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 and Description |
---|---|
Alignment |
PairwiseAligner.Result.alignment |
Modifier and Type | Method and Description |
---|---|
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) |
Modifier and Type | Method and 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 |
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) |
Modifier and Type | Method and Description |
---|---|
Alignment |
Aligner.alignSequences(java.util.Collection<Sequence> sequences) |
Modifier and Type | Class and 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 and Description |
---|---|
Alignment |
ConsensusSequence.getSource() |
Modifier and Type | Method and Description |
---|---|
static State[] |
ConsensusSequence.constructConsensus(Alignment source,
boolean includeAmbiguities) |
void |
ResampledAlignment.init(Alignment srcAlignment,
int[] siteIndices)
Setup resampled alignment.
|
Constructor and 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 and 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 and 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 and Description |
---|---|
void |
NexusExporter.exportAlignment(Alignment alignment)
exportAlignment.
|
void |
MEGAExporter.exportAlignment(Alignment alignment)
Deprecated.
Files created by this export method won't be importable by MEGA (because they don't have titles). Use
MEGAExporter.exportAlignment(jebl.evolution.alignments.Alignment, String) instead. |
void |
PHYLIPExporter.exportAlignment(Alignment alignment) |
void |
AlignmentExporter.exportAlignment(Alignment alignment)
export one alignment.
|
void |
MEGAExporter.exportAlignment(Alignment alignment,
java.lang.String name) |
http://code.google.com/p/jebl2/