org.biojava.nbio.genome.parsers.genename

Class GeneChromosomePositionParser

java.lang.Object

org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser

public class GeneChromosomePositionParser
extends Object

A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positions

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_MAPPING_URL

Constructor Summary

Constructors

Constructor and Description
GeneChromosomePositionParser()

Method Summary

Methods

Modifier and Type	Method and Description
static List<GeneChromosomePosition>	getChromosomeMappings()
static List<GeneChromosomePosition>	getChromosomeMappings(InputStream inStream)
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MAPPING_URL

public static final String DEFAULT_MAPPING_URL

See Also:

Constant Field Values

Constructor Detail

GeneChromosomePositionParser

public GeneChromosomePositionParser()

Method Detail

main

public static void main(String[] args)

getChromosomeMappings

public static List<GeneChromosomePosition> getChromosomeMappings()
                                                          throws IOException

Throws:

IOException

getChromosomeMappings

public static List<GeneChromosomePosition> getChromosomeMappings(InputStream inStream)
                                                          throws IOException

Throws:

IOException