Package org.biojava3.core.sequence.location

Class InsdcParser

java.lang.Object

org.biojava3.core.sequence.location.InsdcParser

public class InsdcParser
extends Object

Parser for working with INSDC style locations. This class supports the full range of location types generated by Genbank, INSDC and ENA.

Author:

ayates

Constructor Summary

Constructors

Constructor	Description
InsdcParser()
InsdcParser(DataSource dataSource)

Method Summary

Modifier and Type	Method	Description
DataSource	getDataSource()
Location	parse(Reader reader)	Reader based version of the parse methods.
Location	parse(String locationString)	Main method for parsing a location from a String instance

Methods inherited from class java.lang.Object

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

Constructor Details

InsdcParser

public InsdcParser()

InsdcParser

public InsdcParser(DataSource dataSource)

Method Details

getDataSource

public DataSource getDataSource()

parse

public Location parse(String locationString)
               throws ParserException

Main method for parsing a location from a String instance

Parameters:

locationString - Represents a logical location

Returns:

The parsed location

Throws:

ParserException - thrown in the event of any error during parsing

parse

public Location parse(Reader reader)
               throws IOException,
ParserException

Reader based version of the parse methods.

Parameters:

reader - The source of the data; assumes that end of the reader stream is the end of the location string to parse

Returns:

The parsed location

Throws:

IOException - Thrown with any reader error

ParserException - Thrown with any error with parsing locations