Uses of Class jebl.evolution.sequences.State (JEBL2 lib API)

Packages that use State

Package

Description

jebl.evolution.alignments

jebl.evolution.parsimony

jebl.evolution.sequences

Uses of State in jebl.evolution.alignments

Methods in jebl.evolution.alignments that return State

Modifier and Type

Method

Description

static State[]

ConsensusSequence.constructConsensus(Alignment source, boolean includeAmbiguities)

State

Pattern.getMostFrequentState()

Returns the most frequent state in this pattern

State

Pattern.getMostFrequentState(boolean includeAmbiguous)

Returns the most frequent state in this pattern, optionally including ambiguous states

State

ConsensusSequence.getState(int site)

State

Pattern.getState(int index)

Get the state for the ith taxon

State[]

ConsensusSequence.getStates()

Methods in jebl.evolution.alignments that return types with arguments of type State

Modifier and Type

Method

Description

List<State>

Pattern.getStates()

Set<State>

Pattern.getStateSet()

Methods in jebl.evolution.alignments with parameters of type State

Modifier and Type

Method

Description

int

Pattern.getStateCount(State state)

Returns the count of the given state in this pattern

double

Pattern.getStateFrequency(State state)

Returns the frequent of the given state in this pattern
Uses of State in jebl.evolution.parsimony

Methods in jebl.evolution.parsimony that return State

Modifier and Type

Method

Description

State[]

FitchParsimony.getStates(Tree tree, Node node)

Returns the reconstructed character states for a given node in the tree.

State[]

ParsimonyCriterion.getStates(Tree tree, Node node)

Returns the reconstructed character states for a given node in the tree.
Uses of State in jebl.evolution.sequences

Subclasses of State in jebl.evolution.sequences

Modifier and Type

Class

Description

final class

AminoAcidState

final class

CodonState

As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - see Codons.

final class

NucleotideState

Methods in jebl.evolution.sequences that return State

Modifier and Type

Method

Description

static State[]

Utils.cleanSequence(CharSequence seq, SequenceType type)

Produce a clean sequence filtered of spaces and digits.

State

SequenceType.getGapState()

Get state corresponding to a gap

State

BasicSequence.getState(int site)

State

CanonicalSequence.getState(int site)

State

CodonSequence.getState(int site)

State

FilteredSequence.getState(int site)

State

Sequence.getState(int site)

State

SequenceType.getState(char code)

Get state whose code is the one-character string consisting only of code.

State

SequenceType.getState(int index)

Get state corresponding to a state index

State

SequenceType.getState(String code)

Get state corresponding to a string code

State[]

BasicSequence.getStates()

State[]

CanonicalSequence.getStates()

State[]

CodonSequence.getStates()

State[]

FilteredSequence.getStates()

State[]

Sequence.getStates()

State

SequenceType.getUnknownState()

Get state corresponding to an unknown

static State[]

Utils.replaceStates(State[] sequence, List<State> searchStates, State replaceState)

Searchers and replaces a sequence of any states given

static State[]

Utils.reverse(State[] sequence)

static State[]

Utils.stripGaps(State[] sequence)

Strips a sequence of gaps

static State[]

Utils.stripStates(State[] sequence, List<State> stripStates)

Strips a sequence of any states given

State[]

SequenceType.toStateArray(byte[] indexArray)

Converts an array of state indices into an array of State objects for this SequenceType

State[]

SequenceType.toStateArray(String sequenceString)

Converts a string of state codes into an array of State objects for this SequenceType

Methods in jebl.evolution.sequences that return types with arguments of type State

Modifier and Type

Method

Description

static List<State>

AminoAcids.getCanonicalStates()

static List<State>

Codons.getCanonicalStates()

List<? extends State>

SequenceType.getCanonicalStates()

Get a list of canonical states ordered by their indices.

Set<State>

State.getCanonicalStates()

static List<State>

Codons.getStates()

static List<State>

Nucleotides.getStates()

List<? extends State>

SequenceType.getStates()

Get a list of states ordered by their indices.

Set<State>

StateClassification.Default.getStateSet(String setName)

Set<State>

StateClassification.getStateSet(String setName)

Methods in jebl.evolution.sequences with parameters of type State

Modifier and Type

Method

Description

double

State.fractionEqual(State other)

Determine how much in common these potentially ambigous states have as a fraction between 0 and 1 2 non-ambiguous states will return 0.

String

StateClassification.Default.getSetName(State state)

String

StateClassification.getSetName(State state)

static int

Sequence.getStateCount(Sequence sequence, State state)

Counts the number of occurances of a state

static byte[]

Utils.getStateIndices(State[] sequence)

static boolean

Nucleotides.isATstate(State state)

boolean

SequenceType.isGap(State state)

static boolean

Nucleotides.isGCstate(State state)

static boolean

Nucleotides.isPossibleTransition(State s1, State s2)

static boolean

Nucleotides.isPossibleTransversion(State s1, State s2)

static boolean

Nucleotides.isPurine(State state)

static boolean

Nucleotides.isPyrimidine(State state)

static boolean

Nucleotides.isTransition(State state1, State state2)

static boolean

Nucleotides.isTransversion(State state1, State state2)

boolean

SequenceType.isUnknown(State state)

boolean

NucleotideState.possiblyEqual(State other)

boolean

State.possiblyEqual(State other)

static Sequence

Sequence.replaceStates(Sequence sequence, List<State> searchStates, State replaceState)

Searchers and replaces a sequence of any states given

static State[]

Utils.replaceStates(State[] sequence, List<State> searchStates, State replaceState)

Searchers and replaces a sequence of any states given

static State[]

Utils.reverse(State[] sequence)

static State[]

Utils.stripGaps(State[] sequence)

Strips a sequence of gaps

static State[]

Utils.stripStates(State[] sequence, List<State> stripStates)

Strips a sequence of any states given

static CodonState[]

Nucleotides.toCodons(State[] states, int readingFrame)

Convert an array of nucleotide states into an array of codon states

static NucleotideState[]

Codons.toNucleotides(State[] states)

static String

Utils.toString(State[] states)

static AminoAcidState[]

Utils.translate(State[] states, GeneticCode geneticCode)

Translates each of a given sequence of NucleotideStates or CodonStates to the AminoAcidState corresponding to it under the given genetic code.

static AminoAcidState[]

Utils.translate(State[] states, GeneticCode geneticCode, int readingFrame)

Translates each of a given sequence of NucleotideStates or CodonStates to the AminoAcidState corresponding to it under the given genetic code.

Method parameters in jebl.evolution.sequences with type arguments of type State

Modifier and Type

Method

Description

static Sequence

Sequence.replaceStates(Sequence sequence, List<State> searchStates, State replaceState)

Searchers and replaces a sequence of any states given

static State[]

Utils.replaceStates(State[] sequence, List<State> searchStates, State replaceState)

Searchers and replaces a sequence of any states given

static Sequence

Sequence.stripStates(Sequence sequence, List<State> stripStates)

Strips a sequence of any states given

static State[]

Utils.stripStates(State[] sequence, List<State> stripStates)

Strips a sequence of any states given

static Sequence

Sequence.trimSequence(Sequence sequence, List<State> trimStates)

Constructors in jebl.evolution.sequences with parameters of type State

Modifier

Constructor

Description

BasicSequence(SequenceType sequenceType, Taxon taxon, State[] states)

Creates a sequence with a name corresponding to the taxon name

CanonicalSequence(SequenceType sequenceType, Taxon taxon, State[] states)

Creates a sequence with a name corresponding to the taxon name

CodonSequence(Taxon taxon, State[] states)

Creates a sequence with a name corresponding to the taxon name

Default(String name, String[] setNames, State[][] stateSets)

Uses of Classjebl.evolution.sequences.State

Uses of State in jebl.evolution.alignments

Uses of State in jebl.evolution.parsimony

Uses of State in jebl.evolution.sequences

Uses of Class
jebl.evolution.sequences.State