org.biojava.nbio.core.sequence.io

Class IUPACParser

java.lang.Object

org.biojava.nbio.core.sequence.io.IUPACParser

public class IUPACParser
extends Object

Available translations

• 1 - UNIVERSAL
• 2 - VERTEBRATE_MITOCHONDRIAL
• 3 - YEAST_MITOCHONDRIAL
• 4 - MOLD_MITOCHONDRIAL
• 5 - INVERTEBRATE_MITOCHONDRIAL
• 6 - CILIATE_NUCLEAR
• 9 - ECHINODERM_MITOCHONDRIAL
• 10 - EUPLOTID_NUCLEAR
• 11 - BACTERIAL
• 12 - ALTERNATIVE_YEAST_NUCLEAR
• 13 - ASCIDIAN_MITOCHONDRIAL
• 14 - FLATWORM_MITOCHONDRIAL
• 15 - BLEPHARISMA_MACRONUCLEAR
• 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL
• 21 - TREMATODE_MITOCHONDRIAL
• 23 - SCENEDESMUS_MITOCHONDRIAL

Taken from NCBI with slight modification and put into the classpath resource. Takes in an ID, name, amino acid string and the locations of amino acids which acts as start codons in the translation table. You can give the 3 codon position strings that correspond to the amino acid string or if you are using the default IUPAC codes you can use the hardcoded ones which are consistent amongst all codon tables. The generated IUPACParser.IUPACTable objects do not parse the data further until requested so if you do not use a translation table your only penalty is the loading of the IUPAC data from the classpath.

Author:

Andy Yates

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IUPACParser.IUPACTable Holds the concept of a codon table from the IUPAC format

Field Summary

Fields

Modifier and Type	Field and Description
static String	IUPAC_LOCATION

Constructor Summary

Constructors

Constructor and Description
IUPACParser() Default version and uses the classpath based IUPAC table
IUPACParser(InputStream is) Allows you to specify a different IUPAC table.

Method Summary

Modifier and Type	Method and Description
static IUPACParser	getInstance()
IUPACParser.IUPACTable	getTable(Integer id) Returns a table by its identifier i.e. 1 means universal codon tables
IUPACParser.IUPACTable	getTable(String name) Returns a table by its name
List<IUPACParser.IUPACTable>	getTables() Returns a list of all available IUPAC tables

Methods inherited from class java.lang.Object

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

Field Detail

IUPAC_LOCATION

public static final String IUPAC_LOCATION

See Also:

Constant Field Values

Constructor Detail

IUPACParser

public IUPACParser()

Default version and uses the classpath based IUPAC table

IUPACParser

public IUPACParser(InputStream is)

Allows you to specify a different IUPAC table.

Method Detail

getInstance

public static IUPACParser getInstance()

getTables

public List<IUPACParser.IUPACTable> getTables()

Returns a list of all available IUPAC tables

getTable

public IUPACParser.IUPACTable getTable(String name)

Returns a table by its name

getTable

public IUPACParser.IUPACTable getTable(Integer id)

Returns a table by its identifier i.e. 1 means universal codon tables