edu.sdsc.mbt.util
Class AminoAcidInfo

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

public class AminoAcidInfo

extends java.lang.Object

Provides static information about Amino Acids such as character codes, 3-letter codes, and full names.

Author:

John L. Moreland

See Also:

Constructor Summary

AminoAcidInfo()

Method Summary

static java.lang.String	getCodeFromLetter(byte letter) Returns the 3-letter code equivalent for the given letter.
static java.lang.String	getCodeFromLetter(java.lang.String letter) Returns the 3-letter code equivalent for the given letter.
static float	getHydrophobicityFromCode(java.lang.String code) Returns hydrophobicity given the 3-letter code.
static java.lang.String	getLetterFromCode(java.lang.String code) Returns the character code equivalent for the given 3-letter code.
static int	getNameCount() Returns the number of amino acid name tuples in the database.
static java.lang.String	getNameFromCode(java.lang.String code) Returns the full name equivalent for the given 3-letter code.
static java.lang.String	getNameFromLetter(byte letter) Returns the full name equivalent for the given letter.
static java.lang.String	getNameFromLetter(java.lang.String letter) Returns the full name equivalent for the given character code.

Methods inherited from class java.lang.Object

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

Constructor Detail

AminoAcidInfo

public AminoAcidInfo()

Method Detail

getNameCount

public static int getNameCount()

Returns the number of amino acid name tuples in the database.

getCodeFromLetter

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

Returns the 3-letter code equivalent for the given letter.

getCodeFromLetter

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

Returns the 3-letter code equivalent for the given letter.

getNameFromLetter

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

Returns the full name equivalent for the given letter.

getLetterFromCode

public static java.lang.String getLetterFromCode(java.lang.String code)

Returns the character code equivalent for the given 3-letter code.

getNameFromCode

public static java.lang.String getNameFromCode(java.lang.String code)

Returns the full name equivalent for the given 3-letter code.

getNameFromLetter

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

Returns the full name equivalent for the given character code.

getHydrophobicityFromCode

public static float getHydrophobicityFromCode(java.lang.String code)

Returns hydrophobicity given the 3-letter code.

Hydrophobicity of an amino acid may be obtained experimentally or may be computed using one of 37 different algorithms. There are many sources of hydrophobicity methods/scales: http://psyche.uthct.edu/shaun/SBlack/aagrease.html http://bioinformatics.weizmann.ac.il/hydroph/data_used.html http://prowl.rockefeller.edu/aainfo/hydro.htm http://blanco.biomol.uci.edu/hydrophobicity_scales.html etc...