org.jbei.ice.lib.utils

Class SequenceUtils

java.lang.Object

org.jbei.ice.lib.utils.SequenceUtils

public class SequenceUtils
extends Object

Utility methods for sequences.

Author:

Zinovii Dmytriv, Timothy Ham

Constructor Summary

Constructors

Constructor and Description
SequenceUtils()

Method Summary

Modifier and Type	Method and Description
static String	breakUpLines(String input) Format into 6 column, 10 basepairs per column display.
static String	calculateReverseComplementSequenceHash(String sequence) Calculate the SHA-1 sequence hash of the reverse complement of the given sequence.
static String	calculateSequenceHash(String sequence) Calculate the SHA-1 sequence hash of the given sequence.
static String	reverseComplement(String sequence) Calculate the reverse complement of the given DNA sequence.
static String	translateToProtein(String dnaSequence) Calculate the amino acid translation of the given dnaSequence string.

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceUtils

public SequenceUtils()

Method Detail

calculateSequenceHash

public static String calculateSequenceHash(String sequence)

Calculate the SHA-1 sequence hash of the given sequence.

Normalize by trimming and converting to lower case. Does not verify valid symbol.

Parameters:

sequence - sequence to hash.

Returns:

Hex digest of SHA-1 hash.

calculateReverseComplementSequenceHash

public static String calculateReverseComplementSequenceHash(String sequence)
                                                     throws UtilityException

Calculate the SHA-1 sequence hash of the reverse complement of the given sequence.

Normalize by trimming and converting to lower case. Does not verify valid symbol.

Parameters:

sequence - sequence to hash.

Returns:

Hex digest of SHA-1 hash.

Throws:

UtilityException

reverseComplement

public static String reverseComplement(String sequence)
                                throws UtilityException

Calculate the reverse complement of the given DNA sequence.

Parameters:

sequence - DNA sequence to reverse complement.

Returns:

Reversed, complemented sequence.

Throws:

UtilityException

translateToProtein

public static String translateToProtein(String dnaSequence)
                                 throws UtilityException

Calculate the amino acid translation of the given dnaSequence string.

Parameters:

dnaSequence - DNA sequence to translate.

Returns:

String of amino acid symbols.

Throws:

UtilityException

breakUpLines

public static String breakUpLines(String input)

Format into 6 column, 10 basepairs per column display.

Parameters:

input - sequence string.

Returns:

Formatted sequence output.