Uses of Class
jebl.evolution.sequences.State

Packages that use State

jebl.evolution.alignments
jebl.evolution.parsimony
jebl.evolution.sequences

Uses of State in jebl.evolution.alignments

Methods in jebl.evolution.alignments that return State

static State[]	ConsensusSequence.constructConsensus(Alignment source)
State	Pattern.getMostFrequentState() Returns the most frequent state in this pattern
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

List<State>	Pattern.getStates()
Set<State>	Pattern.getStateSet()

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

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

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

class	AminoAcidState
class	CodonState
class	NucleotideState

Methods in jebl.evolution.sequences that return State

protected abstract State[]	FilteredSequence.filterSequence(Sequence source)
protected State[]	GaplessSequence.filterSequence(Sequence source)
protected State[]	TranslatedSequence.filterSequence(Sequence source)
State	SequenceType.getGapState() Get state corresponding to a gap
State	SequenceType.getState(char code)
State	BasicSequence.getState(int site)
State	FilteredSequence.getState(int site)
State	Sequence.getState(int site)
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[]	FilteredSequence.getStates()
State[]	Sequence.getStates()
State	SequenceType.getUnknownState() Get state corresponding to an unknown
static State[]	Utils.reverse(State[] sequence)
static State[]	Utils.stripGaps(State[] sequence)
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

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.getStateSet(String setName)
Set<State>	StateClassification.Default.getStateSet(String setName)

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

String	StateClassification.getSetName(State state)
String	StateClassification.Default.getSetName(State 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.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	State.possiblyEqual(State other)
static State[]	Utils.reverse(State[] sequence)
static State[]	Utils.stripGaps(State[] sequence)
static AminoAcidState[]	Utils.translate(State[] states, GeneticCode geneticCode)

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

BasicSequence(SequenceType sequenceType, Taxon taxon, State[] states)
Creates a sequence with a name corresponding to the taxon name

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