edu.unc.csbio.data
Class Insertion

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

public class Insertion
extends Feature

The class for insertion variant. This class is to be developed.

Version:
0.1
Author:
Shunping Huang , Jack Wang

Field Summary
(package private)  char[] insertedSequence
          An char array of sequences to be inserted
 
Fields inherited from class edu.unc.csbio.data.Feature
chrom, end, start
 
Constructor Summary
Insertion(java.lang.String chrom, int insertedPos, java.lang.String sequence)
          A constructor for Insertion object The end position is smaller than start position.
 
Method Summary
 char[] getInserted()
           
 int getLength()
          Get the length of the insertion, which is the length of the inserted sequence.
 java.lang.String toString()
          A stub method for toString()
 
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
 

Field Detail

insertedSequence

char[] insertedSequence
An char array of sequences to be inserted

Constructor Detail

Insertion

public Insertion(java.lang.String chrom,
                 int insertedPos,
                 java.lang.String sequence)
A constructor for Insertion object The end position is smaller than start position. Because the effective range of an insertion is zero on the reference coordinate.

Parameters:
chrom - name of the chromosome
insertedPos - the first position for the inserted sequence
sequence - the sequence to be inserted
Method Detail

getLength

public int getLength()
Get the length of the insertion, which is the length of the inserted sequence.

Overrides:
getLength in class Feature
Returns:
The length of an insertion (i.e. the length of the inserted sequence)
See Also:
Feature

getInserted

public char[] getInserted()

toString

public java.lang.String toString()
A stub method for toString()

Specified by:
toString in class Feature
See Also:
Object.toString()