edu.unc.csbio.data
Class Exon

java.lang.Object
  extended by edu.unc.csbio.data.Feature
      extended by edu.unc.csbio.data.Exon
All Implemented Interfaces:
java.lang.Comparable<Feature>

public class Exon
extends Feature

The class Exon inherits abstract class Feature. Each exon belongs to only one chromosome, and it is in the region between its start position (inclusively) and end position(inclusively) in the chromosome. The unit of a position is a base pair.

Version:
0.1
Author:
Shunping Huang , Jack Wang

Field Summary
 
Fields inherited from class edu.unc.csbio.data.Feature
chrom, end, start
 
Constructor Summary
Exon(java.lang.String _chrom, int _start, int _end)
          A constructor for Exon object
 
Method Summary
 int getLength()
          A method to get exon length
 java.lang.String getSequence(SequenceBuffer motherSequence)
          A method to get the sequence of an exon from a mother sequence (a sequence buffer).
 java.lang.String toString()
          A method to get exon information
 
Methods inherited from class edu.unc.csbio.data.Feature
compareTo, getChromosome, getEnd, getRange, getStart
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Exon

public Exon(java.lang.String _chrom,
            int _start,
            int _end)
A constructor for Exon object

Parameters:
_chrom - name of the chromosome
_start - start position of exon
_end - end position of exon
Method Detail

getSequence

public java.lang.String getSequence(SequenceBuffer motherSequence)
A method to get the sequence of an exon from a mother sequence (a sequence buffer).

Parameters:
motherSequence - a sequence buffer
Returns:
exon sequence

getLength

public int getLength()
A method to get exon length

Overrides:
getLength in class Feature
Returns:
exon length
See Also:
Object.toString()

toString

public java.lang.String toString()
A method to get exon information

Specified by:
toString in class Feature
Returns:
a string containing chromosome name, start position and end position
See Also:
Object.toString()