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)	Attempts to parse String as a DNA sequence first. If this fails it tries to parse as a ProteinSequence.
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.
static String	permuteCyclic2(String string, int n)	Improved implementation that is generally 10-100x faster, and fixes some edge-case bugs.

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

permuteCyclic2

public static String permuteCyclic2(String string,
                                    int n)

Improved implementation that is generally 10-100x faster, and fixes some edge-case bugs.

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

Returns:

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

Attempts to parse String as a DNA sequence first.
If this fails it tries to parse as a ProteinSequence.
This method does not attempt to create an RNASequence.

Also, a sequence such as 'ATCGTA' which is both a peptide sequence and a DNA sequence, will always be returned as a DNA sequence.

An empty string argument returns a ProteinSequence of length 0. A null argument throws a NullPointerException

Parameters:

sequence -

Returns:

Either a DNASequence or a ProteinSequence

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