edu.unc.csbio.RNASim
Class ReadGenerator

java.lang.Object
  extended by edu.unc.csbio.RNASim.ReadGenerator

public class ReadGenerator
extends java.lang.Object

The class generates pair-end reads from a sequence.

Version:
0.1
Author:
Shunping Huang , Jack Wang

Field Summary
private  int fragMaxLength
          maximum sequence length
private  int fragMinLength
          minimum sequence length
private  int readLength
          read length
 
Constructor Summary
ReadGenerator(int _readLength, int _fragMinLength, int _fragMaxLength)
          A constructor for ReadGenerator object
 
Method Summary
 Read[] generate(java.lang.String sequence)
          Randomly sample a fragment from a transcript sequence, and then return its both ends.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

readLength

private final int readLength
read length


fragMinLength

private final int fragMinLength
minimum sequence length


fragMaxLength

private final int fragMaxLength
maximum sequence length

Constructor Detail

ReadGenerator

public ReadGenerator(int _readLength,
                     int _fragMinLength,
                     int _fragMaxLength)
A constructor for ReadGenerator object

Parameters:
_readLength - read length
_fragMinLength - minimum sequence length
_fragMaxLength - maximum sequence length
Method Detail

generate

public Read[] generate(java.lang.String sequence)
Randomly sample a fragment from a transcript sequence, and then return its both ends.

Parameters:
sequence - the transcript sequence.
Returns:
an array for pair-end reads, null if the sequence is too short to get reads