Uses of Interface pal.datatype.DataType

Packages that use DataType
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

Uses of DataType in pal.alignment

Fields in pal.alignment declared as DataType
Modifier and Type	Field	Description
`DataType[]`	MultiLocusAnnotatedAlignment.`siteDataType`	provides datatype for each locus separately

Methods in pal.alignment that return DataType
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

Methods in pal.alignment with parameters of type DataType
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]

Constructors in pal.alignment with parameters of type DataType
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)`

Uses of DataType in pal.datatype

Subinterfaces of DataType in pal.datatype
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).

Classes in pal.datatype that implement DataType
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

Fields in pal.datatype declared as DataType
Modifier and Type	Field	Description
`static DataType`	NumericDataType.`DEFAULT_INSTANCE`

Methods in pal.datatype that return DataType
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()`

Methods in pal.datatype with parameters of type DataType
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

Constructors in pal.datatype with parameters of type DataType
Constructor	Description
`StateRemover(DataType toAdjust, int[] statesToRemove)`	A translation array -> originalToAdjusted_["adjusted State"] = "original state"

Uses of DataType in pal.eval

Methods in pal.eval with parameters of type DataType
Modifier and Type	Method	Description
`LHCalculator.Generator`	LHCalculator.Factory.`createSeries(int numberOfCategories, DataType dt)`

Constructors in pal.eval with parameters of type DataType
Constructor	Description
`LikelihoodSummary(DataType dt, double overallLogLikelihood, double[] categoryProbabilities, double[][] individualLikelihoods, int[] sitePatternMatchup)`

Uses of DataType in pal.substmodel

Methods in pal.substmodel that return DataType
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()`

Methods in pal.substmodel with parameters of type DataType
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)`

Constructors in pal.substmodel with parameters of type DataType
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)`

Uses of DataType in pal.treesearch

Methods in pal.treesearch that return DataType
Modifier and Type Method Description

DataType GeneralConstructionTool.getDataType()