Uses of Interface
pal.datatype.DataType
Packages that use DataType
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes describing substitution models, i.e.
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Uses of DataType in pal.alignment
Fields in pal.alignment declared as DataTypeModifier and TypeFieldDescriptionDataType[]
MultiLocusAnnotatedAlignment.siteDataType
provides datatype for each locus separatelyMethods in pal.alignment that return DataTypeModifier and TypeMethodDescriptionfinal DataType
AbstractAlignment.getDataType()
Returns the datatype of this alignmentAlignment.getDataType()
Return DataType of this alignment.AnnotationAlignment.getDataType
(int site) Returns the datatype for a specific site, which could differ by site in complex alignmentsConcatenatedAnnotatedAlignment.getDataType
(int site) Return the datatype for a given site, which can differ between source alignmentsIndelAnnotatedAlignment.getDataType
(int site) Returns the datatypeMultiLocusAnnotatedAlignment.getDataType
(int site) Returns the datatypeSimpleAnnotatedAlignment.getDataType
(int site) Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)StrippedAnnotatedAlignment.getDataType
(int site) Returns the datatypestatic DataType
AlignmentUtils.getSuitableInstance
(char[][] sequences) guess data type suitable for a given sequence data setstatic DataType
AlignmentUtils.getSuitableInstance
(String[] sequences) guess data type suitable for a given sequence data setstatic DataType
AlignmentUtils.getSuitableInstance
(Alignment alignment) guess data type suitable for a given sequence data setMethods in pal.alignment with parameters of type DataTypeModifier and TypeMethodDescriptionstatic final 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 otherstatic final 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 final 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'AlignmentBuilder.generateAlignment
(DataType dt) Build an alignment based on sequences stored.static final 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 final 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 final Alignment
AlignmentTool.readAlignment
(Reader r, DataType dt) Attempt to read a file from a reader objectstatic final Alignment[]
AlignmentReaders.readAllPhylipClustalAlignments
(Reader r, DataType dt) Read an alignment in phylip/clustal/simple format.static final Alignment
AlignmentReaders.readFastaSequences
(Reader r, DataType dt) Read an a set of unaligned Fasta sequencesstatic final Alignment
AlignmentReaders.readNewLineSeperatedSequences
(Reader r, DataType dt) Read an a set of unaligned Fasta sequencesstatic final Alignment
AlignmentReaders.readPhylipClustalAlignment
(Reader r, DataType dt) Read an alignment in phylip/clustal/simple format.static final void
AlignmentReaders.readPhylipClustalAlignment
(Reader r, DataType dt, AlignmentReceiver receiver) Read an alignment in phylip/clustal/simple format.final void
AbstractAlignment.setDataType
(DataType d) Sets the datatype of this alignmentstatic final char[][]
Converts an state matrix to a char matrix Stored as [sequnce][site]static final int[][]
Converts an alignment to a state matrix Stored as [sequnce][site]Constructors in pal.alignment with parameters of type DataTypeModifierConstructorDescriptionMultiLocusAnnotatedAlignment
(Identifier[] ids, String[] sequences, String gaps, DataType dt) MultiLocusAnnotatedAlignment
(IdGroup group, String[] sequences, String gaps, DataType dt) MultiLocusAnnotatedAlignment
(IdGroup group, String[] sequences, DataType dt) PhylipClustalAlignment
(String[] names, String[] sequences, DataType dt) SimpleAlignment
(Identifier[] ids, String[] sequences, String gaps, DataType dt) SimpleAlignment
(Identifier[] ids, String[] sequences, DataType dt) SimpleAlignment
(Identifier id, String sequence, DataType dataType) Constructor taking single identifier and sequence.SimpleAlignment
(IdGroup group, char[][] cSequences, String gaps, DataType dt) SimpleAlignment
(IdGroup group, char[][] cSequences, DataType dt) SimpleAlignment
(IdGroup ids, String[] sequences, String gaps, DataType dt) SimpleAlignment
(IdGroup ids, String[] sequences, DataType dt) SimpleAlignment
(IdGroup group, DataType dt, int[][] sSequences) SimpleAnnotatedAlignment
(Identifier[] ids, String[] sequences, String gaps, DataType dt) This constructor creates a basic SimpleAnnotatedAlignment.SimpleAnnotatedAlignment
(IdGroup group, String[] sequences, String gaps, DataType dt) This constructor creates a basic SimpleAnnotatedAlignment.SimpleAnnotatedAlignment
(IdGroup group, 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 scratchUnalignedAlignment
(String[] names, String[] sequences, DataType dt) -
Uses of DataType in pal.datatype
Subinterfaces of DataType in pal.datatypeModifier and TypeInterfaceDescriptioninterface
Additional interface information for data types which represent ambiguity in sub types.interface
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 DataTypeModifier and TypeClassDescriptionclass
implements DataType for amino acidsclass
implements DataType for all Codons (including terminators).class
implements a ResidueDataType for GapBalanced notation.class
implements DataType for nucleotides with ambiguous charactersclass
implements DataType for nucleotidesclass
This datatype stores numeric values.class
interface for sequence data typesclass
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
A standard data type, but with characters removedclass
implements DataType for two-state dataFields in pal.datatype declared as DataTypeMethods in pal.datatype that return DataTypeModifier and TypeMethodDescriptionfinal DataType
IUPACPenaltyTable.getDataType()
TransitionPenaltyTable.getDataType()
static DataType
DataType.Utils.getInstance
(int typeID) create object according to this codeAmbiguousDataType.getSpecificDataType()
IUPACNucleotides.getSpecificDataType()
Methods in pal.datatype with parameters of type DataTypeModifier and TypeMethodDescriptionstatic final 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 sequencestatic final byte[]
DataType.Utils.getByteStates
(String sequence, DataType dt) For converting a sequence to an array of bytes where each byte represents the state of the corresponding character in sequencestatic final char[][]
For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequencestatic final char[]
For converting a sequence of ints representing states to an array of charsstatic final char[]
For converting a sequence of ints representing states to an array of charsstatic final MolecularDataType
MolecularDataType.Utils.getMolecularDataType
(DataType dt) Converts (if possible) a DataType into a MolecularDataType.static final char[]
DataType.Utils.getPreferredChars
(char[] sequence, DataType dt) Converts a sequence of characters to the preferred form for a data typestatic final char[]
DataType.Utils.getPreferredChars
(char[] sequence, DataType dt, boolean specialDots) Converts a sequence of characters to the preferred form for a data typestatic final String
DataType.Utils.getPreferredChars
(String sequence, DataType dt) Converts a sequence of characters to the preferred form for a data type (using Strings)static final String
DataType.Utils.getPreferredChars
(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 typestatic final int[][]
For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequencestatic final int[][]
For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequencestatic final int[]
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 statesstatic final int[]
For converting a sequence to an array of ints where each int represents the state of the corresponding character in sequencestatic final boolean
Deprecated.use DataType.isGapChar()static final 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 final String
For converting an array of states into a String of characters, based on a DataTypeConstructors in pal.datatype with parameters of type DataTypeModifierConstructorDescriptionStateRemover
(DataType toAdjust, int[] statesToRemove) A translation array -> originalToAdjusted_["adjusted State"] = "original state" -
Uses of DataType in pal.eval
Modifier and TypeMethodDescriptionLHCalculator.Factory.createSeries
(int numberOfCategories, DataType dt) ModifierConstructorDescriptionLikelihoodSummary
(DataType dt, double overallLogLikelihood, double[] categoryProbabilities, double[][] individualLikelihoods, int[] sitePatternMatchup) -
Uses of DataType in pal.substmodel
Methods in pal.substmodel that return DataTypeModifier and TypeMethodDescriptionAbstractRateMatrix.getDataType()
final DataType
CachedRateMatrix.getDataType()
GeneralRateDistributionSubstitutionModel.getDataType()
NeutralSelectionRateMatrixGroup.getDataType()
PositiveSelectionRateMatrixGroup.getDataType()
RateMatrix.getDataType()
Get the data type of this rate matrixRateMatrixGroup.getDataType()
SimpleRateMatrixGroup.getDataType()
SingleClassSubstitutionModel.getDataType()
SubstitutionModel.getDataType()
YangCodonModel.SimpleNeutralSelection.getDataType()
YangCodonModel.SimplePositiveSelection.getDataType()
Methods in pal.substmodel with parameters of type DataTypeModifier and TypeMethodDescriptionstatic final 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 matrixboolean
GeneralREVRateMatrix.isDataTypeCompatible
(DataType dt) Check the compatibility of a data type to be used with the rate matrixboolean
NeoRateMatrix.isDataTypeCompatible
(DataType dt) Check the compatibility of a data type to be used with the rate matrixprotected final void
AbstractRateMatrix.setDataType
(DataType dt) Constructors in pal.substmodel with parameters of type DataTypeModifierConstructorDescriptionGeneralRateDistributionSubstitutionModel
(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