| 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 | 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 acid
|
static 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) |
| 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) |
| Modifier and Type | Method | Description |
|---|---|---|
void |
Aligner.addProgressListener(ProgressListener listener) |
|
void |
Aligner.removeProgressListener(ProgressListener listener) |
| 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) |
| 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.
|
| 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) |
| Modifier and Type | Class | 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 | Description |
|---|---|---|
static ProgressListener |
ProgressListener.EMPTY |
A ProgressListener that ignores all events and always returns false from
isCanceled(). |
| Modifier and Type | Method | Description |
|---|---|---|
ProgressListener |
CompositeProgressListener.getRootProgressListener() |
| Modifier and Type | Method | Description |
|---|---|---|
static CompositeProgressListener |
CompositeProgressListener.forFiles(ProgressListener listener,
java.util.List<java.io.File> files) |
| 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) |
http://code.google.com/p/jebl2/