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Packages that use State | |
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jebl.evolution.alignments | |
jebl.evolution.parsimony | |
jebl.evolution.sequences |
Uses of State in jebl.evolution.alignments |
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Methods in jebl.evolution.alignments that return State | |
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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 | |
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java.util.List<State> |
Pattern.getStates()
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java.util.Set<State> |
Pattern.getStateSet()
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Methods in jebl.evolution.alignments with parameters of type State | |
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double |
Pattern.getStateFrequency(State state)
Returns the frequent of the given state in this pattern |
Uses of State in jebl.evolution.parsimony |
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Methods in jebl.evolution.parsimony that return State | |
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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 |
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Subclasses of State in jebl.evolution.sequences | |
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class |
AminoAcidState
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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 | |
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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 |
FilteredSequence.getState(int site)
|
State |
SequenceType.getState(int index)
Get state corresponding to a state index |
State |
BasicSequence.getState(int site)
|
State |
Sequence.getState(int site)
|
State |
CanonicalSequence.getState(int site)
|
State |
SequenceType.getState(java.lang.String code)
Get state corresponding to a string code |
State[] |
FilteredSequence.getStates()
|
State[] |
BasicSequence.getStates()
|
State[] |
Sequence.getStates()
|
State[] |
CanonicalSequence.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 | |
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java.util.List<? extends State> |
SequenceType.getCanonicalStates()
Get a list of canonical states ordered by their indices. |
java.util.Set<State> |
State.getCanonicalStates()
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static java.util.List<State> |
AminoAcids.getCanonicalStates()
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static java.util.List<State> |
Codons.getCanonicalStates()
|
java.util.List<? extends State> |
SequenceType.getStates()
Get a list of states ordered by their indices. |
static java.util.List<State> |
Nucleotides.getStates()
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static java.util.List<State> |
Codons.getStates()
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java.util.Set<State> |
StateClassification.getStateSet(java.lang.String setName)
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java.util.Set<State> |
StateClassification.Default.getStateSet(java.lang.String setName)
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Methods in jebl.evolution.sequences with parameters of type State | |
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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)
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java.lang.String |
StateClassification.Default.getSetName(State state)
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static byte[] |
Utils.getStateIndices(State[] sequence)
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static boolean |
Nucleotides.isATstate(State state)
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boolean |
SequenceType.isGap(State state)
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static boolean |
Nucleotides.isGCstate(State state)
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static boolean |
Nucleotides.isPossibleTransition(State s1,
State s2)
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static boolean |
Nucleotides.isPossibleTransversion(State s1,
State s2)
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static boolean |
Nucleotides.isPurine(State state)
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static boolean |
Nucleotides.isPyrimidine(State state)
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static boolean |
Nucleotides.isTransition(State state1,
State state2)
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static boolean |
Nucleotides.isTransversion(State state1,
State state2)
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boolean |
SequenceType.isUnknown(State state)
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boolean |
State.possiblyEqual(State other)
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static State[] |
Utils.reverse(State[] sequence)
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static State[] |
Utils.stripGaps(State[] sequence)
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static java.lang.String |
Utils.toString(State[] states)
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static AminoAcidState[] |
Utils.translate(State[] states,
GeneticCode geneticCode)
Translates each of a given sequence of NucleotideState s or CodonState s
to the AminoAcidState corresponding to it under the given genetic code. |
Constructors in jebl.evolution.sequences with parameters of type State | |
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BasicSequence(SequenceType sequenceType,
Taxon taxon,
State[] states)
Creates a sequence with a name corresponding to the taxon name |
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CanonicalSequence(SequenceType sequenceType,
Taxon taxon,
State[] states)
Creates a sequence with a name corresponding to the taxon name |
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StateClassification.Default(java.lang.String name,
java.lang.String[] setNames,
State[][] stateSets)
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