IUPACParser (biojava 5.2.0 API)

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 Description

static class IUPACParser.IUPACTable
Holds the concept of a codon table from the IUPAC format

Field Summary

Fields
Modifier and Type Field Description

static String IUPAC_LOCATION

Constructor Summary

Constructors
Constructor Description

IUPACParser()
Default version and uses the classpath based IUPAC table

IUPACParser(InputStream is)
Allows you to specify a different IUPAC table.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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