ProfileProfileScorer (biojava-alignment 5.2.0 API)

Type Parameters:

S - each Sequence in the pair of alignment Profiles is of type S

C - each element of an AlignedSequence is a Compound of type C

All Superinterfaces:

Scorer

All Known Subinterfaces:

PartitionRefiner<S,C>, ProfileProfileAligner<S,C>

All Known Implementing Classes:

AbstractProfileProfileAligner, SimpleProfileProfileAligner
```
public interface ProfileProfileScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
extends Scorer
```
Defines an algorithm which computes a score for a pairing of alignment profiles.

Author:

Mark Chapman

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`org.biojava.nbio.core.alignment.template.Profile<S,C>`	`getQuery()`	Returns the first profile of the pair.
`org.biojava.nbio.core.alignment.template.Profile<S,C>`	`getTarget()`	Returns the second profile of the pair.

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

- Method Detail
  - getQuery
```
org.biojava.nbio.core.alignment.template.Profile<S,C> getQuery()
```
    Returns the first profile of the pair.
    
    Returns:
    
    the first profile of the pair
  - getTarget
```
org.biojava.nbio.core.alignment.template.Profile<S,C> getTarget()
```
    Returns the second profile of the pair.
    
    Returns:
    
    the second profile of the pair