Uses of Class
jebl.evolution.sequences.State
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Packages that use State Package Description jebl.evolution.alignments jebl.evolution.parsimony jebl.evolution.sequences -
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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)StatePattern. getMostFrequentState()Returns the most frequent state in this patternStatePattern. getMostFrequentState(boolean includeAmbiguous)Returns the most frequent state in this pattern, optionally including ambiguous statesStateConsensusSequence. getState(int site)StatePattern. getState(int index)Get the state for the ith taxonState[]ConsensusSequence. getStates()Methods in jebl.evolution.alignments that return types with arguments of type State Modifier and Type Method Description java.util.List<State>Pattern. getStates()java.util.Set<State>Pattern. getStateSet()Methods in jebl.evolution.alignments with parameters of type State Modifier and Type Method Description intPattern. getStateCount(State state)Returns the count of the given state in this patterndoublePattern. 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 classAminoAcidStateclassCodonStateAs of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - seeCodons.classNucleotideStateMethods in jebl.evolution.sequences that return State Modifier and Type Method Description static State[]Utils. cleanSequence(java.lang.CharSequence seq, SequenceType type)Produce a clean sequence filtered of spaces and digits.StateSequenceType. getGapState()Get state corresponding to a gapStateBasicSequence. getState(int site)StateCanonicalSequence. getState(int site)StateCodonSequence. getState(int site)StateFilteredSequence. getState(int site)StateSequence. getState(int site)StateSequenceType. getState(char code)Get state whose code is the one-character string consisting only of code.StateSequenceType. getState(int index)Get state corresponding to a state indexStateSequenceType. getState(java.lang.String code)Get state corresponding to a string codeState[]BasicSequence. getStates()State[]CanonicalSequence. getStates()State[]CodonSequence. getStates()State[]FilteredSequence. getStates()State[]Sequence. getStates()StateSequenceType. getUnknownState()Get state corresponding to an unknownstatic State[]Utils. replaceStates(State[] sequence, java.util.List<State> searchStates, State replaceState)Searchers and replaces a sequence of any states givenstatic State[]Utils. reverse(State[] sequence)static State[]Utils. stripGaps(State[] sequence)Strips a sequence of gapsstatic State[]Utils. stripStates(State[] sequence, java.util.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(java.lang.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 State Modifier and Type Method Description static java.util.List<State>AminoAcids. getCanonicalStates()static java.util.List<State>Codons. getCanonicalStates()java.util.List<? extends State>SequenceType. getCanonicalStates()Get a list of canonical states ordered by their indices.java.util.Set<State>State. getCanonicalStates()static java.util.List<State>Codons. getStates()static java.util.List<State>Nucleotides. getStates()java.util.List<? extends State>SequenceType. getStates()Get a list of states ordered by their indices.java.util.Set<State>StateClassification.Default. getStateSet(java.lang.String setName)java.util.Set<State>StateClassification. getStateSet(java.lang.String setName)Methods in jebl.evolution.sequences with parameters of type State Modifier and Type Method Description doubleState. 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.java.lang.StringStateClassification.Default. getSetName(State state)java.lang.StringStateClassification. getSetName(State state)static intSequence. getStateCount(Sequence sequence, State state)Counts the number of occurances of a statestatic byte[]Utils. getStateIndices(State[] sequence)static booleanNucleotides. isATstate(State state)booleanSequenceType. isGap(State state)static booleanNucleotides. isGCstate(State state)static booleanNucleotides. isPossibleTransition(State s1, State s2)static booleanNucleotides. isPossibleTransversion(State s1, State s2)static booleanNucleotides. isPurine(State state)static booleanNucleotides. isPyrimidine(State state)static booleanNucleotides. isTransition(State state1, State state2)static booleanNucleotides. isTransversion(State state1, State state2)booleanSequenceType. isUnknown(State state)booleanNucleotideState. possiblyEqual(State other)booleanState. possiblyEqual(State other)static SequenceSequence. replaceStates(Sequence sequence, java.util.List<State> searchStates, State replaceState)Searchers and replaces a sequence of any states givenstatic State[]Utils. replaceStates(State[] sequence, java.util.List<State> searchStates, State replaceState)Searchers and replaces a sequence of any states givenstatic State[]Utils. reverse(State[] sequence)static State[]Utils. stripGaps(State[] sequence)Strips a sequence of gapsstatic State[]Utils. stripStates(State[] sequence, java.util.List<State> stripStates)Strips a sequence of any states givenstatic CodonState[]Nucleotides. toCodons(State[] states, int readingFrame)Convert an array of nucleotide states into an array of codon statesstatic NucleotideState[]Codons. toNucleotides(State[] states)static java.lang.StringUtils. toString(State[] states)static AminoAcidState[]Utils. translate(State[] states, GeneticCode geneticCode)Translates each of a given sequence ofNucleotideStates orCodonStates to theAminoAcidStatecorresponding to it under the given genetic code.static AminoAcidState[]Utils. translate(State[] states, GeneticCode geneticCode, int readingFrame)Translates each of a given sequence ofNucleotideStates orCodonStates to theAminoAcidStatecorresponding 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 SequenceSequence. replaceStates(Sequence sequence, java.util.List<State> searchStates, State replaceState)Searchers and replaces a sequence of any states givenstatic State[]Utils. replaceStates(State[] sequence, java.util.List<State> searchStates, State replaceState)Searchers and replaces a sequence of any states givenstatic SequenceSequence. stripStates(Sequence sequence, java.util.List<State> stripStates)Strips a sequence of any states givenstatic State[]Utils. stripStates(State[] sequence, java.util.List<State> stripStates)Strips a sequence of any states givenstatic SequenceSequence. trimSequence(Sequence sequence, java.util.List<State> trimStates)Constructors in jebl.evolution.sequences with parameters of type State Constructor Description BasicSequence(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 nameDefault(java.lang.String name, java.lang.String[] setNames, State[][] stateSets)
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