Package | Description |
---|---|
jebl.evolution.alignments | |
jebl.evolution.parsimony | |
jebl.evolution.sequences |
Modifier and Type | Method and Description |
---|---|
static State[] |
ConsensusSequence.constructConsensus(Alignment source,
boolean includeAmbiguities) |
State |
Pattern.getMostFrequentState()
Returns the most frequent state in this pattern
|
State |
Pattern.getMostFrequentState(boolean includeAmbiguous)
Returns the most frequent state in this pattern, optionally including ambiguous states
|
State |
ConsensusSequence.getState(int site) |
State |
Pattern.getState(int index)
Get the state for the ith taxon
|
State[] |
ConsensusSequence.getStates() |
Modifier and Type | Method and Description |
---|---|
java.util.List<State> |
Pattern.getStates() |
java.util.Set<State> |
Pattern.getStateSet() |
Modifier and Type | Method and Description |
---|---|
int |
Pattern.getStateCount(State state)
Returns the count of the given state in this pattern
|
double |
Pattern.getStateFrequency(State state)
Returns the frequent of the given state in this pattern
|
Modifier and Type | Method and Description |
---|---|
State[] |
ParsimonyCriterion.getStates(Tree tree,
Node node)
Returns the reconstructed character states for a given node in the tree.
|
State[] |
FitchParsimony.getStates(Tree tree,
Node node)
Returns the reconstructed character states for a given node in the tree.
|
Modifier and Type | Class and Description |
---|---|
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 |
Modifier and Type | Method and 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 gap
|
State |
SequenceType.getState(char code)
Get state whose code is the one-character string consisting only of code.
|
State |
CanonicalSequence.getState(int site) |
State |
Sequence.getState(int site) |
State |
BasicSequence.getState(int site) |
State |
CodonSequence.getState(int site) |
State |
SequenceType.getState(int index)
Get state corresponding to a state index
|
State |
FilteredSequence.getState(int site) |
State |
SequenceType.getState(java.lang.String code)
Get state corresponding to a string code
|
State[] |
CanonicalSequence.getStates() |
State[] |
Sequence.getStates() |
State[] |
BasicSequence.getStates() |
State[] |
CodonSequence.getStates() |
State[] |
FilteredSequence.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
|
Modifier and Type | Method and Description |
---|---|
static java.util.List<State> |
Codons.getCanonicalStates() |
java.util.Set<State> |
State.getCanonicalStates() |
static java.util.List<State> |
AminoAcids.getCanonicalStates() |
java.util.List<? extends State> |
SequenceType.getCanonicalStates()
Get a list of canonical states ordered by their indices.
|
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.getStateSet(java.lang.String setName) |
java.util.Set<State> |
StateClassification.Default.getStateSet(java.lang.String setName) |
Modifier and Type | Method and 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.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
NucleotideState s or CodonState s
to the AminoAcidState corresponding to it under the given genetic code. |
static AminoAcidState[] |
Utils.translate(State[] states,
GeneticCode geneticCode,
int readingFrame)
Translates each of a given sequence of
NucleotideState s or CodonState s
to the AminoAcidState corresponding to it under the given genetic code. |
Constructor and Description |
---|
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
|
CodonSequence(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/