util.bio.digest
Class REDigest

java.lang.Object
  util.bio.digest.REDigest

public class REDigest

extends java.lang.Object

StandAlone class to perform a restriction digestion on a sequence, a hack, uses as a template.

Constructor Summary

REDigest()

Method Summary

static java.lang.String	getRestrictionMapString(java.lang.String seq, Enzyme[] enzymes)
static void	main(java.lang.String[] args)
static Enzyme[]	restrictionMap(java.lang.String DNA, Enzyme[] e) Runs thru an enzyme array attempting to cut a particular sequence
static java.util.ArrayList	restrictionMapHTML(java.lang.String DNA, Enzyme[] e) Returns an arraylist of enzymes found to cut the sequence
static java.lang.String	restrictionMapList(java.lang.String DNA, Enzyme[] e) Restriction map a sequence.

Methods inherited from class java.lang.Object

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

Constructor Detail

REDigest

public REDigest()

Method Detail

main

public static void main(java.lang.String[] args)

restrictionMapHTML

public static java.util.ArrayList restrictionMapHTML(java.lang.String DNA,
                                                     Enzyme[] e)

Returns an arraylist of enzymes found to cut the sequence

getRestrictionMapString

public static java.lang.String getRestrictionMapString(java.lang.String seq,
                                                       Enzyme[] enzymes)

restrictionMap

public static Enzyme[] restrictionMap(java.lang.String DNA,
                                      Enzyme[] e)

Runs thru an enzyme array attempting to cut a particular sequence

restrictionMapList

public static java.lang.String restrictionMapList(java.lang.String DNA,
                                                  Enzyme[] e)

Restriction map a sequence. Makes an ordered list of enzymes. First by number of cuts, second alphabetically.