org.biojavax.bio.seq.io

Class GenbankLocationParser

java.lang.Object

org.biojavax.bio.seq.io.GenbankLocationParser

public class GenbankLocationParser
extends Object

Parses Genbank location strings into RichLocation objects.

Since:

1.5

Author:

Richard Holland

Method Summary

Modifier and Type	Method and Description
static RichLocation	parseLocation(Namespace featureNS, String featureAccession, String locationString) Parses a location.
static String	writeLocation(RichLocation l) Writes a location in Genbank format.

Methods inherited from class java.lang.Object

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

Method Detail

parseLocation

public static RichLocation parseLocation(Namespace featureNS,
                                         String featureAccession,
                                         String locationString)
                                  throws ParseException

Parses a location.

Parameters:

featureNS - the namespace of the feature this location lives on.

featureAccession - the accession of the sequence of the feature this location lives on.

locationString - the GenBank location string.

Returns:

RichLocation the equivalent RichLocation object.

Throws:

ParseException - if the parsing failed.

writeLocation

public static String writeLocation(RichLocation l)

Writes a location in Genbank format.

Parameters:

l - the location to write

Returns:

the formatted string representing the location.