Package org.biojava.nbio.data.sequence

Class SequenceUtil

java.lang.Object

org.biojava.nbio.data.sequence.SequenceUtil

public final class SequenceUtil
extends Object

Utility class for operations on sequences

Since:

3.0.2

Version:

1.0

Author:

Peter Troshin

Field Summary

Fields

Modifier and Type	Field	Description
static final Pattern	AA	Valid Amino acids
static final Pattern	AMBIGUOUS_AA	Same as AA pattern but with one additional letters - X
static final Pattern	AMBIGUOUS_NUCLEOTIDE	Ambiguous nucleotide
static final Pattern	DIGIT	A digit
static final Pattern	NON_AA	inversion of AA pattern
static final Pattern	NON_NUCLEOTIDE	Non nucleotide
static final Pattern	NONWORD	Non word
static final Pattern	NUCLEOTIDE	Nucleotides a, t, g, c, u
static final Pattern	WHITE_SPACE	A whitespace character: [\t\n\x0B\f\r]

Method Summary

Modifier and Type	Method	Description
static String	cleanSequence(String sequence)	Removes all whitespace chars in the sequence string
static String	deepCleanSequence(String sequence)	Removes all special characters and digits as well as whitespace chars from the sequence
static boolean	isAmbiguosProtein(String sequence)	Check whether the sequence confirms to amboguous protein sequence
static boolean	isNonAmbNucleotideSequence(String sequence)	Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!)
static boolean	isNucleotideSequence(FastaSequence s)
static boolean	isProteinSequence(String sequence)
static List<FastaSequence>	readFasta(InputStream inStream)	Reads fasta sequences from inStream into the list of FastaSequence objects
static void	writeFasta(OutputStream os, List<FastaSequence> sequences)	Writes FastaSequence in the file, each sequence will take one line only
static void	writeFasta(OutputStream outstream, List<FastaSequence> sequences, int width)	Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line

Methods inherited from class java.lang.Object

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

Field Details

WHITE_SPACE

public static final Pattern WHITE_SPACE

A whitespace character: [\t\n\x0B\f\r]

DIGIT

public static final Pattern DIGIT

A digit

NONWORD

public static final Pattern NONWORD

Non word

AA

public static final Pattern AA

Valid Amino acids

NON_AA

public static final Pattern NON_AA

inversion of AA pattern

AMBIGUOUS_AA

public static final Pattern AMBIGUOUS_AA

Same as AA pattern but with one additional letters - X

NUCLEOTIDE

public static final Pattern NUCLEOTIDE

Nucleotides a, t, g, c, u

AMBIGUOUS_NUCLEOTIDE

public static final Pattern AMBIGUOUS_NUCLEOTIDE

Ambiguous nucleotide

NON_NUCLEOTIDE

public static final Pattern NON_NUCLEOTIDE

Non nucleotide

Method Details

isNucleotideSequence

public static boolean isNucleotideSequence(FastaSequence s)

Returns:

true is the sequence contains only letters a,c, t, g, u

isNonAmbNucleotideSequence

public static boolean isNonAmbNucleotideSequence(String sequence)

Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char

cleanSequence

public static String cleanSequence(String sequence)

Removes all whitespace chars in the sequence string

Parameters:

sequence -

Returns:

cleaned up sequence

deepCleanSequence

public static String deepCleanSequence(String sequence)

Removes all special characters and digits as well as whitespace chars from the sequence

Parameters:

sequence -

Returns:

cleaned up sequence

isProteinSequence

public static boolean isProteinSequence(String sequence)

Parameters:

sequence -

Returns:

true is the sequence is a protein sequence, false overwise

isAmbiguosProtein

public static boolean isAmbiguosProtein(String sequence)

Check whether the sequence confirms to amboguous protein sequence

Parameters:

sequence -

Returns:

return true only if the sequence if ambiguous protein sequence Return false otherwise. e.g. if the sequence is non-ambiguous protein or DNA

writeFasta

public static void writeFasta(OutputStream outstream,
 List<FastaSequence> sequences,
 int width)
                       throws IOException

Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line

Parameters:

outstream -

sequences -

width - - the maximum number of characters to write in one line

Throws:

IOException

readFasta

public static List<FastaSequence> readFasta(InputStream inStream)
                                     throws IOException

Reads fasta sequences from inStream into the list of FastaSequence objects

Parameters:

inStream - from

Returns:

list of FastaSequence objects

Throws:

IOException

writeFasta

public static void writeFasta(OutputStream os,
 List<FastaSequence> sequences)
                       throws IOException

Writes FastaSequence in the file, each sequence will take one line only

Parameters:

os -

sequences -

Throws:

IOException