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Packages that use ProgressListener | |
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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 |
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Methods in jebl.evolution.align with parameters of type ProgressListener | |
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java.lang.String[] |
BartonSternberg.align(java.util.List<Sequence> sourceSequences,
ProgressListener progress,
boolean refineOnly,
boolean estimateMatchMismatchCosts)
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static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(Alignment alignment,
TreeBuilderFactory.Method method,
TreeBuilderFactory.DistanceModel model,
ProgressListener progressListener)
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static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(Alignment alignment,
TreeBuilderFactory.Method method,
TreeBuilderFactory.DistanceModel model,
ProgressListener progressListener,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs,
TreeBuilderFactory.Method method,
MultipleAligner aligner,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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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 acid |
static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs,
TreeBuilderFactory.Method method,
PairwiseAligner aligner,
ProgressListener progressListener,
TreeBuilderFactory.DistanceModel model)
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Alignment |
MultipleAligner.doAlign(Alignment a1,
Alignment a2,
ProgressListener progress)
|
Alignment |
BartonSternberg.doAlign(Alignment a1,
Alignment a2,
ProgressListener progress)
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Alignment |
MultipleAligner.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress)
|
Alignment |
BartonSternberg.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress)
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Alignment |
MultipleAligner.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress)
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Alignment |
BartonSternberg.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress)
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jebl.evolution.align.AlignmentResult[] |
NeedlemanWunschLinearSpaceAffine.doAlignment(jebl.evolution.align.Profile profile1,
jebl.evolution.align.Profile profile2,
ProgressListener progress,
boolean scoreOnly)
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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)
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void |
NeedlemanWunschLinearSpaceAffine.doAlignment(java.lang.String sq1,
java.lang.String sq2,
ProgressListener progress)
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void |
SmithWatermanLinearSpaceAffine.doAlignment(java.lang.String sq1,
java.lang.String sq2,
ProgressListener progress)
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void |
NeedlemanWunschLinearSpaceAffine.doAlignment(java.lang.String sq1,
java.lang.String sq2,
ProgressListener progress,
boolean scoreOnly)
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Constructors in jebl.evolution.align with parameters of type ProgressListener | |
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SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress)
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SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress,
TreeBuilderFactory.DistanceModel model)
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Uses of ProgressListener in jebl.evolution.aligners |
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Methods in jebl.evolution.aligners with parameters of type ProgressListener | |
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void |
Aligner.addProgressListener(ProgressListener listener)
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void |
Aligner.removeProgressListener(ProgressListener listener)
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Uses of ProgressListener in jebl.evolution.distances |
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Constructors in jebl.evolution.distances with parameters of type ProgressListener | |
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F84DistanceMatrix(Alignment alignment,
ProgressListener progress)
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HKYDistanceMatrix(Alignment alignment,
ProgressListener progress)
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HKYDistanceMatrix(Alignment alignment,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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JukesCantorDistanceMatrix(Alignment alignment,
ProgressListener progress)
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JukesCantorDistanceMatrix(Alignment alignment,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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TamuraNeiDistanceMatrix(Alignment alignment,
ProgressListener progress)
|
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TamuraNeiDistanceMatrix(Alignment alignment,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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Uses of ProgressListener in jebl.evolution.io |
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Methods in jebl.evolution.io with parameters of type ProgressListener | |
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void |
ImmediateSequenceImporter.importSequences(ImmediateSequenceImporter.Callback callback,
ProgressListener progressListener)
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void |
FastaImporter.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 |
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Methods in jebl.evolution.trees with parameters of type ProgressListener | |
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void |
TreeBuilder.addProgressListener(ProgressListener listener)
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void |
ClusteringTreeBuilder.addProgressListener(ProgressListener listener)
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void |
ConsensusTreeBuilder.addProgressListener(ProgressListener listener)
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void |
TreeBuilder.removeProgressListener(ProgressListener listener)
|
void |
ClusteringTreeBuilder.removeProgressListener(ProgressListener listener)
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void |
ConsensusTreeBuilder.removeProgressListener(ProgressListener listener)
Stops a ProgressListener from receiving progress. |
Uses of ProgressListener in jebl.util |
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Subclasses of ProgressListener in jebl.util | |
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class |
BasicProgressListener
A basic ProgressListener implementation that allows the caller to set the canceled
status. |
class |
CompositeProgressListener
A ProgressListener 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 | |
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static ProgressListener |
ProgressListener.EMPTY
A ProgressListener that ignores all events and always returns false from isCanceled() . |
Methods in jebl.util that return ProgressListener | |
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ProgressListener |
CompositeProgressListener.getRootProgressListener()
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Methods in jebl.util with parameters of type ProgressListener | |
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static CompositeProgressListener |
CompositeProgressListener.forFiles(ProgressListener listener,
java.util.List<java.io.File> files)
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Constructors in jebl.util with parameters of type ProgressListener | |
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CompositeProgressListener(ProgressListener listener,
double... operationDuration)
construct a new composite ProgressListener. |
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CompositeProgressListener(ProgressListener listener,
int numberOfEvenlyWeightedSubTasks)
Construct a CompositeProgressListener with a number of evenly weighted subtasks. |
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ProgressListener.Wrapper(ProgressListener internalProgressListener)
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