Package org.biojava.bio.symbol
Class CodonPrefTools
java.lang.Object
org.biojava.bio.symbol.CodonPrefTools
An utility class for codon preferences
- Since:
- 1.3
- Author:
- David Huen, Mark Schreiber
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic String
Saccharomyces cerevisiae codon preferencesstatic String
Drosophila melanogaster codon preferencesstatic String
Escherichia coli codon preferencesstatic String
Takifugu rubripes codon preferencesstatic String
Homo sapiens codon preferencesstatic String
Mus musculus codon preferencesstatic String
Schizosaccharomyces pombe codon preferencesstatic String
Rattus norvegicus codon preferencesstatic String
Caenorhabditis elegans codon preferences -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic CodonPref
get the specified codon preference.static FiniteAlphabet
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.
-
Field Details
-
DROSOPHILA_MELANOGASTER_NUCLEAR
Drosophila melanogaster codon preferences -
MAN_NUCLEAR
Homo sapiens codon preferences -
MOUSE_NUCLEAR
Mus musculus codon preferences -
RAT_NUCLEAR
Rattus norvegicus codon preferences -
FUGU_NUCLEAR
Takifugu rubripes codon preferences -
WORM_NUCLEAR
Caenorhabditis elegans codon preferences -
CEREVISIAE_NUCLEAR
Saccharomyces cerevisiae codon preferences -
POMBE_NUCLEAR
Schizosaccharomyces pombe codon preferences -
ECOLI
Escherichia coli codon preferences
-
-
Constructor Details
-
CodonPrefTools
public CodonPrefTools()
-
-
Method Details
-
getCodonPreference
get the specified codon preference. -
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. -
readFromXML
reads a specified CodonPref from an file.- Parameters:
name
- name of organism- Throws:
BioException
-
readFromXML
- Throws:
BioException
-
readFromXML
read an CodonPref XML stream and handle it with a CodonPrefFilter object.- Throws:
BioException
-
translateCUD
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
-