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
 java.lang.String[] BartonSternberg.align(java.util.List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts)
           
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)
           
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 acid
static AlignmentTreeBuilderFactory.Result AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model)
           
 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(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
           
 Alignment MultipleAligner.doAlign(java.util.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 SmithWaterman.doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
           
 void NeedlemanWunschLinearSpaceAffine.doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
           
 void SmithWatermanLinearSpaceAffine.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)
           
 

Constructors in jebl.evolution.align with parameters of type ProgressListener
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
 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)
           
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
 void ImmediateSequenceImporter.importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
           
 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
 

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)
          Stops a ProgressListener from receiving progress.
 void TreeBuilder.removeProgressListener(ProgressListener listener)
           
 

Uses of ProgressListener in jebl.util
 

Subclasses of ProgressListener in jebl.util
 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
static ProgressListener ProgressListener.EMPTY
          A ProgressListener that ignores all events and always returns false from isCanceled().
 

Methods in jebl.util that return ProgressListener
 ProgressListener CompositeProgressListener.getRootProgressListener()
           
 

Methods in jebl.util with parameters of type ProgressListener
static CompositeProgressListener CompositeProgressListener.forFiles(ProgressListener listener, java.util.List<java.io.File> files)
           
 

Constructors in jebl.util with parameters of type ProgressListener
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.
ProgressListener.Wrapper(ProgressListener internalProgressListener)
           
 



http://code.google.com/p/jebl2/