Package | Description |
---|---|
jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
jebl.evolution.aligners | |
jebl.evolution.alignments | |
jebl.evolution.io | |
jebl.evolution.sequences |
Modifier and Type | Method and Description |
---|---|
Alignment |
MultipleAligner.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress) |
Alignment |
BartonSternberg.doAlign(Alignment alignment,
Sequence sequence,
ProgressListener progress) |
PairwiseAligner.Result |
NeedlemanWunschLinearSpaceAffine.doAlignment(Sequence seq1,
Sequence seq2,
ProgressListener progress) |
PairwiseAligner.Result |
PairwiseAligner.doAlignment(Sequence seq1,
Sequence seq2,
ProgressListener progress) |
double |
NeedlemanWunschLinearSpaceAffine.getScore(Sequence seq1,
Sequence seq2) |
double |
PairwiseAligner.getScore(Sequence seq1,
Sequence seq2) |
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(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(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress) |
Alignment |
BartonSternberg.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress) |
static TreeBuilderFactory.DistanceModel |
SequenceAlignmentsDistanceMatrix.getDefaultDistanceModel(java.util.List<Sequence> seqs) |
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 |
---|---|
Alignment |
Aligner.alignSequences(java.util.Collection<Sequence> sequences) |
Modifier and Type | Class and Description |
---|---|
class |
ConsensusSequence |
Modifier and Type | Method and Description |
---|---|
Sequence |
ResampledAlignment.getSequence(Taxon taxon) |
Sequence |
BasicAlignment.getSequence(Taxon taxon) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Sequence> |
Alignment.getSequenceList() |
java.util.List<Sequence> |
ResampledAlignment.getSequenceList() |
java.util.List<Sequence> |
BasicAlignment.getSequenceList() |
java.util.Set<Sequence> |
ResampledAlignment.getSequences() |
java.util.Set<Sequence> |
BasicAlignment.getSequences() |
Modifier and Type | Method and Description |
---|---|
void |
BasicAlignment.addSequence(Sequence sequence)
Adds a sequence to this alignment
|
Constructor and Description |
---|
BasicAlignment(Sequence[] sequences)
Constructs a basic alignment from an array of sequences.
|
Constructor and Description |
---|
BasicAlignment(java.util.Collection<? extends Sequence> sequences)
Constructs a basic alignment from a collection of sequences.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Sequence> |
SequenceImporter.importSequences()
importSequences.
|
java.util.List<Sequence> |
NexusImporter.importSequences()
Import all sequences in the input from the current position
|
java.util.List<Sequence> |
PhylipSequentialImporter.importSequences()
importSequences.
|
java.util.List<Sequence> |
FastaImporter.importSequences() |
java.util.List<Sequence> |
NexusImporter.parseCharactersBlock(java.util.List<Taxon> taxonList)
Parse the next 'CHARACTERS' block encountered in the input.
|
java.util.List<Sequence> |
NexusImporter.parseDataBlock(java.util.List<Taxon> taxonList)
Parse the next 'DATA' block encountered in the input.
|
Modifier and Type | Method and Description |
---|---|
void |
ImmediateSequenceImporter.Callback.add(Sequence seq) |
Modifier and Type | Method and Description |
---|---|
void |
FastaExporter.exportSequences(java.util.Collection<? extends Sequence> sequences)
export alignment or set of sequences.
|
void |
SequenceExporter.exportSequences(java.util.Collection<? extends Sequence> sequences)
exportSequences.
|
void |
NexusExporter.exportSequences(java.util.Collection<? extends Sequence> sequences)
export alignment.
|
Modifier and Type | Class and Description |
---|---|
class |
BasicSequence
A default implementation of the Sequence interface.
|
class |
CanonicalSequence
A default implementation of the Sequence interface
that converts sequence characters to
States such that calling getString() will always return
uppercase residues with nucleotide U residues converted to T
|
class |
CodonSequence
A codon implementation of the Sequence interface.
|
class |
FilteredSequence |
class |
GaplessSequence |
class |
TranslatedSequence |
Modifier and Type | Method and Description |
---|---|
Sequence |
Sequences.getSequence(Taxon taxon) |
static Sequence |
SequenceTester.getTestSequence1() |
static Sequence |
SequenceTester.getTestSequence2() |
static Sequence |
Utils.translate(Sequence sequence,
GeneticCode geneticCode)
|
static Sequence |
Utils.translate(Sequence sequence,
GeneticCode geneticCode,
int readingFrame)
|
Modifier and Type | Method and Description |
---|---|
java.util.Set<Sequence> |
Sequences.getSequences() |
Modifier and Type | Method and Description |
---|---|
static int |
Utils.getGaplessLocation(Sequence sequence,
int gappedLocation)
Gets the site location index for this sequence excluding
any gaps.
|
static int |
Utils.getGappedLocation(Sequence sequence,
int gaplessLocation)
Gets the site location index for this sequence that corresponds
to a location given excluding all gaps.
|
static Sequence |
Utils.translate(Sequence sequence,
GeneticCode geneticCode)
|
static Sequence |
Utils.translate(Sequence sequence,
GeneticCode geneticCode,
int readingFrame)
|
Constructor and Description |
---|
FilteredSequence(Sequence source)
Creates a FilteredSequence wrapper to the given source sequence.
|
GaplessSequence(Sequence source) |
TranslatedSequence(Sequence source,
GeneticCode geneticCode) |
http://code.google.com/p/jebl2/