public class CodonPrefTools
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
CEREVISIAE_NUCLEAR
Saccharomyces cerevisiae codon preferences
|
static java.lang.String |
DROSOPHILA_MELANOGASTER_NUCLEAR
Drosophila melanogaster codon preferences
|
static java.lang.String |
ECOLI
Escherichia coli codon preferences
|
static java.lang.String |
FUGU_NUCLEAR
Takifugu rubripes codon preferences
|
static java.lang.String |
MAN_NUCLEAR
Homo sapiens codon preferences
|
static java.lang.String |
MOUSE_NUCLEAR
Mus musculus codon preferences
|
static java.lang.String |
POMBE_NUCLEAR
Schizosaccharomyces pombe codon preferences
|
static java.lang.String |
RAT_NUCLEAR
Rattus norvegicus codon preferences
|
static java.lang.String |
WORM_NUCLEAR
Caenorhabditis elegans codon preferences
|
Constructor and Description |
---|
CodonPrefTools() |
Modifier and Type | Method and Description |
---|---|
static CodonPref |
getCodonPreference(java.lang.String id)
get the specified codon preference.
|
static FiniteAlphabet |
getDinucleotideAlphabet()
returns an RNA dinucleotide alphabet.
|
static CodonPref[] |
readFromXML(java.io.InputStream prefStream) |
static void |
readFromXML(java.io.InputStream prefStream,
CodonPrefFilter filter)
read an CodonPref XML stream and handle it with a CodonPrefFilter object.
|
static CodonPref |
readFromXML(java.io.InputStream prefStream,
java.lang.String name)
reads a specified CodonPref from an file.
|
static void |
translateCUD(java.io.InputStream input,
java.io.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,
java.io.PrintWriter writer)
write out a specified CodonPref object in XML format.
|
public static java.lang.String DROSOPHILA_MELANOGASTER_NUCLEAR
public static java.lang.String MAN_NUCLEAR
public static java.lang.String MOUSE_NUCLEAR
public static java.lang.String RAT_NUCLEAR
public static java.lang.String FUGU_NUCLEAR
public static java.lang.String WORM_NUCLEAR
public static java.lang.String CEREVISIAE_NUCLEAR
public static java.lang.String POMBE_NUCLEAR
public static java.lang.String ECOLI
public static CodonPref getCodonPreference(java.lang.String id)
public static FiniteAlphabet getDinucleotideAlphabet()
public static void writeToXML(CodonPref codonPref, java.io.PrintWriter writer) throws java.lang.NullPointerException, java.io.IOException, IllegalSymbolException, BioException
java.lang.NullPointerException
java.io.IOException
IllegalSymbolException
BioException
public static CodonPref readFromXML(java.io.InputStream prefStream, java.lang.String name) throws BioException
name
- name of organismBioException
public static CodonPref[] readFromXML(java.io.InputStream prefStream) throws BioException
BioException
public static void readFromXML(java.io.InputStream prefStream, CodonPrefFilter filter) throws BioException
BioException
public static void translateCUD(java.io.InputStream input, java.io.OutputStream output) throws java.io.IOException
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.
java.io.IOException