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.ResultAlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)static AlignmentTreeBuilderFactory.ResultAlignmentTreeBuilderFactory. 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.ResultAlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model)static AlignmentTreeBuilderFactory.ResultAlignmentTreeBuilderFactory. build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener)static AlignmentTreeBuilderFactory.ResultAlignmentTreeBuilderFactory. build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)AlignmentBartonSternberg. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)AlignmentBartonSternberg. doAlign(Alignment a1, Alignment a2, ProgressListener progress)AlignmentBartonSternberg. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)AlignmentMultipleAligner. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)AlignmentMultipleAligner. doAlign(Alignment a1, Alignment a2, ProgressListener progress)AlignmentMultipleAligner. doAlign(Alignment alignment, Sequence sequence, ProgressListener progress)voidNeedlemanWunschLinearSpaceAffine. doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)voidNeedlemanWunschLinearSpaceAffine. 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.ResultNeedlemanWunschLinearSpaceAffine. doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)PairwiseAligner.ResultPairwiseAligner. doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)voidSmithWaterman. doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)voidSmithWatermanLinearSpaceAffine. 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) -
Uses of ProgressListener in jebl.evolution.aligners
Methods in jebl.evolution.aligners with parameters of type ProgressListener Modifier and Type Method Description voidAligner. addProgressListener(ProgressListener listener)voidAligner. removeProgressListener(ProgressListener listener) -
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) -
Uses of ProgressListener in jebl.evolution.io
Methods in jebl.evolution.io with parameters of type ProgressListener Modifier and Type Method Description voidFastaImporter. importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)voidImmediateSequenceImporter. importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)voidImportHelper. 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)voidImportHelper. 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 voidClusteringTreeBuilder. addProgressListener(ProgressListener listener)voidConsensusTreeBuilder. addProgressListener(ProgressListener listener)voidTreeBuilder. addProgressListener(ProgressListener listener)voidClusteringTreeBuilder. removeProgressListener(ProgressListener listener)voidConsensusTreeBuilder. removeProgressListener(ProgressListener listener)Stops a ProgressListener from receiving progress.voidTreeBuilder. removeProgressListener(ProgressListener listener) -
Uses of ProgressListener in jebl.util
Subclasses of ProgressListener in jebl.util Modifier and Type Class Description classBasicProgressListenerA basicProgressListenerimplementation that allows the caller to set the canceled status.classCompositeProgressListenerAProgressListenerthat is suitable for a task that consists of several subtasks.static classProgressListener.WrapperA 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 ProgressListenerProgressListener. EMPTYA ProgressListener that ignores all events and always returns false fromisCanceled().Methods in jebl.util that return ProgressListener Modifier and Type Method Description ProgressListenerCompositeProgressListener. getRootProgressListener()Methods in jebl.util with parameters of type ProgressListener Modifier and Type Method Description static CompositeProgressListenerCompositeProgressListener. 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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