jebl.evolution.sequences
Interface Sequence

All Superinterfaces:

Attributable, Comparable

All Known Implementing Classes:

BasicSequence, ConsensusSequence, FilteredSequence, GaplessSequence, TranslatedSequence

public interface Sequence
extends Attributable, Comparable

A biomolecular sequence.

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

Nested classes/interfaces inherited from interface jebl.util.Attributable

Attributable.Utils

Method Summary

int	getLength() Get the length of the sequence
SequenceType	getSequenceType()
State	getState(int site)
byte[]	getStateIndices()
State[]	getStates()
String	getString()
Taxon	getTaxon()

Methods inherited from interface jebl.util.Attributable

getAttribute, getAttributeMap, getAttributeNames, removeAttribute, setAttribute

Methods inherited from interface java.lang.Comparable

compareTo

Method Detail

getTaxon

Taxon getTaxon()

Returns:

the taxon that this sequence represents (primarily used to match sequences with tree nodes)

getSequenceType

SequenceType getSequenceType()

Returns:

the type of symbols that this sequence is made up of.

getString

String getString()

Returns:

a string representing the sequence of symbols.

getStates

State[] getStates()

Returns:

an array of state objects.

getStateIndices

byte[] getStateIndices()

Returns:

an array of state indices.

getState

State getState(int site)

Returns:

the state at site.

getLength

int getLength()

Get the length of the sequence

Returns:

the length