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AtchleyDistance Class Reference

Calculate scores for profile to profile alignment using sequence metric factor. More...

+ Inheritance diagram for AtchleyDistance:
+ Collaboration diagram for AtchleyDistance:

Public Member Functions

 AtchleyDistance (Profile *pro1, Profile *pro2)
 Default constructor. More...
 
 AtchleyDistance (Profile *pro1, Profile *pro2, double offset)
 Constructor assigning offset. More...
 
 AtchleyDistance (const AtchleyDistance &orig)
 Copy constructor. More...
 
virtual ~AtchleyDistance ()
 Destructor.
 
virtual void copy (const ScoringFunction &orig)
 Copy orig object to this object ("deep copy").
 
virtual void copy (const AtchleyDistance &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual double getOffset ()
 Return offset.
 
virtual AtchleyDistancenewCopy ()
 Construct a new "deep copy" of this object. More...
 
AtchleyDistanceoperator= (const AtchleyDistance &orig)
 Assignment operator. More...
 
virtual void pLoadFactor ()
 Helper function used to load Atchley metric factor.
 
virtual double scoringSeq (int i, int j)
 Calculate scores to create matrix values. More...
 
virtual void setOffset (double off)
 Set offset.
 

Detailed Description

Calculate scores for profile to profile alignment using sequence metric factor.

Some explanations can be found in:

          William R. Atchley, Jieping Zhao, Andrew D. Fernandes, Tanja Druke
          Solving the protein sequence metric problem.
          Edited by Walter M. Fitch, University of California, Irvine, CA,
          and approved March 22, 2005 (received for review December 14, 2004).

Constructor & Destructor Documentation

AtchleyDistance ( Profile pro1,
Profile pro2 
)

Default constructor.

Parameters
pro1
pro2
AtchleyDistance ( Profile pro1,
Profile pro2,
double  offset 
)

Constructor assigning offset.

Parameters
pro1
pro2
offset
AtchleyDistance ( const AtchleyDistance orig)

Copy constructor.

Parameters
orig

Member Function Documentation

void copy ( const AtchleyDistance orig)
virtual

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

Parameters
orig
AtchleyDistance * newCopy ( )
virtual

Construct a new "deep copy" of this object.

Returns

Implements ScoringFunction.

AtchleyDistance & operator= ( const AtchleyDistance 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: