Package org.biojava.bio.symbol

Class CodonPrefTools

java.lang.Object

org.biojava.bio.symbol.CodonPrefTools

public class CodonPrefTools
extends Object

An utility class for codon preferences

Since:

1.3

Author:

David Huen, Mark Schreiber

Field Summary

Fields

Modifier and Type	Field	Description
static String	CEREVISIAE_NUCLEAR	Saccharomyces cerevisiae codon preferences
static String	DROSOPHILA_MELANOGASTER_NUCLEAR	Drosophila melanogaster codon preferences
static String	ECOLI	Escherichia coli codon preferences
static String	FUGU_NUCLEAR	Takifugu rubripes codon preferences
static String	MAN_NUCLEAR	Homo sapiens codon preferences
static String	MOUSE_NUCLEAR	Mus musculus codon preferences
static String	POMBE_NUCLEAR	Schizosaccharomyces pombe codon preferences
static String	RAT_NUCLEAR	Rattus norvegicus codon preferences
static String	WORM_NUCLEAR	Caenorhabditis elegans codon preferences

Constructor Summary

Constructors

Constructor	Description
CodonPrefTools()

Method Summary

Modifier and Type	Method	Description
static CodonPref	getCodonPreference(String id)	get the specified codon preference.
static FiniteAlphabet	getDinucleotideAlphabet()	returns an RNA dinucleotide alphabet.
static CodonPref[]	readFromXML(InputStream prefStream)
static CodonPref	readFromXML(InputStream prefStream, String name)	reads a specified CodonPref from an file.
static void	readFromXML(InputStream prefStream, CodonPrefFilter filter)	read an CodonPref XML stream and handle it with a CodonPrefFilter object.
static void	translateCUD(InputStream input, OutputStream output)	reads in a file in Codon Usage Database format and translate it into our XML format These can be obtained from the Codon Usage Database.
static void	writeToXML(CodonPref codonPref, PrintWriter writer)	write out a specified CodonPref object in XML format.

Methods inherited from class java.lang.Object

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

Field Detail

DROSOPHILA_MELANOGASTER_NUCLEAR

public static String DROSOPHILA_MELANOGASTER_NUCLEAR

Drosophila melanogaster codon preferences

MAN_NUCLEAR

public static String MAN_NUCLEAR

Homo sapiens codon preferences

MOUSE_NUCLEAR

public static String MOUSE_NUCLEAR

Mus musculus codon preferences

RAT_NUCLEAR

public static String RAT_NUCLEAR

Rattus norvegicus codon preferences

FUGU_NUCLEAR

public static String FUGU_NUCLEAR

Takifugu rubripes codon preferences

WORM_NUCLEAR

public static String WORM_NUCLEAR

Caenorhabditis elegans codon preferences

CEREVISIAE_NUCLEAR

public static String CEREVISIAE_NUCLEAR

Saccharomyces cerevisiae codon preferences

POMBE_NUCLEAR

public static String POMBE_NUCLEAR

Schizosaccharomyces pombe codon preferences

ECOLI

public static String ECOLI

Escherichia coli codon preferences

Constructor Detail

CodonPrefTools

public CodonPrefTools()

Method Detail

getCodonPreference

public static CodonPref getCodonPreference(String id)

get the specified codon preference.

getDinucleotideAlphabet

public static FiniteAlphabet getDinucleotideAlphabet()

returns an RNA dinucleotide alphabet. Used to represent the non-wobble bases in WobbleDistribution

writeToXML

public static void writeToXML(CodonPref codonPref,
                              PrintWriter writer)
                       throws NullPointerException,
                              IOException,
                              IllegalSymbolException,
                              BioException

write out a specified CodonPref object in XML format.

Throws:

NullPointerException

IOException

IllegalSymbolException

BioException

readFromXML

public static CodonPref readFromXML(InputStream prefStream,
                                    String name)
                             throws BioException

reads a specified CodonPref from an file.

Parameters:

name - name of organism

Throws:

BioException

readFromXML

public static CodonPref[] readFromXML(InputStream prefStream)
                               throws BioException

Throws:

BioException

readFromXML

public static void readFromXML(InputStream prefStream,
                               CodonPrefFilter filter)
                        throws BioException

read an CodonPref XML stream and handle it with a CodonPrefFilter object.

Throws:

BioException

translateCUD

public static void translateCUD(InputStream input,
                                OutputStream output)
                         throws IOException

reads in a file in Codon Usage Database format and translate it into our XML format These can be obtained from the Codon Usage Database.

Note that the output assumes that the universal genetic code is used as that is not encoded in the CUD files. Edit the output appropriately to modify the genetic code if necessary.

Throws:

IOException