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 | Description |
---|---|---|
DataType[] |
MultiLocusAnnotatedAlignment.siteDataType |
provides datatype for each locus separately
|
Modifier and Type | Method | Description |
---|---|---|
DataType |
AbstractAlignment.getDataType() |
Returns the datatype of this alignment
|
DataType |
Alignment.getDataType() |
Return DataType of this alignment.
|
DataType |
AnnotationAlignment.getDataType(int site) |
Returns the datatype for a specific site, which could differ by site in complex alignments
|
DataType |
ConcatenatedAnnotatedAlignment.getDataType(int site) |
Return the datatype for a given site, which can differ between source alignments
|
DataType |
IndelAnnotatedAlignment.getDataType(int site) |
Returns the datatype
|
DataType |
MultiLocusAnnotatedAlignment.getDataType(int site) |
Returns the datatype
|
DataType |
SimpleAnnotatedAlignment.getDataType(int site) |
Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)
|
DataType |
StrippedAnnotatedAlignment.getDataType(int site) |
Returns the datatype
|
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
|
static DataType |
AlignmentUtils.getSuitableInstance(Alignment alignment) |
guess data type suitable for a given sequence data set
|
Modifier and Type | Method | 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 | Description |
---|---|
MultiLocusAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
|
MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
|
MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
DataType dt) |
|
PhylipClustalAlignment(java.lang.String[] names,
java.lang.String[] sequences,
DataType dt) |
|
SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
|
SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
DataType dt) |
|
SimpleAlignment(Identifier id,
java.lang.String sequence,
DataType dataType) |
Constructor taking single identifier and sequence.
|
SimpleAlignment(IdGroup group,
char[][] cSequences,
java.lang.String gaps,
DataType dt) |
|
SimpleAlignment(IdGroup group,
char[][] cSequences,
DataType dt) |
|
SimpleAlignment(IdGroup ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
|
SimpleAlignment(IdGroup ids,
java.lang.String[] sequences,
DataType dt) |
|
SimpleAlignment(IdGroup group,
DataType dt,
int[][] sSequences) |
|
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,
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.
|
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 | 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 | 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 | Description |
---|---|---|
static DataType |
NumericDataType.DEFAULT_INSTANCE |
Modifier and Type | Method | Description |
---|---|---|
DataType |
IUPACPenaltyTable.getDataType() |
|
DataType |
TransitionPenaltyTable.getDataType() |
|
static DataType |
DataType.Utils.getInstance(int typeID) |
create object according to this code
|
DataType |
AmbiguousDataType.getSpecificDataType() |
|
DataType |
IUPACNucleotides.getSpecificDataType() |
Modifier and Type | Method | 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,
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[][] 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[] 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 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 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 | Description |
---|---|
StateRemover(DataType toAdjust,
int[] statesToRemove) |
A translation array -> originalToAdjusted_["adjusted State"] = "original state"
|
Modifier and Type | Method | Description |
---|---|---|
LHCalculator.Generator |
LHCalculator.Factory.createSeries(int numberOfCategories,
DataType dt) |
Constructor | Description |
---|---|
LikelihoodSummary(DataType dt,
double overallLogLikelihood,
double[] categoryProbabilities,
double[][] individualLikelihoods,
int[] sitePatternMatchup) |
Modifier and Type | Method | Description |
---|---|---|
DataType |
AbstractRateMatrix.getDataType() |
|
DataType |
CachedRateMatrix.getDataType() |
|
DataType |
GeneralRateDistributionSubstitutionModel.getDataType() |
|
DataType |
NeutralSelectionRateMatrixGroup.getDataType() |
|
DataType |
PositiveSelectionRateMatrixGroup.getDataType() |
|
DataType |
RateMatrix.getDataType() |
Get the data type of this rate matrix
|
DataType |
RateMatrixGroup.getDataType() |
|
DataType |
SimpleRateMatrixGroup.getDataType() |
|
DataType |
SingleClassSubstitutionModel.getDataType() |
|
DataType |
SubstitutionModel.getDataType() |
|
DataType |
YangCodonModel.SimpleNeutralSelection.getDataType() |
|
DataType |
YangCodonModel.SimplePositiveSelection.getDataType() |
Modifier and Type | Method | Description |
---|---|---|
static SubstitutionModel |
SubstitutionModel.Utils.createSubstitutionModel(NeoRateMatrix rm,
DataType dt,
double[] equilibriumFrequencies) |
|
boolean |
GeneralPoissonRateMatrix.isDataTypeCompatible(DataType dt) |
Check the compatibility of a data type to be used with the rate matrix
|
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
|
protected void |
AbstractRateMatrix.setDataType(DataType dt) |
Constructor | 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 | Description |
---|---|---|
DataType |
GeneralConstructionTool.getDataType() |