htsjdk.samtools.seekablestream

Class SeekableStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.seekablestream.SeekableStream

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

Direct Known Subclasses:

ByteArraySeekableStream, SeekableBufferedStream, SeekableFileStream, SeekableFTPStream, SeekableHTTPStream, SeekableMemoryStream

public abstract class SeekableStream
extends java.io.InputStream

Constructor Summary

Constructors

Constructor and Description
SeekableStream()

Method Summary

Modifier and Type	Method and Description
abstract void	close()
abstract boolean	eof()
abstract java.lang.String	getSource()
abstract long	length()
abstract long	position()
abstract int	read(byte[] buffer, int offset, int length)
void	readFully(byte[] b) Read enough bytes to fill the input buffer.
abstract void	seek(long position)

Methods inherited from class java.io.InputStream

available, mark, markSupported, read, read, reset, skip

Methods inherited from class java.lang.Object

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

Constructor Detail

SeekableStream

public SeekableStream()

Method Detail

length

public abstract long length()

position

public abstract long position()
                       throws java.io.IOException

Throws:

java.io.IOException

seek

public abstract void seek(long position)
                   throws java.io.IOException

Throws:

java.io.IOException

read

public abstract int read(byte[] buffer,
                         int offset,
                         int length)
                  throws java.io.IOException

Overrides:

read in class java.io.InputStream

Throws:

java.io.IOException

close

public abstract 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

eof

public abstract boolean eof()
                     throws java.io.IOException

Throws:

java.io.IOException

getSource

public abstract java.lang.String getSource()

Returns:

String representation of source (e.g. URL, file path, etc.), or null if not available.

readFully

public void readFully(byte[] b)
               throws java.io.IOException

Read enough bytes to fill the input buffer.

Parameters:

b -

Throws:

java.io.EOFException - If EOF is reached before buffer is filled

java.io.IOException