util.bio.digest
Class REDigest

java.lang.Object
  extended byutil.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.