Uses of Interface
pal.alignment.Alignment
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Packages that use Alignment 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.coalescent Classes to model population genetic processes using the coalescent.pal.distance Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.popgen Classes for providing 'classical' population genetics analyses.pal.statistics Classes with useful for statistics (normal distribution, Gamma distribution, chi-square distribution, exponential distribution, likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).pal.treesearch pal.xml Utility classes for converting PAL objects to and from XML documents. -
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Uses of Alignment in pal.alignment
Subinterfaces of Alignment in pal.alignment Modifier and Type Interface Description interface
AnnotationAlignment
The AnnotationAlignment interface is designed to provide annotation for an alignment.Classes in pal.alignment that implement Alignment Modifier and Type Class Description class
AbstractAlignment
abstract base class for any alignment data.static class
AlignmentReaders.PhylipClustalAlignment
static class
AlignmentReaders.UnalignedAlignment
class
BootstrappedAlignment
generates bootstrapped alignments from a raw alignmentclass
ConcatenatedAlignment
concatenates a list of alignments to one single alignment, increasing the number of sitesclass
ConcatenatedAnnotatedAlignment
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.class
GapBalancedAlignment
Creates a "Gap-Balanced" alignment.class
IndelAlignment
This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.class
IndelAnnotatedAlignment
an extension of the IndelAlignment that includes annotation.class
JumbledAlignment
generates jumbled alignments (randomizing input order of sequences)class
MultiLocusAnnotatedAlignment
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.class
ReadAlignment
reads aligned sequence data from plain text files.class
ReadAlignmentOld
reads aligned sequence data from plain text files.class
SimpleAlignment
An alignment class that can be efficiently constructed from an array of strings.class
SimpleAnnotatedAlignment
This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.class
SitePattern
takes an Alignment and determines its site patternsclass
StrippedAlignment
takes an alignment and repeatedly removes sitesclass
StrippedAnnotatedAlignment
This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.Fields in pal.alignment declared as Alignment Modifier and Type Field Description protected Alignment
StrippedAlignment. rawAlignment
Methods in pal.alignment that return Alignment 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 Alignment
AlignmentTool. convertToUniversalAminoAcids(Alignment base, int startingIndex)
Convert an alignment to one of amino acids (using Universal Translation)static Alignment
AlignmentTool. createBootstrapReplicate(Alignment base)
A simple approach to creating a bootstrap replicatestatic Alignment
AlignmentTool. createGapBalanced(Alignment base, int startingIndex)
Create a gap balanced alignment.Alignment
AlignmentBuilder. generateAlignment(DataType dt)
Build an alignment based on sequences stored.Alignment
Genotype. getAlignment(int i)
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.Alignment
AlignmentReceiver.SingleReceiver. getLastReceivedAlignment()
static Alignment
AlignmentUtils. getLeadingIncompleteCodonsStripped(Alignment base)
Creates a new nucleotide alignment based on the input that has any leading incomplete codons (that is, the first codon of the sequence that is not a gap/unknown but is not complete - has a nucleotide unknown) replaced by a triplet of unknownsAlignment
AlignmentGenerator. getNextAlignment(AlgorithmCallback callback)
Alignment[]
AlignmentReceiver.BucketReceiver. getReceivedAlignments()
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 Alignment
AlignmentUtils. removeRedundantSites(Alignment a)
Alignment
DataTranslator. toAlignment(MolecularDataType dt, int startingIndex)
Alignment
DataTranslator. toLeftAlignedReverseComplementNucleotides(int startingIndex)
Alignment
DataTranslator. toReverseComplementNucleotides(int startingIndex)
Methods in pal.alignment with parameters of type Alignment 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 Alignment
AlignmentTool. convertToUniversalAminoAcids(Alignment base, int startingIndex)
Convert an alignment to one of amino acids (using Universal Translation)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 AlignmentGenerator
AlignmentGenerator.Utils. createBootstrapGenerator(Alignment baseAlignment)
static Alignment
AlignmentTool. createBootstrapReplicate(Alignment base)
A simple approach to creating a bootstrap replicatestatic Alignment
AlignmentTool. createGapBalanced(Alignment base, int startingIndex)
Create a gap balanced alignment.static double[]
AlignmentUtils. estimateCodonFrequenciesF1X4(Alignment a)
Estimate the frequencies of codons, calculated from the average nucleotide frequencies.static double[]
AlignmentUtils. estimateCodonFrequenciesF3X4(Alignment a)
Estimate the frequencies of codons, calculated from the average nucleotide frequencies at the three codon positions.static double[]
AlignmentUtils. estimateFrequencies(Alignment a)
count statesstatic double[][]
AlignmentUtils. estimateTupletFrequencies(Alignment a, int tupletSize)
Estimates frequencies via tuplets.static void
AlignmentUtils. getAlignedSequenceIndices(Alignment a, int i, int[] indices, DataType dataType, int unknownState)
Returns state indices for a sequence.static int[][]
AlignmentUtils. getAlignedStates(Alignment base)
Unknown characters are given the state of -1static int[][]
AlignmentUtils. getAlignedStates(Alignment base, int unknownState)
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 double
AlignmentUtils. getAlignmentPenalty(Alignment a, TransitionPenaltyTable penalties, double gapCreation, double gapExtension)
Returns total sum of pairs alignment penalty using gap creation and extension penalties and transition penalties 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 double
AlignmentUtils. getConsistency(Alignment a, Alignment b)
static Alignment
AlignmentUtils. getLeadingIncompleteCodonsStripped(Alignment base)
Creates a new nucleotide alignment based on the input that has any leading incomplete codons (that is, the first codon of the sequence that is not a gap/unknown but is not complete - has a nucleotide unknown) replaced by a triplet of unknownsstatic void
AlignmentUtils. getPositionMisalignmentInfo(Alignment a, java.io.PrintWriter out, int startingCodonPosition)
static void
AlignmentUtils. getPositionMisalignmentInfo(Alignment a, java.io.PrintWriter out, int startingCodonPosition, CodonTable translator, boolean removeIncompleteCodons)
static char[]
AlignmentUtils. getSequenceCharArray(Alignment a, int sequence)
Returns a particular sequence of an alignment as a char arraystatic java.lang.String
AlignmentUtils. getSequenceString(Alignment a, int sequence)
Returns a particular sequence of an alignment as a Stringstatic SitePattern
SitePattern. getSitePattern(Alignment a)
static DataType
AlignmentUtils. getSuitableInstance(Alignment alignment)
guess data type suitable for a given sequence data setstatic boolean
AlignmentUtils. isGap(Alignment a, int seq, int site)
Returns true if the alignment has a gap at the site in the sequence specified.static boolean
AlignmentUtils. isSiteRedundant(Alignment a, int site)
void
AlignmentReceiver.BucketReceiver. newAlignment(Alignment a)
void
AlignmentReceiver. newAlignment(Alignment a)
void
AlignmentReceiver.SingleReceiver. newAlignment(Alignment a)
static void
AlignmentUtils. print(Alignment a, java.io.PrintWriter out)
print alignment (default format: INTERLEAVED)static void
AlignmentUtils. printCLUSTALW(Alignment a, java.io.PrintWriter out)
Print alignment (in CLUSTAL W format)static void
AlignmentUtils. printInterleaved(Alignment a, java.io.PrintWriter out)
print alignment (in PHYLIP 3.4 INTERLEAVED format)static void
AlignmentUtils. printPlain(Alignment a, java.io.PrintWriter out)
print alignment (in plain format)static void
AlignmentUtils. printPlain(Alignment a, java.io.PrintWriter out, boolean relaxed)
print alignment (in plain format)static void
AlignmentUtils. printSequential(Alignment a, java.io.PrintWriter out)
print alignment (in PHYLIP SEQUENTIAL format)static Alignment
AlignmentUtils. removeRedundantSites(Alignment a)
static void
AlignmentUtils. report(Alignment a, java.io.PrintWriter out)
Report number of sequences, sites, and data typestatic int[][]
DataTranslator. toStates(Alignment a)
Converts an alignment to a state matrix Stored as [sequnce][site]static int[][]
DataTranslator. toStates(Alignment a, int gapUnknownState)
Converts an alignment to a state matrix Stored as [sequnce][site]Constructors in pal.alignment with parameters of type Alignment Constructor Description BootstrappedAlignment(Alignment raw)
ConstructorConcatenatedAlignment(Alignment[] list)
concatenate alignmentsDataTranslator(Alignment base)
GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap)
The standard GapBalanced constructorGapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap, int codonLength)
GapBalanced power user constructorGapBalancedAlignment(Alignment base, int startingCodonPosition, int codonLength)
GapBalanced power user constructorGenotype(Alignment a1, Alignment a2)
IndelAlignment(Alignment a, boolean anchored)
Basic constructor.JumbledAlignment(Alignment raw)
MultiLocusAnnotatedAlignment(Alignment a)
Basic constructor.SimpleAlignment(Alignment a)
Clone constructor.SimpleAlignment(Alignment a, int sequenceToIgnore)
Clone constructor.SimpleAlignment(Alignment a, Alignment b, java.lang.String guide1, java.lang.String guide2, char gap)
This constructor combines to alignments given two guide strings.SimpleAlignment(Alignment a, LabelMapping lm)
Clone constructor.SimpleAnnotatedAlignment(Alignment a)
Clone constructor from an unannotated alignment.SitePattern(Alignment a)
infer site patterns for a given alignmentStrippedAlignment(Alignment raw)
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Uses of Alignment in pal.coalescent
Methods in pal.coalescent that return Alignment Modifier and Type Method Description Alignment[]
SerialCoalescentGenerator.Results. getAlignments()
Constructors in pal.coalescent with parameters of type Alignment Constructor Description Results(Tree[] trees, Alignment[] alignments)
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Uses of Alignment in pal.distance
Methods in pal.distance with parameters of type Alignment Modifier and Type Method Description static DistanceMatrix
DistanceTool. constructEvolutionaryDistances(Alignment a, SubstitutionModel sm)
Construct a distance matrix object such that the distance between sequence A, and sequence B, is the evolutionary distance by a given substitution model.static DistanceMatrixAccess
DistanceMatrixAccess.Utils. createEvolutionary(Alignment a, SubstitutionModel sm)
static DistanceMatrixGenerator
DistanceMatrixGenerator.Utils. createEvolutionary(Alignment a, SubstitutionModel sm)
Constructors in pal.distance with parameters of type Alignment Constructor Description JukesCantorDistanceMatrix(Alignment alignment)
compute jukes-cantor corrected distances -
Uses of Alignment in pal.eval
Methods in pal.eval that return Alignment Modifier and Type Method Description static Alignment
LikelihoodTool. getMatchingDataType(Alignment alignment, SubstitutionModel model)
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)Methods in pal.eval with parameters of type Alignment Modifier and Type Method Description static double
LikelihoodTool. calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model)
Calculate the log likelihood of a particular set of phylogenetic datastatic Alignment
LikelihoodTool. getMatchingDataType(Alignment alignment, SubstitutionModel model)
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)static double
LikelihoodOptimiser. optimiseAlternate(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
Optimise parameters to acheive maximum likelihood using an alternating stategy.static double
LikelihoodOptimiser. optimiseAlternate(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
Optimise parameters to acheive maximum likelihood using an alternating stategy.static Tree
LikelihoodTool. optimiseClockConstrained(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
Optimise the branches of a tree with regard to maximum likelihood, with a molecular clock assumption, that is, constrained such that all tips are contemporaneous, the tree is treated as rooted.static double
LikelihoodOptimiser. optimiseCombined(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
Optimise parameters to acheive maximum likelihood using a combined stategy.static double
LikelihoodOptimiser. optimiseCombined(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
Optimise parameters to acheive maximum likelihood using a combined stategy.static double
LikelihoodOptimiser. optimiseModel(Tree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
Optimise model parameters only to acheive maximum likelihood using a combined stategy.static Tree
LikelihoodTool. optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval.static Tree
LikelihoodTool. optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateChangeTimes, double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals.static Tree
LikelihoodTool. optimiseSRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter.static double
LikelihoodOptimiser. optimiseTree(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.static double
LikelihoodOptimiser. optimiseTree(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.static Tree
LikelihoodTool. optimiseUnrooted(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).Constructors in pal.eval with parameters of type Alignment Constructor Description GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model)
Constructor taking site pattern, tree and a rate matrix.GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model, RateDistribution distribution)
Constructor taking site pattern, tree rate matrix, and a rate distributionGeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, SubstitutionModel model)
Constructor taking site pattern, tree and a general substitution model.LikelihoodOptimiser(Tree tree, Alignment alignment, SubstitutionModel model)
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Uses of Alignment in pal.popgen
Fields in pal.popgen declared as Alignment Modifier and Type Field Description protected Alignment
LinkageDisequilibrium. theAlignment
Constructors in pal.popgen with parameters of type Alignment Constructor Description LinkageDisequilibrium(Alignment alignment)
compute LD based on an alignment.LinkageDisequilibrium(Alignment alignment, boolean rapidPermute, int numberOfPermutations)
compute LD based on an alignment -
Uses of Alignment in pal.statistics
Methods in pal.statistics with parameters of type Alignment Modifier and Type Method Description double
LikelihoodEvaluator. calculateLikelihood(Tree tree, Alignment alignment)
LikelihoodEvaluator.MLResult
LikelihoodEvaluator. getMLOptimised(Tree tree, Alignment alignment, AlgorithmCallback callback)
double
ReplicateLikelihoodEvaluator. getReplicateLogLikelihood(Tree tree, Alignment alignment)
Constructors in pal.statistics with parameters of type Alignment Constructor Description GeneralTopologyPool(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator)
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Uses of Alignment in pal.tree
Classes in pal.tree that implement Alignment Modifier and Type Class Description class
SimulatedAlignment
generates an artificial data setMethods in pal.tree that return Alignment Modifier and Type Method Description static Alignment
TreeUtils. extractAlignment(Tree tree)
Extracts an alignment from a tree.static Alignment
TreeUtils. extractAlignment(Tree tree, boolean leaveSeqsInTree)
Extracts an alignment from a tree. -
Uses of Alignment in pal.treesearch
Methods in pal.treesearch that return Alignment Modifier and Type Method Description static Alignment
TreeSearchTool. getMatchingDataType(Alignment alignment, SubstitutionModel model)
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)Methods in pal.treesearch with parameters of type Alignment Modifier and Type Method Description UnrootedMLSearcher
BranchAccess. attach(java.lang.String newSequence, Alignment fullAlignment)
Create a new Tree Searcher with a new sub tree attachedUnrootedMLSearcher
BranchAccess. attach(java.lang.String newSequence, Alignment fullAlignment, SubstitutionModel model)
Create a new Tree Searcher with a new sub tree attachedUnrootedMLSearcher
BranchAccess. attach(Node subTree, Alignment fullAlignment)
Create a new Tree Searcher with a new sub tree attachedUnrootedMLSearcher
BranchAccess. attach(Node subTree, Alignment fullAlignment, SubstitutionModel model)
Create a new Tree Searcher with a new sub tree attachedTree
TreeSearchTool. basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel)
Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting treeTree
TreeSearchTool. basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback)
Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting treeTree
TreeSearchTool. basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel)
Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting treeTree
TreeSearchTool. basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback)
Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting treestatic double
TreeSearchTool. calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model)
Calculate the log likelihood of a particular set of phylogenetic datastatic Alignment
TreeSearchTool. getMatchingDataType(Alignment alignment, SubstitutionModel model)
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)static Tree
TreeSearchTool. optimiseClockConstrainedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point.static Tree
TreeSearchTool. optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).static Tree
TreeSearchTool. optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).Constructors in pal.treesearch with parameters of type Alignment Constructor Description GeneralConstructionTool(ConstraintModel constraints, Alignment alignment)
The constructorGeneralLikelihoodSearcher(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel)
UnrootedMLSearcher(Alignment alignment, SubstitutionModel model)
Build an unconstrained optimiser based on a randomly generated tree.UnrootedMLSearcher(Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model)
UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
UnrootedMLSearcher(Tree t, Alignment alignment, SubstitutionModel model)
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Uses of Alignment in pal.xml
Methods in pal.xml that return Alignment Modifier and Type Method Description static Alignment
ElementParser. parseAlignmentElement(org.w3c.dom.Element e)
Parses an alignment element and returns an alignment object.Methods in pal.xml with parameters of type Alignment Modifier and Type Method Description static org.w3c.dom.Element
ElementFactory. createAlignmentElement(Alignment a, org.w3c.dom.Document document)
protected static RateMatrix
ElementParser. parseRateMatrix(org.w3c.dom.Element e, Alignment a)
Reads a rate matrix from a DOM Document element.
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