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 |
Modifier and Type | Method and Description |
---|---|
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 |
MultipleAligner.doAlign(Alignment a1,
Alignment a2,
ProgressListener progress) |
Alignment |
BartonSternberg.doAlign(Alignment a1,
Alignment a2,
ProgressListener progress) |
Alignment |
MultipleAligner.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress) |
Alignment |
BartonSternberg.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress) |
Alignment |
MultipleAligner.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress) |
Alignment |
BartonSternberg.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 |
PairwiseAligner.doAlignment(Sequence seq1,
Sequence seq2,
ProgressListener progress) |
PairwiseAligner.Result |
NeedlemanWunschLinearSpaceAffine.doAlignment(Sequence seq1,
Sequence seq2,
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) |
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,
boolean scoreOnly) |
Constructor and Description |
---|
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress) |
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress,
TreeBuilderFactory.DistanceModel model) |
Modifier and Type | Method and Description |
---|---|
void |
Aligner.addProgressListener(ProgressListener listener) |
void |
Aligner.removeProgressListener(ProgressListener listener) |
Constructor and 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) |
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
void |
TreeBuilder.addProgressListener(ProgressListener listener) |
void |
ConsensusTreeBuilder.addProgressListener(ProgressListener listener) |
void |
ClusteringTreeBuilder.addProgressListener(ProgressListener listener) |
void |
TreeBuilder.removeProgressListener(ProgressListener listener) |
void |
ConsensusTreeBuilder.removeProgressListener(ProgressListener listener)
Stops a ProgressListener from receiving progress.
|
void |
ClusteringTreeBuilder.removeProgressListener(ProgressListener listener) |
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Field and Description |
---|---|
static ProgressListener |
ProgressListener.EMPTY
A ProgressListener that ignores all events and always returns false from
isCanceled() . |
Modifier and Type | Method and Description |
---|---|
ProgressListener |
CompositeProgressListener.getRootProgressListener() |
Modifier and Type | Method and Description |
---|---|
static CompositeProgressListener |
CompositeProgressListener.forFiles(ProgressListener listener,
java.util.List<java.io.File> files) |
Constructor and 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.
|
ProgressListener.Wrapper(ProgressListener internalProgressListener) |
http://code.google.com/p/jebl2/