org.strbio.mol
Class Nucleotide

java.lang.Object
  org.strbio.mol.Monomer
      org.strbio.mol.Nucleotide

All Implemented Interfaces:

DLinkedList.Node

public class Nucleotide
extends Monomer

Class to represent a single nucleotide

 Version 1.0, 8/17/01 - original version, based on org.strbio.mol.Residue
 

Version:

1.0, 8/17/01

Author:

JMC

Field Summary

static java.lang.String

oneLetter unlike Residue, don't make - a valid type

Fields inherited from class org.strbio.mol.Monomer

atoms, n, type

Constructor Summary

Nucleotide()

Nucleotide(char t)
Make a new nucleotide of a given type.

Nucleotide(Nucleotide q)
copy another residue, including the atoms.

Method Summary

static char	complement(char dna) complement of a dna base
static java.lang.String	complement(java.lang.String dna) complement of a dna chain
DLinkedList.Node	copyNode() copy contents of a residue
boolean	isGap() is the character used to represent a gap?
static boolean	isGap(char x) Is a character a gap code?
static boolean	isNuc(char x) Is your character a valid 1-letter code?
boolean	isValidType() is the character in 'type' valid for this residue?
static java.lang.String	reverse(java.lang.String dna) reverse
static java.lang.String	reverseComplement(java.lang.String dna) reverse complement

Methods inherited from class org.strbio.mol.Monomer

atomSearch, centerOfMass, centerOfMass, copyAtoms, copyDataFrom, isValidNonGap, molecularWeight, nAtoms, nAtomsWithCoord, next, prev, readAtomRecord, readFasta, readSeqRecord, rotate, setNext, setPrev, stripAllAtoms, stripAllBut, stripAllButFirstAtom, stripAtomsByName, transform, translate, typeName, writePDBAtom, writePts, writeSeqRecord, writeYAPFAtom

Methods inherited from class java.lang.Object

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

Field Detail

oneLetter

public static final java.lang.String oneLetter

unlike Residue, don't make - a valid type

See Also:

Constant Field Values

Constructor Detail

Nucleotide

public Nucleotide()

Nucleotide

public Nucleotide(char t)

Make a new nucleotide of a given type.

Nucleotide

public Nucleotide(Nucleotide q)

copy another residue, including the atoms. This makes another copy of the data.

Method Detail

complement

public static final char complement(char dna)

complement of a dna base

complement

public static final java.lang.String complement(java.lang.String dna)

complement of a dna chain

reverseComplement

public static final java.lang.String reverseComplement(java.lang.String dna)

reverse complement

reverse

public static final java.lang.String reverse(java.lang.String dna)

reverse

isNuc

public static final boolean isNuc(char x)

Is your character a valid 1-letter code?

isGap

public static final boolean isGap(char x)

Is a character a gap code?

copyNode

public DLinkedList.Node copyNode()

copy contents of a residue

Specified by:

copyNode in interface DLinkedList.Node

Overrides:

copyNode in class Monomer

isValidType

public boolean isValidType()

is the character in 'type' valid for this residue?

Overrides:

isValidType in class Monomer

isGap

public boolean isGap()

is the character used to represent a gap?

Overrides:

isGap in class Monomer