Uses of Class
jebl.util.ProgressListener
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Packages that use ProgressListener Package Description 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 -
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Uses of ProgressListener in jebl.evolution.align
Methods in jebl.evolution.align with parameters of type ProgressListener Modifier and Type Method Description java.lang.String[]
BartonSternberg. align(java.util.List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts)
static AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
static AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener)
Will use model F84 for nucleotides and Jukes-Cantor for amino acidstatic AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model)
static AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener)
static AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
Alignment
BartonSternberg. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment
BartonSternberg. doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment
BartonSternberg. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
Alignment
MultipleAligner. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment
MultipleAligner. doAlign(Alignment a1, Alignment a2, ProgressListener progress)
Alignment
MultipleAligner. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)
void
NeedlemanWunschLinearSpaceAffine. doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
void
NeedlemanWunschLinearSpaceAffine. doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress, boolean scoreOnly)
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
SmithWaterman. doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
void
SmithWatermanLinearSpaceAffine. doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
Constructors in jebl.evolution.align with parameters of type ProgressListener Constructor Description SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress)
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress, TreeBuilderFactory.DistanceModel model)
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Uses of ProgressListener in jebl.evolution.aligners
Methods in jebl.evolution.aligners with parameters of type ProgressListener Modifier and Type Method Description void
Aligner. addProgressListener(ProgressListener listener)
void
Aligner. removeProgressListener(ProgressListener listener)
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Uses of ProgressListener in jebl.evolution.distances
Constructors in jebl.evolution.distances with parameters of type ProgressListener Constructor Description F84DistanceMatrix(Alignment alignment, ProgressListener progress)
HKYDistanceMatrix(Alignment alignment, ProgressListener progress)
HKYDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress)
JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress)
TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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Uses of ProgressListener in jebl.evolution.io
Methods in jebl.evolution.io with parameters of type ProgressListener Modifier and Type Method Description void
FastaImporter. importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
void
ImmediateSequenceImporter. importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
void
ImportHelper. readSequence(java.lang.StringBuilder sequence, SequenceType sequenceType, java.lang.String delimiters, int maxSites, java.lang.String gapCharacters, java.lang.String missingCharacters, java.lang.String matchCharacters, java.lang.String matchSequence, ProgressListener progress)
void
ImportHelper. readSequence(java.lang.StringBuilder sequence, SequenceType sequenceType, java.lang.String delimiters, int maxSites, java.lang.String gapCharacters, java.lang.String missingCharacters, java.lang.String matchCharacters, java.lang.String matchSequence, ProgressListener progress, boolean stopAtDoubleNewLine)
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 Modifier and Type Method Description 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)
Stops a ProgressListener from receiving progress.void
TreeBuilder. removeProgressListener(ProgressListener listener)
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Uses of ProgressListener in jebl.util
Subclasses of ProgressListener in jebl.util Modifier and Type Class Description class
BasicProgressListener
A basicProgressListener
implementation that allows the caller to set the canceled status.class
CompositeProgressListener
AProgressListener
that is suitable for a task that consists of several subtasks.static class
ProgressListener.Wrapper
A decorator progress listener which delegates all method calls to an internal progress listener.Fields in jebl.util declared as ProgressListener Modifier and Type Field Description static ProgressListener
ProgressListener. EMPTY
A ProgressListener that ignores all events and always returns false fromisCanceled()
.Methods in jebl.util that return ProgressListener Modifier and Type Method Description ProgressListener
CompositeProgressListener. getRootProgressListener()
Methods in jebl.util with parameters of type ProgressListener Modifier and Type Method Description static CompositeProgressListener
CompositeProgressListener. forFiles(ProgressListener listener, java.util.List<java.io.File> files)
Constructors in jebl.util with parameters of type ProgressListener Constructor Description CompositeProgressListener(ProgressListener listener, double... operationDuration)
construct a new composite ProgressListener.CompositeProgressListener(ProgressListener listener, int numberOfEvenlyWeightedSubTasks)
Construct a CompositeProgressListener with a number of evenly weighted subtasks.Wrapper(ProgressListener internalProgressListener)
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