org.broad.tribble
Interface Feature

All Known Subinterfaces:

LocusScore

All Known Implementing Classes:

BasicScore

public interface Feature

Represents a locus on a reference sequence. The coordiante conventions are 1-based fully closed. For example, a features spanning the second and third base of a sequence would have coordinates start = 2, end = 3, and a length of 2.

Method Summary

java.lang.String	getChr() Return the features reference sequence name, e.g chromosome or contig
int	getEnd() Return the end position following 1-based fully closed conventions.
int	getStart() Return the start position in 1-based coordinates (first base is 1)

Method Detail

getChr

java.lang.String getChr()

Return the features reference sequence name, e.g chromosome or contig

getStart

int getStart()

Return the start position in 1-based coordinates (first base is 1)

getEnd

int getEnd()

Return the end position following 1-based fully closed conventions. The length of a feature is end - start + 1;