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java.lang.Objectorg.biojava.bio.symbol.CodonPrefTools
public class CodonPrefTools
An utility class for codon preferences
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 | |
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CodonPrefTools()
|
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static String DROSOPHILA_MELANOGASTER_NUCLEAR
public static String MAN_NUCLEAR
public static String MOUSE_NUCLEAR
public static String RAT_NUCLEAR
public static String FUGU_NUCLEAR
public static String WORM_NUCLEAR
public static String CEREVISIAE_NUCLEAR
public static String POMBE_NUCLEAR
public static String ECOLI
Constructor Detail |
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public CodonPrefTools()
Method Detail |
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public static CodonPref getCodonPreference(String id)
public static FiniteAlphabet getDinucleotideAlphabet()
public static void writeToXML(CodonPref codonPref, PrintWriter writer) throws NullPointerException, IOException, IllegalSymbolException, BioException
NullPointerException
IOException
IllegalSymbolException
BioException
public static CodonPref readFromXML(InputStream prefStream, String name) throws BioException
name
- name of organism
BioException
public static CodonPref[] readFromXML(InputStream prefStream) throws BioException
BioException
public static void readFromXML(InputStream prefStream, CodonPrefFilter filter) throws BioException
BioException
public static void translateCUD(InputStream input, OutputStream output) throws 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.
IOException
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