mobios.type
Class DNA

java.lang.Object
  mobios.type.Sequence
      mobios.type.DNA

All Implemented Interfaces:

Serializable

public class DNA
extends Sequence

A DNA is a compact representation of a DNA sequence.

Version:

2003.06.06

Author:

Rui Mao, Willard

See Also:

Serialized Form

Nested Class Summary

static class

DNA.DNASymbol

Field Summary

static Alphabet	ALPHABET The alphabet of DNASymbols.
static WeightMatrix	EditDistanceWeightMatrix A complete EditDistanceWeightMatrix: { 0, 1, 1, 1, 0.5, 1, 0.5, 1, 0.5, 1, 1, 0.5, 0.5, 0.5, 0.5 },// A Adenine { 1, 0, 1, 1, 1, 0.5, 0.5, 1, 1, 0.5, 0.5, 1, 0.5, 0.5, 0.5 },// C Cytosine { 1, 1, 0, 1, 0.5, 1, 1, 0.5, 1, 0.5, 0.5, 0.5, 1, 0.5, 0.5 },// G Guanine { 1, 1, 1, 0, 1, 0.5, 1, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 1, 0.5 },// T Thymine { 0.5, 1, 0.5, 1, 0, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5 }, // R Purine (A or G) { 1, 0.5, 1, 0.5, 1, 0, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5 },// Y Pyrimidine (C, T, or U) { 0.5, 0.5, 1, 1, 0.5, 0.5, 0, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5 },// M C or A { 1, 1, 0.5, 0.5, 0.5, 0.5, 1, 0, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5 },// K T, U, or G { 0.5, 1, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 1, 0.5, 0.5, 0.5, 0.5, 0.5 },// W T, U, or A { 1, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 1, 0, 0.5, 0.5, 0.5, 0.5, 0.5 },// S C or G { 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 0.5, 0.5, 0.5, 0.5 },// B C, T, U, or G (not A) { 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 0.5, 0.5, 0.5 },// D A, T, U, or G (not C) { 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 0.5, 0.5 },// H A, T, U, or C (not G) { 0.5, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 0.5 },// V A, C, or G (not T, not U) { 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0 }// N Anybase (A,C,G,T,or U)
static Alphabet	SIMPLE_ALPHABET A simple alphabet of DNASymbols.
static WeightMatrix	SimpleDNAEditDistanceMatrix The SimpleDNAEditDistanceMatrix looks like: {0,1,1,1}, {1,0,1,1}, {1,1,0,1}, {1,1,1,0}
static WeightMatrix	SimpleWeightedDNAMatrix A simpleWeightedDNAMatrix.

Constructor Summary

DNA(String sequenceID, String sequence)
Construct a DNA.

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

The alphabet of DNASymbols. Includes all of the symbols in DNASymbol.

SIMPLE_ALPHABET

public static final Alphabet SIMPLE_ALPHABET

A simple alphabet of DNASymbols. Only includes A,C, T, and G.

SimpleDNAEditDistanceMatrix

public static final WeightMatrix SimpleDNAEditDistanceMatrix

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

SimpleWeightedDNAMatrix

public static final WeightMatrix SimpleWeightedDNAMatrix

A simpleWeightedDNAMatrix. { 0, 2 / 3, 2 / 3, 2 / 3 }, { 2 / 3, 0, 2 / 3, 2 / 3 }, { 2 / 3, 2 / 3, 0, 1 }, { 2 / 3, 2 / 3, 1, 0 } }

EditDistanceWeightMatrix

public static final WeightMatrix EditDistanceWeightMatrix

A complete EditDistanceWeightMatrix: { 0, 1, 1, 1, 0.5, 1, 0.5, 1, 0.5, 1, 1, 0.5, 0.5, 0.5, 0.5 },// A Adenine { 1, 0, 1, 1, 1, 0.5, 0.5, 1, 1, 0.5, 0.5, 1, 0.5, 0.5, 0.5 },// C Cytosine { 1, 1, 0, 1, 0.5, 1, 1, 0.5, 1, 0.5, 0.5, 0.5, 1, 0.5, 0.5 },// G Guanine { 1, 1, 1, 0, 1, 0.5, 1, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 1, 0.5 },// T Thymine { 0.5, 1, 0.5, 1, 0, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5 }, // R Purine (A or G) { 1, 0.5, 1, 0.5, 1, 0, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5 },// Y Pyrimidine (C, T, or U) { 0.5, 0.5, 1, 1, 0.5, 0.5, 0, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5 },// M C or A { 1, 1, 0.5, 0.5, 0.5, 0.5, 1, 0, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5 },// K T, U, or G { 0.5, 1, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 1, 0.5, 0.5, 0.5, 0.5, 0.5 },// W T, U, or A { 1, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 1, 0, 0.5, 0.5, 0.5, 0.5, 0.5 },// S C or G { 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 0.5, 0.5, 0.5, 0.5 },// B C, T, U, or G (not A) { 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 0.5, 0.5, 0.5 },// D A, T, U, or G (not C) { 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 0.5, 0.5 },// H A, T, U, or C (not G) { 0.5, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0, 0.5 },// V A, C, or G (not T, not U) { 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0 }// N Anybase (A,C,G,T,or U)

Constructor Detail

DNA

public DNA(String sequenceID,
           String sequence)

Construct a DNA.

Parameters:

sequenceID - the sequence ID of the DNA sequence. can be the accession number, or a user assigned ID.

sequence - a string representing a DNA 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