Uses of Interface
pal.datatype.DataType

Packages that use DataType
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
 DataType[] MultiLocusAnnotatedAlignment.siteDataType
          provides datatype for each locus separately
 

Methods in pal.alignment that return DataType
 DataType Alignment.getDataType()
          Return DataType of this alignment.
 DataType AbstractAlignment.getDataType()
          Returns the datatype of this alignment
 DataType ConcatenatedAnnotatedAlignment.getDataType(int site)
          Return the datatype for a given site, which can differ between source alignments
 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 MultiLocusAnnotatedAlignment.getDataType(int site)
          Returns the datatype
 DataType SimpleAnnotatedAlignment.getDataType(int site)
          Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)
 DataType IndelAnnotatedAlignment.getDataType(int site)
          Returns the 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
 

Methods in pal.alignment with parameters of type DataType
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
AlignmentReaders.PhylipClustalAlignment(java.lang.String[] names, java.lang.String[] sequences, DataType dt)
           
AlignmentReaders.UnalignedAlignment(java.lang.String[] names, java.lang.String[] sequences, DataType dt)
           
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)
           
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
 

Uses of DataType in pal.datatype
 

Subinterfaces of DataType in pal.datatype
 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
 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
static DataType NumericDataType.DEFAULT_INSTANCE
           
 

Methods in pal.datatype that return DataType
 DataType TransitionPenaltyTable.getDataType()
           
 DataType IUPACPenaltyTable.getDataType()
           
static DataType DataType.Utils.getInstance(int typeID)
          create object according to this code
 DataType IUPACNucleotides.getSpecificDataType()
           
 DataType AmbiguousDataType.getSpecificDataType()
           
 

Methods in pal.datatype with parameters of type DataType
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
 

Constructors in pal.datatype with parameters of type DataType
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
 LHCalculator.Generator LHCalculator.Factory.createSeries(int numberOfCategories, DataType dt)
           
 

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

Uses of DataType in pal.substmodel
 

Methods in pal.substmodel that return DataType
 DataType CachedRateMatrix.getDataType()
           
 DataType SingleClassSubstitutionModel.getDataType()
           
 DataType PositiveSelectionRateMatrixGroup.getDataType()
           
 DataType SubstitutionModel.getDataType()
           
 DataType RateMatrix.getDataType()
          Get the data type of this rate matrix
 DataType NeutralSelectionRateMatrixGroup.getDataType()
           
 DataType SimpleRateMatrixGroup.getDataType()
           
 DataType YangCodonModel.SimplePositiveSelection.getDataType()
           
 DataType YangCodonModel.SimpleNeutralSelection.getDataType()
           
 DataType GeneralRateDistributionSubstitutionModel.getDataType()
           
 DataType RateMatrixGroup.getDataType()
           
 DataType AbstractRateMatrix.getDataType()
           
 

Methods in pal.substmodel with parameters of type DataType
static SubstitutionModel SubstitutionModel.Utils.createSubstitutionModel(NeoRateMatrix rm, DataType dt, double[] equilibriumFrequencies)
           
 boolean NeoRateMatrix.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 GeneralPoissonRateMatrix.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
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
 DataType GeneralConstructionTool.getDataType()