org.biojava.bio.symbol
Class CodonPrefTools

java.lang.Object
  extended by 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
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
CodonPrefTools()
           
 
Method Summary
static CodonPref getCodonPreference(String id)
          get the specified codon preference.
static FiniteAlphabet getDinucleotideAlphabet()
          returns an RNA dinucleotide alphabet.
static CodonPref[] readFromXML(InputStream prefStream)
           
static void readFromXML(InputStream prefStream, CodonPrefFilter filter)
          read an CodonPref XML stream and handle it with a CodonPrefFilter object.
static CodonPref readFromXML(InputStream prefStream, String name)
          reads a specified CodonPref from an file.
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