jebl.evolution.sequences
Interface SequenceType

public interface SequenceType

Interface for sequences data types.

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

static class

SequenceType.Utils

Field Summary

static SequenceType	AMINO_ACID
static SequenceType	CODON
static SequenceType	NUCLEOTIDE

Method Summary

int	getCanonicalStateCount() Get number of canonical states
List<? extends State>	getCanonicalStates() Get a list of canonical states ordered by their indices.
int	getCodeLength()
State	getGapState() Get state corresponding to a gap
String	getName() name of data type
String	getNexusDataType()
State	getState(char code)
State	getState(int index) Get state corresponding to a state index
State	getState(String code) Get state corresponding to a string code
int	getStateCount() Get number of states including ambiguous states
List<? extends State>	getStates() Get a list of states ordered by their indices.
State	getUnknownState() Get state corresponding to an unknown
boolean	isGap(State state)
boolean	isUnknown(State state)
State[]	toStateArray(byte[] indexArray) Converts an array of state indices into an array of State objects for this SequenceType
State[]	toStateArray(String sequenceString) Converts a string of state codes into an array of State objects for this SequenceType

Field Detail

NUCLEOTIDE

static final SequenceType NUCLEOTIDE

AMINO_ACID

static final SequenceType AMINO_ACID

CODON

static final SequenceType CODON

Method Detail

getStateCount

int getStateCount()

Get number of states including ambiguous states

Returns:

number of states

getStates

List<? extends State> getStates()

Get a list of states ordered by their indices.

Returns:

a list of states

getCanonicalStateCount

int getCanonicalStateCount()

Get number of canonical states

Returns:

number of states

getCanonicalStates

List<? extends State> getCanonicalStates()

Get a list of canonical states ordered by their indices.

Returns:

a list of states

getState

State getState(String code)

Get state corresponding to a string code

Parameters:

code - a string code

Returns:

the state

getState

State getState(char code)

getCodeLength

int getCodeLength()

Returns:

the length, in characters, of a state, when encoded as a string. i.e. 1 for Nucleotides and AminoAcids and 3 for Codons.

getState

State getState(int index)

Get state corresponding to a state index

Parameters:

index - a state index

Returns:

the state

getUnknownState

State getUnknownState()

Get state corresponding to an unknown

Returns:

the state

getGapState

State getGapState()

Get state corresponding to a gap

Returns:

state

isUnknown

boolean isUnknown(State state)

Returns:

true if this state is an unknown state

isGap

boolean isGap(State state)

Returns:

true if this state is a gap

getName

String getName()

name of data type

Returns:

string describing the data type

getNexusDataType

String getNexusDataType()

Returns:

datatype inside a nexus characters block, if any.

toStateArray

State[] toStateArray(String sequenceString)

Converts a string of state codes into an array of State objects for this SequenceType

Parameters:

sequenceString -

Returns:

the State array

toStateArray

State[] toStateArray(byte[] indexArray)

Converts an array of state indices into an array of State objects for this SequenceType

Parameters:

indexArray -

Returns:

the State array