Uses of Class
org.biojava.nbio.alignment.template.AlignedSequence.Step

Packages that use AlignedSequence.Step

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template

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 and Description
protected void	SimpleProfileProfileAligner.setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
protected void	SimpleProfileProfileAligner.setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
protected void	SmithWaterman.setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
protected void	SmithWaterman.setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)

Constructor parameters in org.biojava.nbio.alignment with type arguments of type AlignedSequence.Step

Constructor and Description
SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps) Creates a new AlignedSequence for the given AlignedSequence in a global alignment.
SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps, int numBefore, int numAfter) Creates a new AlignedSequence for the given AlignedSequence in a local alignment.
SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps) Creates an AlignedSequence for the given Sequence in a global alignment.
SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps, int numBefore, int numAfter) Creates an AlignedSequence for the given Sequence 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(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.
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.
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, 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.
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.alignment.routines

Method parameters in org.biojava.nbio.alignment.routines with type arguments of type AlignedSequence.Step

Modifier and Type	Method and Description
protected void	AnchoredPairwiseSequenceAligner.setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
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 matrix
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 matrix
static int[]	AlignerHelper.setSteps(AlignerHelper.Last[][][] traceback, int[][][] scores, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Find global alignment path through traceback matrix
static int[]	AlignerHelper.setSteps(AlignerHelper.Last[][][] traceback, int[][][] scores, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Find global alignment path through traceback matrix
static int[]	AlignerHelper.setSteps(AlignerHelper.Last[][][] traceback, int[] xyMax, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Find local alignment path through traceback matrix
static 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

Methods in org.biojava.nbio.alignment.template that return AlignedSequence.Step

Modifier and Type	Method and 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.

Method parameters in org.biojava.nbio.alignment.template with type arguments of type AlignedSequence.Step

Modifier and Type	Method and Description
protected abstract void	AbstractMatrixAligner.setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
protected abstract void	AbstractMatrixAligner.setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)