Uses of Interface
jebl.evolution.alignments.Alignment

Packages that use Alignment

jebl.evolution.align	Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.aligners
jebl.evolution.alignments
jebl.evolution.distances
jebl.evolution.io

Uses of Alignment in jebl.evolution.align

Fields in jebl.evolution.align declared as Alignment

Alignment

PairwiseAligner.Result.alignment

Methods in jebl.evolution.align that return Alignment

Alignment	BartonSternberg.doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment	MultipleAligner.doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment	BartonSternberg.doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Alignment	MultipleAligner.doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Alignment	BartonSternberg.doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment	MultipleAligner.doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)

Methods in jebl.evolution.align with parameters of type Alignment

static AlignmentTreeBuilderFactory.Result	AlignmentTreeBuilderFactory.build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progress)
Alignment	BartonSternberg.doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment	MultipleAligner.doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment	BartonSternberg.doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Alignment	MultipleAligner.doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)

Uses of Alignment in jebl.evolution.aligners

Methods in jebl.evolution.aligners that return Alignment

Alignment

Aligner.alignSequences(Collection<Sequence> sequences)

Uses of Alignment in jebl.evolution.alignments

Classes in jebl.evolution.alignments that implement Alignment

class	BasicAlignment A basic implementation of the Alignment interface.
class	BootrappedAlignment Date: 15/01/2006 Time: 10:13:50
class	JackknifedAlignment Date: 17/01/2006 Time: 08:18:32
class	ResampledAlignment Date: 17/01/2006 Time: 08:08:44

Methods in jebl.evolution.alignments with parameters of type Alignment

static State[]	ConsensusSequence.constructConsensus(Alignment source)
void	ResampledAlignment.init(Alignment srcAlignment, int[] siteIndices) Setup resampled alignment.

Constructors in jebl.evolution.alignments with parameters of type Alignment

BootrappedAlignment(Alignment srcAlignment)

ConsensusSequence(Taxon taxon, Alignment source)
Creates a FilteredSequence wrapper to the given source sequence.

JackknifedAlignment(Alignment srcAlignment, double percent)

Uses of Alignment in jebl.evolution.distances

Methods in jebl.evolution.distances with parameters of type Alignment

protected static double[]	ModelBasedDistanceMatrix.getFrequencies(Alignment alignment)
protected static double[]	ModelBasedDistanceMatrix.getFrequenciesSafe(Alignment alignment)

Constructors in jebl.evolution.distances with parameters of type Alignment

F84DistanceMatrix(Alignment alignment)

F84DistanceMatrix(Alignment alignment, ProgressListener progress)

HKYDistanceMatrix(Alignment alignment, ProgressListener progress)

JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress)

TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress)

Uses of Alignment in jebl.evolution.io

Methods in jebl.evolution.io that return types with arguments of type Alignment

List<Alignment>	AlignmentImporter.importAlignments() importAlignment.
List<Alignment>	NexusImporter.importAlignments() importAlignment.

Methods in jebl.evolution.io with parameters of type Alignment

void	AlignmentExporter.exportAlignment(Alignment alignment) exportAlignment.
void	MEGAExporter.exportAlignment(Alignment alignment)
void	NexusExporter.exportAlignment(Alignment alignment) exportAlignment.
void	PHYLIPExporter.exportAlignment(Alignment alignment)