Uses of Class
jebl.evolution.sequences.State
Packages that use State
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Uses of State in jebl.evolution.alignments
Methods in jebl.evolution.alignments that return StateModifier and TypeMethodDescriptionstatic State[]
ConsensusSequence.constructConsensus
(Alignment source, boolean includeAmbiguities) Pattern.getMostFrequentState()
Returns the most frequent state in this patternPattern.getMostFrequentState
(boolean includeAmbiguous) Returns the most frequent state in this pattern, optionally including ambiguous statesConsensusSequence.getState
(int site) Pattern.getState
(int index) Get the state for the ith taxonState[]
ConsensusSequence.getStates()
Methods in jebl.evolution.alignments that return types with arguments of type StateMethods in jebl.evolution.alignments with parameters of type StateModifier and TypeMethodDescriptionint
Pattern.getStateCount
(State state) Returns the count of the given state in this patterndouble
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 -
Uses of State in jebl.evolution.sequences
Subclasses of State in jebl.evolution.sequencesModifier and TypeClassDescriptionfinal class
final class
As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - seeCodons
.final class
Methods in jebl.evolution.sequences that return StateModifier and TypeMethodDescriptionstatic State[]
Utils.cleanSequence
(CharSequence seq, SequenceType type) Produce a clean sequence filtered of spaces and digits.SequenceType.getGapState()
Get state corresponding to a gapBasicSequence.getState
(int site) CanonicalSequence.getState
(int site) CodonSequence.getState
(int site) FilteredSequence.getState
(int site) Sequence.getState
(int site) SequenceType.getState
(char code) Get state whose code is the one-character string consisting only of code.SequenceType.getState
(int index) Get state corresponding to a state indexGet state corresponding to a string codeState[]
BasicSequence.getStates()
State[]
CanonicalSequence.getStates()
State[]
CodonSequence.getStates()
State[]
FilteredSequence.getStates()
State[]
Sequence.getStates()
SequenceType.getUnknownState()
Get state corresponding to an unknownstatic State[]
Utils.replaceStates
(State[] sequence, List<State> searchStates, State replaceState) Searchers and replaces a sequence of any states givenstatic State[]
static State[]
Strips a sequence of gapsstatic State[]
Utils.stripStates
(State[] sequence, List<State> stripStates) Strips a sequence of any states givenState[]
SequenceType.toStateArray
(byte[] indexArray) Converts an array of state indices into an array of State objects for this SequenceTypeState[]
SequenceType.toStateArray
(String sequenceString) Converts a string of state codes into an array of State objects for this SequenceTypeMethods in jebl.evolution.sequences that return types with arguments of type StateModifier and TypeMethodDescriptionAminoAcids.getCanonicalStates()
Codons.getCanonicalStates()
SequenceType.getCanonicalStates()
Get a list of canonical states ordered by their indices.State.getCanonicalStates()
Codons.getStates()
Nucleotides.getStates()
SequenceType.getStates()
Get a list of states ordered by their indices.StateClassification.Default.getStateSet
(String setName) StateClassification.getStateSet
(String setName) Methods in jebl.evolution.sequences with parameters of type StateModifier and TypeMethodDescriptiondouble
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.StateClassification.Default.getSetName
(State state) StateClassification.getSetName
(State state) static int
Sequence.getStateCount
(Sequence sequence, State state) Counts the number of occurances of a statestatic byte[]
Utils.getStateIndices
(State[] sequence) static boolean
boolean
static boolean
static boolean
Nucleotides.isPossibleTransition
(State s1, State s2) static boolean
Nucleotides.isPossibleTransversion
(State s1, State s2) static boolean
static boolean
Nucleotides.isPyrimidine
(State state) static boolean
Nucleotides.isTransition
(State state1, State state2) static boolean
Nucleotides.isTransversion
(State state1, State state2) boolean
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 givenstatic State[]
Utils.replaceStates
(State[] sequence, List<State> searchStates, State replaceState) Searchers and replaces a sequence of any states givenstatic State[]
static State[]
Strips a sequence of gapsstatic State[]
Utils.stripStates
(State[] sequence, List<State> stripStates) Strips a sequence of any states givenstatic CodonState[]
Convert an array of nucleotide states into an array of codon statesstatic NucleotideState[]
Codons.toNucleotides
(State[] states) static String
static AminoAcidState[]
Utils.translate
(State[] states, GeneticCode geneticCode) Translates each of a given sequence ofNucleotideState
s orCodonState
s to theAminoAcidState
corresponding to it under the given genetic code.static AminoAcidState[]
Utils.translate
(State[] states, GeneticCode geneticCode, int readingFrame) Translates each of a given sequence ofNucleotideState
s orCodonState
s to theAminoAcidState
corresponding to it under the given genetic code.Method parameters in jebl.evolution.sequences with type arguments of type StateModifier and TypeMethodDescriptionstatic Sequence
Sequence.replaceStates
(Sequence sequence, List<State> searchStates, State replaceState) Searchers and replaces a sequence of any states givenstatic State[]
Utils.replaceStates
(State[] sequence, List<State> searchStates, State replaceState) Searchers and replaces a sequence of any states givenstatic Sequence
Sequence.stripStates
(Sequence sequence, List<State> stripStates) Strips a sequence of any states givenstatic State[]
Utils.stripStates
(State[] sequence, List<State> stripStates) Strips a sequence of any states givenstatic Sequence
Sequence.trimSequence
(Sequence sequence, List<State> trimStates) Constructors in jebl.evolution.sequences with parameters of type StateModifierConstructorDescriptionBasicSequence
(SequenceType sequenceType, Taxon taxon, State[] states) Creates a sequence with a name corresponding to the taxon nameCanonicalSequence
(SequenceType sequenceType, Taxon taxon, State[] states) Creates a sequence with a name corresponding to the taxon nameCodonSequence
(Taxon taxon, State[] states) Creates a sequence with a name corresponding to the taxon name