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)
State
Pattern. getMostFrequentState()
Returns the most frequent state in this patternState
Pattern. getMostFrequentState(boolean includeAmbiguous)
Returns the most frequent state in this pattern, optionally including ambiguous statesState
ConsensusSequence. getState(int site)
State
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 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 int
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 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 class
AminoAcidState
class
CodonState
As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - seeCodons
.class
NucleotideState
Methods 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.State
SequenceType. getGapState()
Get state corresponding to a gapState
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 indexState
SequenceType. 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()
State
SequenceType. getUnknownState()
Get state corresponding to an unknownstatic 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 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 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.java.lang.String
StateClassification.Default. getSetName(State state)
java.lang.String
StateClassification. 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. 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
State. possiblyEqual(State other)
static State[]
Utils. reverse(State[] sequence)
static State[]
Utils. stripGaps(State[] sequence)
static java.lang.String
Utils. toString(State[] states)
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.static Sequence
Sequence. trimSequence(Sequence sequence, 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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