Uses of Interface
pal.datatype.DataType
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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 -
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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 separatelyMethods in pal.alignment that return DataType Modifier and Type Method Description DataType
AbstractAlignment. getDataType()
Returns the datatype of this alignmentDataType
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 alignmentsDataType
ConcatenatedAnnotatedAlignment. getDataType(int site)
Return the datatype for a given site, which can differ between source alignmentsDataType
IndelAnnotatedAlignment. getDataType(int site)
Returns the datatypeDataType
MultiLocusAnnotatedAlignment. getDataType(int site)
Returns the datatypeDataType
SimpleAnnotatedAlignment. getDataType(int site)
Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)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(java.lang.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 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 otherstatic 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 objectstatic 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 sequencesstatic Alignment
AlignmentReaders. readNewLineSeperatedSequences(java.io.Reader r, DataType dt)
Read an a set of unaligned Fasta sequencesstatic 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 alignmentstatic 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 scratchUnalignedAlignment(java.lang.String[] names, java.lang.String[] sequences, DataType dt)
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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 acidsclass
Codons
implements DataType for all Codons (including terminators).class
GapBalanced
implements a ResidueDataType for GapBalanced notation.class
IUPACNucleotides
implements DataType for nucleotides with ambiguous charactersclass
Nucleotides
implements DataType for nucleotidesclass
NumericDataType
This datatype stores numeric values.class
SimpleDataType
interface for sequence data typesclass
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 removedclass
TwoStates
implements DataType for two-state dataFields 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 codeDataType
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 sequencestatic 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 sequencestatic 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 sequencestatic char[]
DataType.Utils. getChars(int[] sequence, char unknownChar, char gapChar, DataType dt)
For converting a sequence of ints representing states to an array of charsstatic char[]
DataType.Utils. getChars(int[] sequence, DataType dt)
For converting a sequence of ints representing states to an array of charsstatic 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 typestatic char[]
DataType.Utils. getPreferredChars(char[] sequence, DataType dt, boolean specialDots)
Converts a sequence of characters to the preferred form for a data typestatic 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 typestatic 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 sequencestatic 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 sequencestatic 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 statesstatic 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 sequencestatic 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 DataTypeConstructors 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)
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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 matrixDataType
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 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 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)
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Uses of DataType in pal.treesearch
Methods in pal.treesearch that return DataType Modifier and Type Method Description DataType
GeneralConstructionTool. getDataType()
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