htsjdk.samtools.util

Class Md5CalculatingInputStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.util.Md5CalculatingInputStream

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class Md5CalculatingInputStream
extends java.io.InputStream

Class to generate an MD5 string for a file as it is being read

Constructor Summary

Constructors

Constructor and Description
Md5CalculatingInputStream(java.io.InputStream is, java.io.File digestFile) Constructor that takes in the InputStream that we are wrapping and creates the MD5 MessageDigest

Method Summary

Methods

Modifier and Type	Method and Description
int	available()
void	close()
void	mark(int readlimit)
boolean	markSupported()
java.lang.String	md5()
int	read()
int	read(byte[] b)
int	read(byte[] b, int off, int len)
void	reset()
long	skip(long n)

Methods inherited from class java.lang.Object

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

Constructor Detail

Md5CalculatingInputStream

public Md5CalculatingInputStream(java.io.InputStream is,
                         java.io.File digestFile)

Constructor that takes in the InputStream that we are wrapping and creates the MD5 MessageDigest

Method Detail

read

public int read()
         throws java.io.IOException

Specified by:

read in class java.io.InputStream

Throws:

java.io.IOException

read

public int read(byte[] b)
         throws java.io.IOException

Overrides:

read in class java.io.InputStream

Throws:

java.io.IOException

read

public int read(byte[] b,
       int off,
       int len)
         throws java.io.IOException

Overrides:

read in class java.io.InputStream

Throws:

java.io.IOException

md5

public java.lang.String md5()

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class java.io.InputStream

Throws:

java.io.IOException

markSupported

public boolean markSupported()

Overrides:

markSupported in class java.io.InputStream

mark

public void mark(int readlimit)

Overrides:

mark in class java.io.InputStream

reset

public void reset()
           throws java.io.IOException

Overrides:

reset in class java.io.InputStream

Throws:

java.io.IOException

skip

public long skip(long n)
          throws java.io.IOException

Overrides:

skip in class java.io.InputStream

Throws:

java.io.IOException

available

public int available()
              throws java.io.IOException

Overrides:

available in class java.io.InputStream

Throws:

java.io.IOException