jebl.evolution.sequences

Class State

java.lang.Object

jebl.evolution.sequences.State

All Implemented Interfaces:

java.lang.Comparable

Direct Known Subclasses:

AminoAcidState, CodonState, NucleotideState

public abstract class State
extends java.lang.Object
implements java.lang.Comparable

Version:

$Id: State.java 1002 2009-05-27 03:33:19Z matt_kearse $

Author:

Andrew Rambaut, Alexei Drummond

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(java.lang.Object o)
double	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.util.Set<State>	getCanonicalStates()
java.lang.String	getCode() Returns the 1 letter code for this state.
java.lang.String	getFullName() A descriptive name for this state.
int	getIndex()
java.lang.String	getName() Deprecated. you probably want to use getFullName() or getCode().
boolean	isAmbiguous()
abstract boolean	isGap()
boolean	possiblyEqual(State other)
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Method Detail

getCode

public java.lang.String getCode()

Returns the 1 letter code for this state.

Returns:

the 1 letter code for this state.

getIndex

public int getIndex()

getFullName

public java.lang.String getFullName()

A descriptive name for this state. e.g. "Phenylalanine" or "Adenine".

Returns:

A descriptive name for this state. e.g. "Phenylalanine" or "Adenine".

getName

@Deprecated
public java.lang.String getName()

Deprecated. you probably want to use getFullName() or getCode().

The 1 letter code (for legacy purposes). Same as getCode()

Returns:

The 1 letter code (for legacy purposes). Same as getCode()

See Also:

getFullName()

isAmbiguous

public boolean isAmbiguous()

getCanonicalStates

public java.util.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, i.e. if the ambiguity sets of this and the other state intersect.

compareTo

public int compareTo(java.lang.Object o)

Specified by:

compareTo in interface java.lang.Comparable

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

isGap

public abstract boolean isGap()

fractionEqual

public double 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. 2 identical non-ambigoues states will 1. e.g. for Nucleotides R,A = 0.5 R,G = 0.5 R,M = 0.25

Parameters:

other - another state to compare with

Returns:

the fraction of canonical states that the 2 potentially ambiguous states have in common between 0 and 1.