org.biojava.nbio.alignment.template.AbstractProfileProfileAligner<S,C>

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 Implemented Interfaces:: Aligner<S,C>, MatrixAligner<S,C>, ProfileProfileAligner<S,C>, ProfileProfileScorer<S,C>, Scorer

Direct Known Subclasses:: SimpleProfileProfileAligner

public abstract class AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> extends AbstractMatrixAligner<S,C> implements ProfileProfileAligner<S,C>

Implements common code for an Aligner for a pair of Profiles.

Author:: Mark Chapman

Field Summary

Fields

Modifier and Type

Field

Description

protected ProfilePair<S,C>

pair

Fields inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart
Constructor Summary

Constructors

Modifier

Constructor

Description

protected

AbstractProfileProfileAligner()

Before running a profile-profile alignment, data must be sent in via calls to setQuery(Profile), setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

protected

AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)

Prepares for a profile-profile alignment run concurrently.

protected

AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)

Prepares for a profile-profile alignment run concurrently.

protected

AbstractProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)

Prepares for a profile-profile alignment run concurrently.

protected

AbstractProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)

Prepares for a profile-profile alignment.
Method Summary

Modifier and Type

Method

Description

protected CompoundSet<C>

getCompoundSet()

protected List<C>

getCompoundsOfQuery()

protected List<C>

getCompoundsOfTarget()

ProfilePair<S,C>

getPair()

Returns alignment profile pair.

Profile<S,C>

getQuery()

Returns the first profile of the pair.

protected int[]

getScoreMatrixDimensions()

protected int

getSubstitutionScore(int queryColumn, int targetColumn)

Profile<S,C>

getTarget()

Returns the second profile of the pair.

protected boolean

isReady()

protected void

reset()

Resets output fields; should be overridden to set max and min

void

setQuery(Profile<S,C> query)

Sets the query Profile.

void

setTarget(Profile<S,C> target)

Sets the target Profile.

Methods inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner
align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, setGapPenalty, setProfile, setStoringScoreMatrix, setSubstitutionMatrix

Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer
getDistance, getDistance, getSimilarity, getSimilarity

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.nbio.alignment.template.Aligner
getComputationTime, getProfile

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

Field Details
- pair
  
  protected ProfilePair<S extends Sequence<C>,C extends Compound> pair
Constructor Details
- AbstractProfileProfileAligner
  
  protected AbstractProfileProfileAligner()
  
  Before running a profile-profile alignment, data must be sent in via calls to setQuery(Profile), setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
- AbstractProfileProfileAligner
  
  protected AbstractProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
  
  Prepares for a profile-profile alignment.
  
  Parameters:
  
  query - the first Profile of the pair to align
  
  target - the second Profile of the pair to align
  
  gapPenalty - the gap penalties used during alignment
  
  subMatrix - the set of substitution scores used during alignment
- AbstractProfileProfileAligner
  
  protected AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
  
  Prepares for a profile-profile alignment run concurrently.
  
  Parameters:
  
  query - the first Profile of the pair to align, still to be calculated
  
  target - the second Profile of the pair to align, still to be calculated
  
  gapPenalty - the gap penalties used during alignment
  
  subMatrix - the set of substitution scores used during alignment
- AbstractProfileProfileAligner
  
  protected AbstractProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
  
  Prepares for a profile-profile alignment run concurrently.
  
  Parameters:
  
  query - the first Profile of the pair to align
  
  target - the second Profile of the pair to align, still to be calculated
  
  gapPenalty - the gap penalties used during alignment
  
  subMatrix - the set of substitution scores used during alignment
- AbstractProfileProfileAligner
  
  protected AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
  
  Prepares for a profile-profile alignment run concurrently.
  
  Parameters:
  
  query - the first Profile of the pair to align, still to be calculated
  
  target - the second Profile of the pair to align
  
  gapPenalty - the gap penalties used during alignment
  
  subMatrix - the set of substitution scores used during alignment
Method Details
- setQuery
  
  public void setQuery(Profile<S,C> query)
  
  Sets the query Profile.
  
  Parameters:
  
  query - the first Profile of the pair to align
- setTarget
  
  public void setTarget(Profile<S,C> target)
  
  Sets the target Profile.
  
  Parameters:
  
  target - the second Profile of the pair to align
- getPair
  
  public ProfilePair<S,C> getPair()
  
  Description copied from interface: ProfileProfileAligner
  
  Returns alignment profile pair.
  
  Specified by:
  
  getPair in interface ProfileProfileAligner<S extends Sequence<C>,C extends Compound>
  
  Returns:
  
  alignment profile pair
- getQuery
  
  public Profile<S,C> getQuery()
  
  Description copied from interface: ProfileProfileScorer
  
  Returns the first profile of the pair.
  
  Specified by:
  
  getQuery in interface ProfileProfileScorer<S extends Sequence<C>,C extends Compound>
  
  Returns:
  
  the first profile of the pair
- getTarget
  
  public Profile<S,C> getTarget()
  
  Description copied from interface: ProfileProfileScorer
  
  Returns the second profile of the pair.
  
  Specified by:
  
  getTarget in interface ProfileProfileScorer<S extends Sequence<C>,C extends Compound>
  
  Returns:
  
  the second profile of the pair
- getCompoundSet
  
  protected CompoundSet<C> getCompoundSet()
  
  Specified by:
  
  getCompoundSet in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- getCompoundsOfQuery
  
  protected List<C> getCompoundsOfQuery()
  
  Specified by:
  
  getCompoundsOfQuery in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- getCompoundsOfTarget
  
  protected List<C> getCompoundsOfTarget()
  
  Specified by:
  
  getCompoundsOfTarget in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- getScoreMatrixDimensions
  
  protected int[] getScoreMatrixDimensions()
  
  Specified by:
  
  getScoreMatrixDimensions in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- getSubstitutionScore
  
  protected int getSubstitutionScore(int queryColumn, int targetColumn)
  
  Specified by:
  
  getSubstitutionScore in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- isReady
  
  protected boolean isReady()
  
  Specified by:
  
  isReady in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- reset
  
  protected void reset()
  
  Description copied from class: AbstractMatrixAligner
  
  Resets output fields; should be overridden to set max and min
  
  Overrides:
  
  reset in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>

Class AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound>

Field Summary

Fields inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Constructor Summary

Method Summary

Methods inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner

Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.nbio.alignment.template.Aligner

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

Field Details

pair

Constructor Details

AbstractProfileProfileAligner

AbstractProfileProfileAligner

AbstractProfileProfileAligner

AbstractProfileProfileAligner

AbstractProfileProfileAligner

Method Details

setQuery

setTarget

getPair

getQuery

getTarget

getCompoundSet

getCompoundsOfQuery

getCompoundsOfTarget

getScoreMatrixDimensions

getSubstitutionScore

isReady

reset