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 Pattern.getState(int index)
          Get the state for the ith taxon
 State ConsensusSequence.getState(int site)
           
 State[] ConsensusSequence.getStates()
           
 

Methods in jebl.evolution.alignments that return types with arguments of type State
 java.util.List<State> Pattern.getStates()
           
 java.util.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
          As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - see Codons.
 class NucleotideState
           
 

Methods in jebl.evolution.sequences that return State
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 gap
 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 CanonicalSequence.getState(int site)
           
 State BasicSequence.getState(int site)
           
 State FilteredSequence.getState(int site)
           
 State Sequence.getState(int site)
           
 State SequenceType.getState(java.lang.String code)
          Get state corresponding to a string code
 State[] CanonicalSequence.getStates()
           
 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(java.lang.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
 java.util.List<? extends State> SequenceType.getCanonicalStates()
          Get a list of canonical states ordered by their indices.
static java.util.List<State> AminoAcids.getCanonicalStates()
           
static java.util.List<State> Codons.getCanonicalStates()
           
 java.util.Set<State> State.getCanonicalStates()
           
 java.util.List<? extends State> SequenceType.getStates()
          Get a list of states ordered by their indices.
static java.util.List<State> Nucleotides.getStates()
           
static java.util.List<State> Codons.getStates()
           
 java.util.Set<State> StateClassification.getStateSet(java.lang.String setName)
           
 java.util.Set<State> StateClassification.Default.getStateSet(java.lang.String setName)
           
 

Methods in jebl.evolution.sequences with parameters of type State
 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.getSetName(State state)
           
 java.lang.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.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 of NucleotideStates or CodonStates to the AminoAcidState corresponding to it under the given genetic code.
 

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
CanonicalSequence(SequenceType sequenceType, Taxon taxon, State[] states)
          Creates a sequence with a name corresponding to the taxon name
StateClassification.Default(java.lang.String name, java.lang.String[] setNames, State[][] stateSets)
           
 



http://code.google.com/p/jebl2/