Package 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

  • Field Details

  • Constructor Details

    • 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 Details