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java.lang.Objectorg.biojava3.alignment.template.AbstractScorer
org.biojava3.alignment.template.AbstractMatrixAligner<S,C>
org.biojava3.alignment.template.AbstractProfileProfileAligner<S,C>
S
- each Sequence
in the pair of alignment Profile
s is of type SC
- each element of an AlignedSequence
is a Compound
of type Cpublic abstract class AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound>
Implements common code for an Aligner
for a pair of Profile
s.
Field Summary | |
---|---|
protected ProfilePair<S,C> |
pair
|
Fields inherited from class org.biojava3.alignment.template.AbstractMatrixAligner |
---|
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart |
Constructor Summary | |
---|---|
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 | |
---|---|
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 short |
getSubstitutionScore(int queryColumn,
int targetColumn)
|
Profile<S,C> |
getTarget()
Returns the second profile of the pair. |
protected boolean |
isReady()
|
protected void |
reset()
|
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.biojava3.alignment.template.AbstractMatrixAligner |
---|
align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, resetAnchors, setGapPenalty, setProfile, setStoringScoreMatrix, setSubstitutionMatrix |
Methods inherited from class org.biojava3.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.biojava3.alignment.template.Aligner |
---|
getComputationTime, getProfile |
Methods inherited from interface org.biojava3.alignment.template.Scorer |
---|
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity |
Field Detail |
---|
protected ProfilePair<S extends Sequence<C>,C extends Compound> pair
Constructor Detail |
---|
protected AbstractProfileProfileAligner()
setQuery(Profile)
, setTarget(Profile)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
protected AbstractProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
query
- the first Profile
of the pair to aligntarget
- the second Profile
of the pair to aligngapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentprotected AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
query
- the first Profile
of the pair to align, still to be calculatedtarget
- the second Profile
of the pair to align, still to be calculatedgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentprotected AbstractProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
query
- the first Profile
of the pair to aligntarget
- the second Profile
of the pair to align, still to be calculatedgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentprotected AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
query
- the first Profile
of the pair to align, still to be calculatedtarget
- the second Profile
of the pair to aligngapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentMethod Detail |
---|
public void setQuery(Profile<S,C> query)
Profile
.
query
- the first Profile
of the pair to alignpublic void setTarget(Profile<S,C> target)
Profile
.
target
- the second Profile
of the pair to alignpublic ProfilePair<S,C> getPair()
ProfileProfileAligner
getPair
in interface ProfileProfileAligner<S extends Sequence<C>,C extends Compound>
public Profile<S,C> getQuery()
ProfileProfileScorer
getQuery
in interface ProfileProfileScorer<S extends Sequence<C>,C extends Compound>
public Profile<S,C> getTarget()
ProfileProfileScorer
getTarget
in interface ProfileProfileScorer<S extends Sequence<C>,C extends Compound>
protected CompoundSet<C> getCompoundSet()
getCompoundSet
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
protected List<C> getCompoundsOfQuery()
getCompoundsOfQuery
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
protected List<C> getCompoundsOfTarget()
getCompoundsOfTarget
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
protected int[] getScoreMatrixDimensions()
getScoreMatrixDimensions
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
protected short getSubstitutionScore(int queryColumn, int targetColumn)
getSubstitutionScore
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
protected boolean isReady()
isReady
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
protected void reset()
reset
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
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