javagene.seq
Class Nucleotide

java.lang.Object
  javagene.seq.Nucleotide

public class Nucleotide
extends java.lang.Object

A nucleotide object, with Dna/Rna utility methods. Understands both the standard A C T G U and the "ambiguous" IUPAC nucleotides, ie, R Y B D H V N.

Nested Class Summary

static class

Nucleotide.Type Sequence type: DNA or RNA.

Field Summary

static Nucleotide	A
static Nucleotide	B G or C or T/U (Anything but A).
static Nucleotide	C
static Nucleotide	D A or G or T/U (Anything but C).
static Nucleotide	G
static Nucleotide	H A or C or T/U (Anything but G).
static Nucleotide	N Any nucleotide.
static Nucleotide	R A or G.
static Nucleotide	T
static Nucleotide	U
static Nucleotide	V A or C or G (Anything but T/U).
static Nucleotide	Y C or T/U.

Method Summary

static java.lang.String	complement(java.lang.String s, Nucleotide.Type type) Complement a string of IUPAC nucleotides.
static java.lang.String	dnaComplement(java.lang.String s) Complement a string of IUPAC DNA nucleotides (output A C T G only).
static java.lang.String	dnaReverseComplement(java.lang.String s) Reverse and complement a string of IUPAC DNA nucleotides (A C T G only).
static boolean	isComplement(char a, char b) Check if two symbols complement one another.
static boolean	isWobbleComplement(char a, char b) Check if two symbols complement one another, accepting wobble pairs (G-U, G-T) in addition to standard (A-T, A-U, G-C) pairs.
static Nucleotide	lookup(java.lang.String str) Find the Nucleotide object corresponding to an IUPAC symbol.
boolean	matches(Nucleotide n) Check if a Nucleotide object matches this object, allowing ambiguous matches.
boolean	matches(java.lang.String s) Check if a IUPAC nucleotide symbol matches this object, allowing ambiguous matches.
static java.lang.String	reverseComplement(java.lang.String s, Nucleotide.Type type) Reverse and complement a string of IUPAC DNA nucleotides.
static java.lang.String	rnaComplement(java.lang.String s) Complement a string of IUPAC RNA nucleotides (output A C U G only).
static java.lang.String	rnaReverseComplement(java.lang.String s) Reverse and complement a string of IUPAC RNA nucleotides (A C U G only).
java.lang.String	toString() Get IUPAC representation.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

A

public static final Nucleotide A

B

public static final Nucleotide B

G or C or T/U (Anything but A).

C

public static final Nucleotide C

D

public static final Nucleotide D

A or G or T/U (Anything but C).

G

public static final Nucleotide G

H

public static final Nucleotide H

A or C or T/U (Anything but G).

N

public static final Nucleotide N

Any nucleotide.

R

public static final Nucleotide R

A or G.

T

public static final Nucleotide T

U

public static final Nucleotide U

V

public static final Nucleotide V

A or C or G (Anything but T/U).

Y

public static final Nucleotide Y

C or T/U.

Method Detail

complement

public static java.lang.String complement(java.lang.String s,
                                          Nucleotide.Type type)

Complement a string of IUPAC nucleotides.

Parameters:

s - The string of one-letter upper or lower case IUPAC nucleotides to complement.

type - Nucleotide.Type.DNA or Nucleotide.Type.RNA.

Returns:

A complemented string. Case is preserved.

dnaComplement

public static java.lang.String dnaComplement(java.lang.String s)

Complement a string of IUPAC DNA nucleotides (output A C T G only).

Parameters:

s - The string of one-letter upper or lower case IUPAC nucleotides to complement.

Returns:

A complemented string, ie A->T, T->A, C->G, G->C, U->A. Case is preserved.

dnaReverseComplement

public static java.lang.String dnaReverseComplement(java.lang.String s)

Reverse and complement a string of IUPAC DNA nucleotides (A C T G only).

Parameters:

s - The string of one-letter upper or lower case IUPAC nucleotides to reverse and complement.

Returns:

The reverse-complemented string, ie A->T, T->A, C->G, G->C. Case is preserved.

isComplement

public static boolean isComplement(char a,
                                   char b)

Check if two symbols complement one another. Accepts only standard (A-T, A-U, G-C) pairs.

Parameters:

a - A nucleotide symbol, either upper or lower case.

b - A nucleotide symbol, either upper or lower case.

Returns:

True if the nucleotides complement one another.

isWobbleComplement

public static boolean isWobbleComplement(char a,
                                         char b)

Check if two symbols complement one another, accepting wobble pairs (G-U, G-T) in addition to standard (A-T, A-U, G-C) pairs.

Parameters:

a - A nucleotide symbol, either upper or lower case.

b - A nucleotide symbol, either upper or lower case.

Returns:

True if the nucleotides complement one another.

lookup

public static Nucleotide lookup(java.lang.String str)
                         throws java.lang.IllegalArgumentException

Find the Nucleotide object corresponding to an IUPAC symbol.

Parameters:

str - One-letter IUPAC nucleotide symbol, either upper or lower case.

Returns:

The corresponding Nucleotide object.

Throws:

java.lang.IllegalArgumentException - The parameter did not match a known nucleotide.

matches

public boolean matches(Nucleotide n)

Check if a Nucleotide object matches this object, allowing ambiguous matches. The nucleotides match if their symbol sets overlap. For example Nucleotide.Y and Nucleotide.T match because Y means "C or T", so "T" is in both sets.

Parameters:

n - The other nucleotide object.

Returns:

True if the two symbol sets overlap.

matches

public boolean matches(java.lang.String s)

Check if a IUPAC nucleotide symbol matches this object, allowing ambiguous matches. The nucleotides match if their symbol sets overlap. For example Nucleotide.Y and symbol "T" match because Y means "C or T", so "T" is in both sets.

Parameters:

s - The one-letter symbol, upper or lower case.

Returns:

True if the two symbol sets overlap.

reverseComplement

public static java.lang.String reverseComplement(java.lang.String s,
                                                 Nucleotide.Type type)

Reverse and complement a string of IUPAC DNA nucleotides.

Parameters:

s - The string of one-letter upper or lower case IUPAC nucleotides to reverse complement.

type - Nucleotide.Type.DNA or Nucleotide.Type.RNA.

Returns:

A complemented string. Case is preserved.

rnaComplement

public static java.lang.String rnaComplement(java.lang.String s)

Complement a string of IUPAC RNA nucleotides (output A C U G only).

Parameters:

s - The string of one-letter upper or lower case IUPAC nucleotides to complement.

Returns:

A complemented string, ie A->U, U->A, C->G, G->C, T->A. Case is preserved.

rnaReverseComplement

public static java.lang.String rnaReverseComplement(java.lang.String s)

Reverse and complement a string of IUPAC RNA nucleotides (A C U G only).

Parameters:

s - The string of one-letter upper or lower case IUPAC nucleotides to reverse and complement.

Returns:

The reverse-complemented string, ie A->U, U->A, C->G, G->C. Case is preserved.

toString

public java.lang.String toString()

Get IUPAC representation.

Overrides:

toString in class java.lang.Object

Returns:

One-letter uppercase IUPAC represenation.