org.concord.biologica.engine
Class Base

java.lang.Object
  |
  +--org.concord.biologica.engine.Base

public final class Base

extends java.lang.Object

This class represents a Base object, as in the base purines and pyrimidines which form DNA and RNA.

This class contains mainly static methods.

Version:

$Revision: 1.1.1.1 $ $Date: 2001/04/28 00:39:11 $

Author:

$Author: ed $

Field Summary

static byte	ADENINE A purine which links with thymine in DNA and with uracil in RNA.
static byte	CYTOSINE A purine which links with guanine in DNA and RNA.
static byte	GUANINE A pyrimidine which links with cytosine in DNA and RNA.
static int	IN_DNA Used in various methods to indicate a base or some nucleic acid is in DNA.
static int	IN_DNA_OR_RNA Used in various methods to indicate a base or some nucleic acid is in DNA or RNA.
static java.lang.String	IN_DNA_STRING
static int	IN_RNA Used in various methods to indicate a base or some nucleic acid is in RNA.
static java.lang.String	IN_RNA_STRING
static byte	THYMINE A pyrimidine which links with adenine only in DNA, not RNA.
static byte	URACIL A pyrimidine which links with adenine only in RNA, not DNA.

Constructor Summary

Base()

Method Summary

static int	getInDNAorRNAasInt(java.lang.String inDNAorRNA) Convert an int inDNAorRNA value to a String.
static java.lang.String	getInDNAorRNAasString(int inDNAorRNA) Convert an int inDNAorRNA value to a String.
static byte	getPairBase(byte aBase, int inDNAorRNA) Get pair base value in either DNA or RNA.
static boolean	isValidBase(byte aBase, int inDNAorRNA) Determines if a base value is valid.

Methods inherited from class java.lang.Object

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

Field Detail

URACIL

public static final byte URACIL

A pyrimidine which links with adenine only in RNA, not DNA. Don't change the value of this argument without being sure the array mapping codons to amino acids in Codon.java is okay.

CYTOSINE

public static final byte CYTOSINE

A purine which links with guanine in DNA and RNA. Don't change the value of this argument without being sure the array mapping codons to amino acids in Codon.java is okay.

ADENINE

public static final byte ADENINE

A purine which links with thymine in DNA and with uracil in RNA. Don't change the value of this argument without being sure the array mapping codons to amino acids in Codon.java is okay.

GUANINE

public static final byte GUANINE

A pyrimidine which links with cytosine in DNA and RNA. Don't change the value of this argument without being sure the array mapping codons to amino acids in Codon.java is okay.

THYMINE

public static final byte THYMINE

A pyrimidine which links with adenine only in DNA, not RNA.

IN_DNA

public static final int IN_DNA

Used in various methods to indicate a base or some nucleic acid is in DNA.

IN_DNA_STRING

public static final java.lang.String IN_DNA_STRING

IN_RNA

public static final int IN_RNA

Used in various methods to indicate a base or some nucleic acid is in RNA.

IN_RNA_STRING

public static final java.lang.String IN_RNA_STRING

IN_DNA_OR_RNA

public static final int IN_DNA_OR_RNA

Used in various methods to indicate a base or some nucleic acid is in DNA or RNA.

Constructor Detail

Base

public Base()

Method Detail

isValidBase

public static boolean isValidBase(byte aBase,
                                  int inDNAorRNA)

Determines if a base value is valid.

Parameters:

aBase - byte - a base value

inDNAorRNA - int - indicates if base in DNA or RNA is sought

Returns:

boolean - true if aBase is valid or false if not valid

getPairBase

public static byte getPairBase(byte aBase,
                               int inDNAorRNA)

Get pair base value in either DNA or RNA.

Parameters:

aBase - byte - base value for which pair base is sought, must be a valid base value

inDNAorRNA - int - indicates if pair base in DNA or RNA is sought

Returns:

byte - pair base value

Throws:

java.lang.IllegalArgumentException - - input arguments not valid

getInDNAorRNAasString

public static final java.lang.String getInDNAorRNAasString(int inDNAorRNA)

Convert an int inDNAorRNA value to a String.

Returns:

String - in DNA or RNA as a string

getInDNAorRNAasInt

public static final int getInDNAorRNAasInt(java.lang.String inDNAorRNA)

Convert an int inDNAorRNA value to a String.

Returns:

String - in DNA or RNA as a string