apollo.dataadapter
Class Region

java.lang.Object
  apollo.dataadapter.Region

public class Region
extends java.lang.Object

Has chromosome string and start and end ints. Can parse chrom string 2L:1000-5000 I wanted to name this Location but theres a Location class in ensj.jar so compile errors went flying. it seems Region is safe. The only bummer is theres a basically deprecated method in ApolloDataAdapterI setRegion(String) that ensembl still uses, that has nothing to do with this class. If this is confusing then maybe this should be renamed ApolloLocation or ApolloLoc should this be merged with datamodel.GenomicRange?

Constructor Summary

Region(java.lang.String regionString)

Region(java.lang.String chrom, int start, int end)

Region(java.lang.String chrom, java.lang.String startString, java.lang.String endString)

Method Summary

java.lang.String	getChromosome()
java.lang.String	getColonDashString()
int	getEnd()
int	getStart()
static void	nullCheck(java.lang.String chromString)
void	setEnd(int end)
void	setStart(int start)
static int	stringToInt(java.lang.String intString)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Region

public Region(java.lang.String regionString)

Region

public Region(java.lang.String chrom,
              java.lang.String startString,
              java.lang.String endString)

Region

public Region(java.lang.String chrom,
              int start,
              int end)

Method Detail

getChromosome

public java.lang.String getChromosome()

getStart

public int getStart()

getEnd

public int getEnd()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getColonDashString

public java.lang.String getColonDashString()

setStart

public void setStart(int start)

setEnd

public void setEnd(int end)

nullCheck

public static void nullCheck(java.lang.String chromString)

stringToInt

public static int stringToInt(java.lang.String intString)