mobios.type
Class RNA

java.lang.Object
  mobios.type.Sequence
      mobios.type.RNA

All Implemented Interfaces:

Serializable

public class RNA
extends Sequence

A compact representation of an RNA sequence.

Version:

2006.07.31

Author:

Rui Mao. Willard

See Also:

Serialized Form

Nested Class Summary

static class

RNA.RNASymbol TODO

Field Summary

static Alphabet	ALPHABET
static WeightMatrix	SimpleEditDistanceMatrix The SimpleEditDistanceMatrix looks like: {0,1,1,1}, {1,0,1,1}, {1,1,0,1}, {1,1,1,0}

Constructor Summary

RNA(String sequenceID, String sequence)

Method Summary

Symbol	get(int index)
Alphabet	getAlphabet()
String	toString()

Methods inherited from class mobios.type.Sequence

getSequenceID, numFragments, size

Methods inherited from class java.lang.Object

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

Field Detail

ALPHABET

public static final Alphabet ALPHABET

SimpleEditDistanceMatrix

public static final WeightMatrix SimpleEditDistanceMatrix

The SimpleEditDistanceMatrix looks like: {0,1,1,1}, {1,0,1,1}, {1,1,0,1}, {1,1,1,0}

Constructor Detail

RNA

public RNA(String sequenceID,
           String sequence)

Parameters:

sequenceID -

sequence -

Method Detail

getAlphabet

public Alphabet getAlphabet()

Specified by:

getAlphabet in class Sequence

Returns:

get

public Symbol get(int index)

Specified by:

get in class Sequence

Parameters:

index - an integer index value

Returns:

the Symbol corresponding to that index.

toString

public String toString()

Specified by:

toString in class Sequence