ~DotPOdds ()
 Destructor.
 
virtual void copy (const ScoringFunction &orig)
 Copy orig object to this object ("deep copy").
 
virtual void copy (const DotPOdds &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual DotPOdds * newCopy ()
 Construct a new "deep copy" of this object. More...
 
DotPOdds & operator= (const DotPOdds &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

DotPOdds ( Profile *  pro1,
Profile *  pro2 
)

Default constructor.

Parameters
pro1
pro2
DotPOdds ( const DotPOdds &  orig)

Copy constructor.

Parameters
orig

Member Function Documentation

void copy ( const DotPOdds &  orig)
virtual

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

Parameters
orig
DotPOdds * newCopy ( )
virtual

Construct a new "deep copy" of this object.

Returns

Implements ScoringFunction.

DotPOdds & operator= ( const DotPOdds &  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: