Package | Description |
---|---|
jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
jebl.evolution.aligners | |
jebl.evolution.alignments | |
jebl.evolution.distances | |
jebl.evolution.io |
Modifier and Type | Field | Description |
---|---|---|
Alignment |
PairwiseAligner.Result.alignment |
Modifier and Type | Method | Description |
---|---|---|
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) |
Modifier and Type | Method | Description |
---|---|---|
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(Alignment a1,
Alignment a2,
ProgressListener progress) |
|
Alignment |
BartonSternberg.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress) |
|
Alignment |
MultipleAligner.doAlign(Alignment a1,
Alignment a2,
ProgressListener progress) |
|
Alignment |
MultipleAligner.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress) |
Modifier and Type | Method | Description |
---|---|---|
Alignment |
Aligner.alignSequences(java.util.Collection<Sequence> sequences) |
Modifier and Type | Class | Description |
---|---|---|
class |
BasicAlignment |
A basic implementation of the Alignment interface.
|
class |
BootstrappedAlignment |
Date: 15/01/2006
Time: 10:13:50
|
class |
JackknifedAlignment |
Date: 17/01/2006
Time: 08:18:32
|
class |
ResampledAlignment |
Date: 17/01/2006
Time: 08:08:44
|
Modifier and Type | Method | Description |
---|---|---|
Alignment |
ConsensusSequence.getSource() |
Modifier and Type | Method | Description |
---|---|---|
static State[] |
ConsensusSequence.constructConsensus(Alignment source,
boolean includeAmbiguities) |
|
void |
ResampledAlignment.init(Alignment srcAlignment,
int[] siteIndices) |
Setup resampled alignment.
|
Constructor | Description |
---|---|
BootstrappedAlignment(Alignment srcAlignment) |
|
BootstrappedAlignment(Alignment srcAlignment,
long seed) |
|
BootstrappedAlignment(Alignment srcAlignment,
java.util.Random r) |
|
ConsensusSequence(Taxon taxon,
Alignment source) |
Creates a FilteredSequence wrapper to the given source sequence.
|
ConsensusSequence(Taxon taxon,
Alignment source,
boolean includeAmbiguities) |
Creates a FilteredSequence wrapper to the given source sequence.
|
JackknifedAlignment(Alignment srcAlignment,
double percent) |
|
JackknifedAlignment(Alignment srcAlignment,
double percent,
long seed) |
|
JackknifedAlignment(Alignment srcAlignment,
double percent,
java.util.Random r) |
Constructor | Description |
---|---|
F84DistanceMatrix(Alignment alignment) |
|
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 |
---|---|---|
java.util.List<Alignment> |
AlignmentImporter.importAlignments() |
importAlignment.
|
java.util.List<Alignment> |
NexusImporter.importAlignments() |
Import all alignments in the input from the current position.
|
Modifier and Type | Method | Description |
---|---|---|
void |
AlignmentExporter.exportAlignment(Alignment alignment) |
export one alignment.
|
void |
MEGAExporter.exportAlignment(Alignment alignment) |
Deprecated.
Files created by this export method won't be importable by MEGA (because they don't have titles).
|
void |
MEGAExporter.exportAlignment(Alignment alignment,
java.lang.String name) |
|
void |
NexusExporter.exportAlignment(Alignment alignment) |
exportAlignment.
|
void |
PHYLIPExporter.exportAlignment(Alignment alignment) |
http://code.google.com/p/jebl2/