org.strbio.raf
Class RAFResidue

java.lang.Object
  org.strbio.raf.RAFResidue

public class RAFResidue
extends java.lang.Object

Class to handle modified residues. Based on LLC's map. Could extend Residue but doesn't need to.

   Version 1.0, 11/2/01 - original version
   

Version:

1.0, 11/2/01

Author:

JMC

Field Summary

static java.lang.String	oneLetter one letter code, in same order as 3-letter code.
static java.lang.String	threeLetter three letter code

Constructor Summary

RAFResidue()

Method Summary

void	addTranslation(java.lang.String x, char c) add a custom translation
boolean	customIs3Res(java.lang.String x) Is your string a valid 3-letter code?
char	customThree2One(java.lang.String x) Convert your 3-letter code into 1-letter code.
void	deleteTranslations() delete custom translations
static boolean	is3Res(java.lang.String x) Is your string a valid 3-letter code?
static char	three2One(java.lang.String x) Convert your 3-letter code into 1-letter code.

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

one letter code, in same order as 3-letter code.

See Also:

Constant Field Values

threeLetter

public static final java.lang.String threeLetter

three letter code

See Also:

Constant Field Values

Constructor Detail

RAFResidue

public RAFResidue()

Method Detail

is3Res

public static final boolean is3Res(java.lang.String x)

Is your string a valid 3-letter code? Note that it has to be capitalized.

three2One

public static final char three2One(java.lang.String x)
                            throws java.lang.IllegalArgumentException

Convert your 3-letter code into 1-letter code. Note that it has to be capitalized.

Throws:

java.lang.IllegalArgumentException - if your String is not a valid AA.

addTranslation

public final void addTranslation(java.lang.String x,
                                 char c)

add a custom translation

deleteTranslations

public final void deleteTranslations()

delete custom translations

customIs3Res

public final boolean customIs3Res(java.lang.String x)

Is your string a valid 3-letter code? Note that it has to be capitalized. Checks private mod table first.

customThree2One

public final char customThree2One(java.lang.String x)
                           throws java.lang.IllegalArgumentException

Convert your 3-letter code into 1-letter code. Note that it has to be capitalized. Checks private mod table after standard one.

Throws:

java.lang.IllegalArgumentException - if your String is not a valid AA.