edu.sdsc.mbt.util
Class NucleicAcidInfo

java.lang.Object
  edu.sdsc.mbt.util.NucleicAcidInfo

public class NucleicAcidInfo

extends java.lang.Object

Provides static information about Nucleic Acids for DNA/RNA such as base character codes, base names, and base pairing rules.

Author:

John L. Moreland

See Also:

Field Summary

static java.lang.String[]	dna_bases Letter codes of the 4 nitrogenous bases for DNA.
static java.lang.String[]	rna_bases Letter codes of the 4 nitrogenous bases for RNA.

Constructor Summary

NucleicAcidInfo()

Method Summary

static int	getBaseCount() Returns the number of nucleic acid base name tuples in the database.
static java.lang.String	getCodeFromLetter(byte letter)
static java.lang.String	getDnaPairing(java.lang.String letter) Returns the base pair pairing for DNA.
static java.lang.String	getLetterFromName(java.lang.String name) Returns the full name equivalent for the given character code.
static java.lang.String	getNameFromLetter(java.lang.String letter) Returns the nucleic acid base name equivalent for the given letter.
static java.lang.String	getRnaDnaPairing(java.lang.String letter) Returns the base pair pairing for RNA-DNA interaction.
static java.lang.String	getRnaRnaPairing(java.lang.String letter) Returns the base pair pairing for RNA-RNA interaction.

Methods inherited from class java.lang.Object

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

Field Detail

dna_bases

public static final java.lang.String[] dna_bases

Letter codes of the 4 nitrogenous bases for DNA.

rna_bases

public static final java.lang.String[] rna_bases

Letter codes of the 4 nitrogenous bases for RNA.

Constructor Detail

NucleicAcidInfo

public NucleicAcidInfo()

Method Detail

getBaseCount

public static int getBaseCount()

Returns the number of nucleic acid base name tuples in the database.

getNameFromLetter

public static java.lang.String getNameFromLetter(java.lang.String letter)

Returns the nucleic acid base name equivalent for the given letter.

getLetterFromName

public static java.lang.String getLetterFromName(java.lang.String name)

Returns the full name equivalent for the given character code.

getDnaPairing

public static java.lang.String getDnaPairing(java.lang.String letter)

Returns the base pair pairing for DNA.

getRnaDnaPairing

public static java.lang.String getRnaDnaPairing(java.lang.String letter)

Returns the base pair pairing for RNA-DNA interaction.

getRnaRnaPairing

public static java.lang.String getRnaRnaPairing(java.lang.String letter)

Returns the base pair pairing for RNA-RNA interaction.

getCodeFromLetter

public static java.lang.String getCodeFromLetter(byte letter)