Package | Description |
---|---|
pal.alignment |
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
|
pal.datatype |
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.substmodel |
Classes describing substitution models, i.e.
|
pal.treesearch |
Modifier and Type | Field and Description |
---|---|
DataType[] |
MultiLocusAnnotatedAlignment.siteDataType
provides datatype for each locus separately
|
Modifier and Type | Method and Description |
---|---|
DataType |
AbstractAlignment.getDataType()
Returns the datatype of this alignment
|
DataType |
Alignment.getDataType()
Return DataType of this alignment.
|
DataType |
ConcatenatedAnnotatedAlignment.getDataType(int site)
Return the datatype for a given site, which can differ between source alignments
|
DataType |
MultiLocusAnnotatedAlignment.getDataType(int site)
Returns the datatype
|
DataType |
StrippedAnnotatedAlignment.getDataType(int site)
Returns the datatype
|
DataType |
AnnotationAlignment.getDataType(int site)
Returns the datatype for a specific site, which could differ by site in complex alignments
|
DataType |
IndelAnnotatedAlignment.getDataType(int site)
Returns the datatype
|
DataType |
SimpleAnnotatedAlignment.getDataType(int site)
Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)
|
static DataType |
AlignmentUtils.getSuitableInstance(Alignment alignment)
guess data type suitable for a given sequence data set
|
static DataType |
AlignmentUtils.getSuitableInstance(char[][] sequences)
guess data type suitable for a given sequence data set
|
static DataType |
AlignmentUtils.getSuitableInstance(java.lang.String[] sequences)
guess data type suitable for a given sequence data set
|
Modifier and Type | Method and Description |
---|---|
static Alignment |
AlignmentUtils.concatAlignments(Alignment[] alignments,
DataType dt)
Concatenates an array of alignments such that the resulting alignment is
all of the sub alignments place along side each other
|
static int |
AlignmentUtils.countUnknowns(Alignment a,
DataType dt)
Tests the characters of an alignment to see if there are any characters that
are not within a data type.
|
static void |
DataTranslator.ensureUnknownState(DataType dt,
int[] states,
int unknownState)
Ensures that all states that are "unknown" (according to a certain DataType) get set to the value of 'unknownState'
|
Alignment |
AlignmentBuilder.generateAlignment(DataType dt)
Build an alignment based on sequences stored.
|
static void |
AlignmentUtils.getAlignedSequenceIndices(Alignment a,
int i,
int[] indices,
DataType dataType,
int unknownState)
Returns state indices for a sequence.
|
static double |
AlignmentUtils.getAlignmentPenalty(Alignment a,
DataType dataType,
TransitionPenaltyTable penalties,
double gapCreation,
double gapExtension,
boolean local)
Returns total sum of pairs alignment distance using gap creation
and extension penalties and transition penalties as defined in the
TransitionPenaltyTable provided.
|
static Alignment |
AlignmentUtils.getChangedDataType(Alignment a,
DataType dt)
Returns an alignment which follows the pattern of the input alignment
except that all sites which do not contain states in dt (excluding the
gap character) are removed.
|
static Alignment |
AlignmentTool.readAlignment(java.io.Reader r,
DataType dt)
Attempt to read a file from a reader object
|
static Alignment[] |
AlignmentReaders.readAllPhylipClustalAlignments(java.io.Reader r,
DataType dt)
Read an alignment in phylip/clustal/simple format.
|
static Alignment |
AlignmentReaders.readFastaSequences(java.io.Reader r,
DataType dt)
Read an a set of unaligned Fasta sequences
|
static Alignment |
AlignmentReaders.readNewLineSeperatedSequences(java.io.Reader r,
DataType dt)
Read an a set of unaligned Fasta sequences
|
static Alignment |
AlignmentReaders.readPhylipClustalAlignment(java.io.Reader r,
DataType dt)
Read an alignment in phylip/clustal/simple format.
|
static void |
AlignmentReaders.readPhylipClustalAlignment(java.io.Reader r,
DataType dt,
AlignmentReceiver receiver)
Read an alignment in phylip/clustal/simple format.
|
void |
AbstractAlignment.setDataType(DataType d)
Sets the datatype of this alignment
|
static char[][] |
DataTranslator.toChars(int[][] dtStates,
DataType dt)
Converts an state matrix to a char matrix
Stored as [sequnce][site]
|
static int[][] |
DataTranslator.toStates(char[][] dtChars,
DataType dt)
Converts an alignment to a state matrix
Stored as [sequnce][site]
|
Constructor and Description |
---|
MultiLocusAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
DataType dt) |
MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
PhylipClustalAlignment(java.lang.String[] names,
java.lang.String[] sequences,
DataType dt) |
SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
DataType dt) |
SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
SimpleAlignment(Identifier id,
java.lang.String sequence,
DataType dataType)
Constructor taking single identifier and sequence.
|
SimpleAlignment(IdGroup group,
char[][] cSequences,
DataType dt) |
SimpleAlignment(IdGroup group,
char[][] cSequences,
java.lang.String gaps,
DataType dt) |
SimpleAlignment(IdGroup group,
DataType dt,
int[][] sSequences) |
SimpleAlignment(IdGroup ids,
java.lang.String[] sequences,
DataType dt) |
SimpleAlignment(IdGroup ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
SimpleAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
This constructor creates a basic SimpleAnnotatedAlignment.
|
SimpleAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
DataType dt)
This constructor creates a basic SimpleAnnotatedAlignment.
|
SimpleAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
This constructor creates a basic SimpleAnnotatedAlignment.
|
SitePattern(DataType dataType,
int numSites,
int numSeqs,
IdGroup idGroup,
int numPatterns,
int[] alias,
int[] weight,
byte[][] pattern)
construct SitePattern from scratch
|
UnalignedAlignment(java.lang.String[] names,
java.lang.String[] sequences,
DataType dt) |
Modifier and Type | Interface and Description |
---|---|
interface |
AmbiguousDataType
Additional interface information for data types which represent ambiguity in
sub types.
|
interface |
MolecularDataType
An extension to the generic DataType class for DataTypes
related to genetic residues (by this it is meant Nucleotides,
AminoAcids, and Codons).
|
Modifier and Type | Class and Description |
---|---|
class |
AminoAcids
implements DataType for amino acids
|
class |
Codons
implements DataType for all Codons (including terminators).
|
class |
GapBalanced
implements a ResidueDataType for GapBalanced notation.
|
class |
IUPACNucleotides
implements DataType for nucleotides with ambiguous characters
|
class |
Nucleotides
implements DataType for nucleotides
|
class |
NumericDataType
This datatype stores numeric values.
|
class |
SimpleDataType
interface for sequence data types
|
class |
SpecificAminoAcids
implements a MolecularDataType for amino acids, where we specifiy the Codon Table basis of amino acid by
supplying the CodonTable which is/was used for converting Nucleotide sequences to Amino Acids.
|
class |
StateRemover
A standard data type, but with characters removed
|
class |
TwoStates
implements DataType for two-state data
|
Modifier and Type | Field and Description |
---|---|
static DataType |
NumericDataType.DEFAULT_INSTANCE |
Modifier and Type | Method and Description |
---|---|
DataType |
TransitionPenaltyTable.getDataType() |
DataType |
IUPACPenaltyTable.getDataType() |
static DataType |
DataType.Utils.getInstance(int typeID)
create object according to this code
|
DataType |
AmbiguousDataType.getSpecificDataType() |
DataType |
IUPACNucleotides.getSpecificDataType() |
Modifier and Type | Method and Description |
---|---|
static byte[] |
DataType.Utils.getByteStates(char[] sequence,
DataType dt)
For converting a sequence to an array of bytes where each byte represents the
state of the corresponding character in sequence
|
static byte[] |
DataType.Utils.getByteStates(java.lang.String sequence,
DataType dt)
For converting a sequence to an array of bytes where each byte represents the
state of the corresponding character in sequence
|
static char[][] |
DataType.Utils.getChars(int[][] sequences,
char unknownChar,
char gapChar,
DataType dt)
For converting an array of sequence to arrays of ints where each int represents the
state of the corresponding character in sequence
|
static char[] |
DataType.Utils.getChars(int[] sequence,
char unknownChar,
char gapChar,
DataType dt)
For converting a sequence of ints representing states to an array of chars
|
static char[] |
DataType.Utils.getChars(int[] sequence,
DataType dt)
For converting a sequence of ints representing states to an array of chars
|
static MolecularDataType |
MolecularDataType.Utils.getMolecularDataType(DataType dt)
Converts (if possible) a DataType into a MolecularDataType.
|
static char[] |
DataType.Utils.getPreferredChars(char[] sequence,
DataType dt)
Converts a sequence of characters to the preferred form for a data type
|
static char[] |
DataType.Utils.getPreferredChars(char[] sequence,
DataType dt,
boolean specialDots)
Converts a sequence of characters to the preferred form for a data type
|
static java.lang.String |
DataType.Utils.getPreferredChars(java.lang.String sequence,
DataType dt)
Converts a sequence of characters to the preferred form for a data type (using Strings)
|
static java.lang.String |
DataType.Utils.getPreferredChars(java.lang.String sequence,
DataType dt,
boolean specialDots)
Converts a sequence of characters to the preferred form for a data type (using Strings) * @param specialDots if true then the dot (period) '.' is used even if it is not the prefered character by the data type
|
static int[][] |
DataType.Utils.getStates(char[][] sequences,
DataType dt)
For converting an array of sequence to arrays of ints where each int represents the
state of the corresponding character in sequence
|
static int[][] |
DataType.Utils.getStates(char[][] sequences,
int unknownState,
int gapState,
DataType dt)
For converting an array of sequence to arrays of ints where each int represents the
state of the corresponding character in sequence
|
static int[] |
DataType.Utils.getStates(char[] sequence,
DataType dt)
For converting a sequence to an array of ints where each int represents the
state of the corresponding character in sequence
|
static int[] |
DataType.Utils.getStates(char[] sequence,
int unknownState,
int gapState,
DataType dt)
For converting a sequence to an array of ints where each int represents the
state of the corresponding character in sequence
Allows user selection of unknown and gap states
|
static boolean |
DataType.Utils.isGap(DataType d,
char c)
Deprecated.
use DataType.isGapChar()
|
static void |
DataType.Utils.leftAlignSequence(int[] sequence,
DataType dt)
Realigns a sequence of states so that there are no gaps at the beggining (shifts to the left if necessary)
|
static java.lang.String |
DataType.Utils.toString(DataType dt,
int[] states)
For converting an array of states into a String of characters, based on a
DataType
|
Constructor and Description |
---|
StateRemover(DataType toAdjust,
int[] statesToRemove)
A translation array -> originalToAdjusted_["adjusted State"] = "original state"
|
Modifier and Type | Method and Description |
---|---|
LHCalculator.Generator |
LHCalculator.Factory.createSeries(int numberOfCategories,
DataType dt) |
Constructor and Description |
---|
LikelihoodSummary(DataType dt,
double overallLogLikelihood,
double[] categoryProbabilities,
double[][] individualLikelihoods,
int[] sitePatternMatchup) |
Modifier and Type | Method and Description |
---|---|
DataType |
RateMatrixGroup.getDataType() |
DataType |
SimpleRateMatrixGroup.getDataType() |
DataType |
SubstitutionModel.getDataType() |
DataType |
RateMatrix.getDataType()
Get the data type of this rate matrix
|
DataType |
AbstractRateMatrix.getDataType() |
DataType |
CachedRateMatrix.getDataType() |
DataType |
GeneralRateDistributionSubstitutionModel.getDataType() |
DataType |
PositiveSelectionRateMatrixGroup.getDataType() |
DataType |
NeutralSelectionRateMatrixGroup.getDataType() |
DataType |
SingleClassSubstitutionModel.getDataType() |
DataType |
YangCodonModel.SimplePositiveSelection.getDataType() |
DataType |
YangCodonModel.SimpleNeutralSelection.getDataType() |
Modifier and Type | Method and Description |
---|---|
static SubstitutionModel |
SubstitutionModel.Utils.createSubstitutionModel(NeoRateMatrix rm,
DataType dt,
double[] equilibriumFrequencies) |
boolean |
GeneralREVRateMatrix.isDataTypeCompatible(DataType dt)
Check the compatibility of a data type to be used with the rate matrix
|
boolean |
NeoRateMatrix.isDataTypeCompatible(DataType dt)
Check the compatibility of a data type to be used with the rate matrix
|
boolean |
GeneralPoissonRateMatrix.isDataTypeCompatible(DataType dt)
Check the compatibility of a data type to be used with the rate matrix
|
protected void |
AbstractRateMatrix.setDataType(DataType dt) |
Constructor and Description |
---|
GeneralRateDistributionSubstitutionModel(NeoRateMatrix base,
RateDistribution rateDistribution,
DataType dt,
double[] frequencies) |
SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices,
double[] equilibriumFrequencies,
double[] initialClassProbabilities,
DataType dataType) |
SingleClassSubstitutionModel(NeoRateMatrix base,
DataType dt,
double[] frequencies) |
Modifier and Type | Method and Description |
---|---|
DataType |
GeneralConstructionTool.getDataType() |