ca.ucalgary.seahawk.util
Class Sequence

java.lang.Object
  ca.ucalgary.seahawk.util.Sequence

public class Sequence
extends Object

Utility methods to report properties of DNA and protein sequence.

Constructor Summary

Sequence()

Method Summary

static boolean	isDNA(String sequence)
static boolean	isNucleicAcid(String sequence) Case insensitve search for DNA or RNA like characters in the provid3ed string
static boolean	isProtein(String sequence)
static boolean	isRNA(String sequence)
static String	reverseComplement(String sequence)

Methods inherited from class java.lang.Object

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

Constructor Detail

Sequence

public Sequence()

Method Detail

isNucleicAcid

public static boolean isNucleicAcid(String sequence)

Case insensitve search for DNA or RNA like characters in the provid3ed string

Returns:

true if ACGTUX comprise > 2/3 of the sequence, and all non-IUPAC letters comprise less than 5%

isDNA

public static boolean isDNA(String sequence)

isRNA

public static boolean isRNA(String sequence)

isProtein

public static boolean isProtein(String sequence)

reverseComplement

public static String reverseComplement(String sequence)