Uses of Class
org.biojava.nbio.core.alignment.template.AlignedSequence.Step
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Uses of AlignedSequence.Step in org.biojava.nbio.alignment
Method parameters in org.biojava.nbio.alignment with type arguments of type AlignedSequence.Step Modifier and Type Method Description protected void
SimpleProfileProfileAligner. setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
protected void
SmithWaterman. setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
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Uses of AlignedSequence.Step in org.biojava.nbio.alignment.routines
Method parameters in org.biojava.nbio.alignment.routines with type arguments of type AlignedSequence.Step Modifier and Type Method Description protected void
AnchoredPairwiseSequenceAligner. setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
static int[]
AlignerHelper. setSteps(AlignerHelper.Last[][][] traceback, boolean local, int[] xyMax, AlignerHelper.Last last, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
Find alignment path through traceback matrixstatic int[]
AlignerHelper. setSteps(AlignerHelper.Last[][][] traceback, int[][][] scores, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
Find global alignment path through traceback matrixstatic int[]
AlignerHelper. setSteps(AlignerHelper.Last[][][] traceback, int[] xyMax, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
Find local alignment path through traceback matrix -
Uses of AlignedSequence.Step in org.biojava.nbio.alignment.template
Method parameters in org.biojava.nbio.alignment.template with type arguments of type AlignedSequence.Step Modifier and Type Method Description protected abstract void
AbstractMatrixAligner. setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
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Uses of AlignedSequence.Step in org.biojava.nbio.core.alignment
Constructor parameters in org.biojava.nbio.core.alignment with type arguments of type AlignedSequence.Step Constructor Description SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps)
Creates a newAlignedSequence
for the givenAlignedSequence
in a global alignment.SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps, int numBefore, int numAfter)
Creates a newAlignedSequence
for the givenAlignedSequence
in a local alignment.SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps)
Creates anAlignedSequence
for the givenSequence
in a global alignment.SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps, int numBefore, int numAfter)
Creates anAlignedSequence
for the givenSequence
in a local alignment.SimpleProfile(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
Creates a pair profile for the given profiles.SimpleProfile(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya)
Creates a pair profile for the given sequences.SimpleProfilePair(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
Creates a pair profile for the given profiles.SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya)
Creates a pair profile for the given sequences with a local alignment.SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
Creates a pair profile for the given sequences with a global alignment. -
Uses of AlignedSequence.Step in org.biojava.nbio.core.alignment.template
Methods in org.biojava.nbio.core.alignment.template that return AlignedSequence.Step Modifier and Type Method Description static AlignedSequence.Step
AlignedSequence.Step. valueOf(String name)
Returns the enum constant of this type with the specified name.static AlignedSequence.Step[]
AlignedSequence.Step. values()
Returns an array containing the constants of this enum type, in the order they are declared.
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