Uses of Class
jebl.util.ProgressListener

Packages that use ProgressListener

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

Uses of ProgressListener in jebl.evolution.align

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

String[]	BartonSternberg.align(List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMIsmatchCosts)
static AlignmentTreeBuilderFactory.Result	AlignmentTreeBuilderFactory.build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progress)
static AlignmentTreeBuilderFactory.Result	AlignmentTreeBuilderFactory.build(List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress)
static AlignmentTreeBuilderFactory.Result	AlignmentTreeBuilderFactory.build(List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, 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)
Alignment	BartonSternberg.doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment	MultipleAligner.doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
jebl.evolution.align.AlignmentResult[]	NeedlemanWunschLinearSpaceAffine.doAlignment(jebl.evolution.align.Profile profile1, jebl.evolution.align.Profile profile2, ProgressListener progress, boolean scoreOnly)
PairwiseAligner.Result	NeedlemanWunschLinearSpaceAffine.doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)
PairwiseAligner.Result	PairwiseAligner.doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)
void	NeedlemanWunschLinearSpaceAffine.doAlignment(String sq1, String sq2, ProgressListener progress)
void	SmithWaterman.doAlignment(String sq1, String sq2, ProgressListener progress)
void	SmithWatermanLinearSpaceAffine.doAlignment(String sq1, String sq2, ProgressListener progress)
void	NeedlemanWunschLinearSpaceAffine.doAlignment(String sq1, String sq2, ProgressListener progress, boolean scoreOnly)

Constructors in jebl.evolution.align with parameters of type ProgressListener

SequenceAlignmentsDistanceMatrix(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress)

Uses of ProgressListener in jebl.evolution.aligners

Methods in jebl.evolution.aligners with parameters of type ProgressListener

void	Aligner.addProgressListener(ProgressListener listener)
void	Aligner.removeProgressListener(ProgressListener listener)

Uses of ProgressListener in jebl.evolution.distances

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

F84DistanceMatrix(Alignment alignment, ProgressListener progress)

HKYDistanceMatrix(Alignment alignment, ProgressListener progress)

JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress)

TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress)

Uses of ProgressListener in jebl.evolution.io

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

void	FastaImporter.importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
void	ImmediateSequenceImporter.importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
void	ImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress) Reads sequence, skipping over any comments and filtering using sequenceType.

Uses of ProgressListener in jebl.evolution.trees

Methods in jebl.evolution.trees with parameters of type ProgressListener

void	ClusteringTreeBuilder.addProgressListener(ProgressListener listener)
void	ConsensusTreeBuilder.addProgressListener(ProgressListener listener)
void	TreeBuilder.addProgressListener(ProgressListener listener)
void	ClusteringTreeBuilder.removeProgressListener(ProgressListener listener)
void	ConsensusTreeBuilder.removeProgressListener(ProgressListener listener)
void	TreeBuilder.removeProgressListener(ProgressListener listener)

Uses of ProgressListener in jebl.util

Subclasses of ProgressListener in jebl.util

class

CompositeProgressListener

Fields in jebl.util declared as ProgressListener

static ProgressListener	ProgressListener.EMPTY A ProgressListener that ignores all events and always returns false from isCanceled().
protected ProgressListener	CompositeProgressListener.listener

Methods in jebl.util with parameters of type ProgressListener

static CompositeProgressListener

CompositeProgressListener.forFiles(ProgressListener listener, List<File> files)

Constructors in jebl.util with parameters of type ProgressListener

CompositeProgressListener(ProgressListener listener, double[] operationDuration)