|
Mobios v0.91 | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object mobios.type.Sequence mobios.type.DNA
public class DNA
A DNA
is a compact representation of a DNA sequence.
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 |
---|
public static final Alphabet ALPHABET
public static final Alphabet SIMPLE_ALPHABET
public static final WeightMatrix SimpleDNAEditDistanceMatrix
public static final WeightMatrix SimpleWeightedDNAMatrix
public static final WeightMatrix EditDistanceWeightMatrix
Constructor Detail |
---|
public DNA(String sequenceID, String sequence)
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 |
---|
public Alphabet getAlphabet()
getAlphabet
in class Sequence
public Symbol get(int index)
get
in class Sequence
index
- an integer index value
Symbol
corresponding to that index.public String toString()
toString
in class Sequence
|
Mobios v0.91 | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |