Package org.biojava.nbio.alignment.template

Class AbstractProfileProfileAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

java.lang.Object

org.biojava.nbio.alignment.template.AbstractScorer

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

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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.alignment.template.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<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> query, Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
protected	AbstractProfileProfileAligner(Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> query, org.biojava.nbio.core.alignment.template.Profile<S,C> target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
protected	AbstractProfileProfileAligner(org.biojava.nbio.core.alignment.template.Profile<S,C> query, Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
protected	AbstractProfileProfileAligner(org.biojava.nbio.core.alignment.template.Profile<S,C> query, org.biojava.nbio.core.alignment.template.Profile<S,C> target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment.

Method Summary

Modifier and Type	Method	Description
protected org.biojava.nbio.core.sequence.template.CompoundSet<C>	getCompoundSet()
protected List<C>	getCompoundsOfQuery()
protected List<C>	getCompoundsOfTarget()
org.biojava.nbio.core.alignment.template.ProfilePair<S,C>	getPair()	Returns alignment profile pair.
org.biojava.nbio.core.alignment.template.Profile<S,C>	getQuery()	Returns the first profile of the pair.
protected int[]	getScoreMatrixDimensions()
protected int	getSubstitutionScore(int queryColumn, int targetColumn)
org.biojava.nbio.core.alignment.template.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(org.biojava.nbio.core.alignment.template.Profile<S,C> query)	Sets the query Profile.
void	setTarget(org.biojava.nbio.core.alignment.template.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 Detail

pair

protected org.biojava.nbio.core.alignment.template.ProfilePair<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound> pair

Constructor Detail

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(org.biojava.nbio.core.alignment.template.Profile<S,C> query,
                                        org.biojava.nbio.core.alignment.template.Profile<S,C> target,
                                        GapPenalty gapPenalty,
                                        org.biojava.nbio.core.alignment.template.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<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> query,
                                        Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> target,
                                        GapPenalty gapPenalty,
                                        org.biojava.nbio.core.alignment.template.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(org.biojava.nbio.core.alignment.template.Profile<S,C> query,
                                        Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> target,
                                        GapPenalty gapPenalty,
                                        org.biojava.nbio.core.alignment.template.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<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> query,
                                        org.biojava.nbio.core.alignment.template.Profile<S,C> target,
                                        GapPenalty gapPenalty,
                                        org.biojava.nbio.core.alignment.template.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 Detail

setQuery

public void setQuery(org.biojava.nbio.core.alignment.template.Profile<S,C> query)

Sets the query Profile.

Parameters:

query - the first Profile of the pair to align

setTarget

public void setTarget(org.biojava.nbio.core.alignment.template.Profile<S,C> target)

Sets the target Profile.

Parameters:

target - the second Profile of the pair to align

getPair

public org.biojava.nbio.core.alignment.template.ProfilePair<S,C> getPair()

Description copied from interface: ProfileProfileAligner

Returns alignment profile pair.

Specified by:

getPair in interface ProfileProfileAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

Returns:

alignment profile pair

getQuery

public org.biojava.nbio.core.alignment.template.Profile<S,C> getQuery()

Description copied from interface: ProfileProfileScorer

Returns the first profile of the pair.

Specified by:

getQuery in interface ProfileProfileScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

Returns:

the first profile of the pair

getTarget

public org.biojava.nbio.core.alignment.template.Profile<S,C> getTarget()

Description copied from interface: ProfileProfileScorer

Returns the second profile of the pair.

Specified by:

getTarget in interface ProfileProfileScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

Returns:

the second profile of the pair

getCompoundSet

protected org.biojava.nbio.core.sequence.template.CompoundSet<C> getCompoundSet()

Specified by:

getCompoundSet in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

getCompoundsOfQuery

protected List<C> getCompoundsOfQuery()

Specified by:

getCompoundsOfQuery in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

getCompoundsOfTarget

protected List<C> getCompoundsOfTarget()

Specified by:

getCompoundsOfTarget in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

getScoreMatrixDimensions

protected int[] getScoreMatrixDimensions()

Specified by:

getScoreMatrixDimensions in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

getSubstitutionScore

protected int getSubstitutionScore(int queryColumn,
                                   int targetColumn)

Specified by:

getSubstitutionScore in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

isReady

protected boolean isReady()

Specified by:

isReady in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>