com.milaboratory.core.io.util

Class AbstractRandomAccessReader<T>

java.lang.Object

com.milaboratory.core.io.util.AbstractRandomAccessReader<T>

Type Parameters:

T - type of records

All Implemented Interfaces:

cc.redberry.pipe.OutputPort<T>

Direct Known Subclasses:

RandomAccessFastqReader

public abstract class AbstractRandomAccessReader<T>
extends Object
implements cc.redberry.pipe.OutputPort<T>

Abstract class that allows random access to some records written in file.

Field Summary

Fields

Modifier and Type	Field and Description
protected long	currentRecordNumber Current record number, i.e.
protected RandomAccessFile	file Random access file
protected FileIndex	fileIndex Index of file

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractRandomAccessReader(FileIndex fileIndex, RandomAccessFile file)

Method Summary

Methods

Modifier and Type	Method and Description
long	getCurrentRecordNumber() Returns the number of record that will be returned on take()
protected void	resetBufferOnSeek()
void	seekToRecord(long recordNumber) Sets the file-pointer offset, measured from the beginning of this file, at which the next record occurs.
protected void	skip()
T	take() Returns the next record or null if no more records exist.
T	take(long recordNumber) Returns the specified record or null if recordNumber is greater than actual number of records in file.
protected abstract T	take0()

Methods inherited from class java.lang.Object

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

Field Detail

fileIndex

protected final FileIndex fileIndex

Index of file

file

protected final RandomAccessFile file

Random access file

currentRecordNumber

protected long currentRecordNumber

Current record number, i.e. number of record that will be returned by invocation of take()

Constructor Detail

AbstractRandomAccessReader

protected AbstractRandomAccessReader(FileIndex fileIndex,
                          RandomAccessFile file)

Method Detail

getCurrentRecordNumber

public long getCurrentRecordNumber()

Returns the number of record that will be returned on take()

Returns:

the number of record that will be returned on take()

seekToRecord

public void seekToRecord(long recordNumber)
                  throws IOException

Sets the file-pointer offset, measured from the beginning of this file, at which the next record occurs.

Parameters:

recordNumber - number of record, at which to set the file pointer.

Throws:

IOException - if pos is less than 0 or if an I/O error occurs.

take

public T take(long recordNumber)
       throws IOException

Returns the specified record or null if recordNumber is greater than actual number of records in file.

Parameters:

recordNumber - record number

Returns:

record with specified number or null if recordNumber is greater than actual number of records in file

Throws:

IOException - if I/O occurs

take

public T take()

Returns the next record or null if no more records exist.

Specified by:

take in interface cc.redberry.pipe.OutputPort<T>

Returns:

next record or null if no more records exist

resetBufferOnSeek

protected void resetBufferOnSeek()

skip

protected void skip()

take0

protected abstract T take0()