Package org.biojava.nbio.core.util

Class SequenceTools

java.lang.Object

org.biojava.nbio.core.util.SequenceTools

public class SequenceTools
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	NUCLEOTIDE_LETTERS

Constructor Summary

Constructors

Constructor	Description
SequenceTools()

Method Summary

Modifier and Type	Method	Description
static boolean	equalLengthSequences(ProteinSequence[] sequences)	A method to check whether an array of sequences contains at least two sequences having an equal length.
Sequence<?>	getSequenceFromString(String sequence)
static boolean	isNucleotideSequence(String sequence)
static int	percentNucleotideSequence(String sequence)
static String	permuteCyclic(String string, int n)	Cyclically permute the characters in string forward by n elements.
static <T> void	permuteCyclic(T[] array, T[] fill, int n)	Cyclically permute array forward by n elements.

Methods inherited from class java.lang.Object

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

Field Detail

NUCLEOTIDE_LETTERS

protected static final String NUCLEOTIDE_LETTERS

See Also:

Constant Field Values

Constructor Detail

SequenceTools

public SequenceTools()

Method Detail

permuteCyclic

public static String permuteCyclic(String string,
                                   int n)

Cyclically permute the characters in string forward by n elements.

Parameters:

string - The string to permute

n - The number of characters to permute by; can be positive or negative; values greater than the length of the array are acceptable

permuteCyclic

public static <T> void permuteCyclic(T[] array,
                                     T[] fill,
                                     int n)

Cyclically permute array forward by n elements.

Parameters:

array - The original result; will not be changed

fill - The permuted result will be filled into this array

n - The number of elements to permute by; can be positive or negative; values greater than the length of the array are acceptable

percentNucleotideSequence

public static int percentNucleotideSequence(String sequence)

isNucleotideSequence

public static boolean isNucleotideSequence(String sequence)

getSequenceFromString

public Sequence<?> getSequenceFromString(String sequence)
                                  throws CompoundNotFoundException

Throws:

CompoundNotFoundException

equalLengthSequences

public static boolean equalLengthSequences(ProteinSequence[] sequences)

A method to check whether an array of sequences contains at least two sequences having an equal length.

Parameters:

sequences - the array of ProteinSequence sequences

Returns:

true if any two sequences are of an equal length