jebl.evolution.sequences
Class State

java.lang.Object
  jebl.evolution.sequences.State

All Implemented Interfaces:

Comparable

Direct Known Subclasses:

AminoAcidState, CodonState, NucleotideState

public abstract class State
extends Object
implements Comparable

Author:

Andrew Rambaut, Alexei Drummond

Method Summary

int	compareTo(Object o)
boolean	equals(Object o)
Set<State>	getCanonicalStates()
String	getCode()
int	getIndex()
String	getName()
int	hashCode()
boolean	isAmbiguous()
abstract boolean	isGap()
boolean	possiblyEqual(State other)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Method Detail

getCode

public String getCode()

getIndex

public int getIndex()

getName

public String getName()

isAmbiguous

public boolean isAmbiguous()

getCanonicalStates

public Set<State> getCanonicalStates()

possiblyEqual

public boolean possiblyEqual(State other)

Parameters:

other - another state to check for the quality with.

Returns:

true if the other state is or possibly is equal to this state, taking ambiguities into account.

compareTo

public int compareTo(Object o)

Specified by:

compareTo in interface Comparable

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

isGap

public abstract boolean isGap()