org.biojava.utils

Class FileAsList

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList

org.biojava.utils.FileAsList

All Implemented Interfaces:

java.lang.Iterable, java.util.Collection, java.util.List, Commitable

public abstract class FileAsList
extends java.util.AbstractList
implements Commitable

FileAsList creates a writable List implementation backed by a random access file. There is a restriction on the record length that the string representation of that integer may not be longer than 4 bytes. This is because a fixed 4 byte leader is used to encode the record length in the file.

Author:

Matthew Pocock, Keith James, Greg Cox

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor and Description
FileAsList(java.io.File mappedFile, boolean mutable) Creates a new FileAsList instance from an existing backing file.
FileAsList(java.io.File mappedFile, int recordLength) Creates a new FileAsList and corresponding backing file.

Method Summary

Modifier and Type	Method and Description
boolean	add(java.lang.Object o)
void	clear()
void	commit() commit commits pending changes.
protected abstract void	generateRecord(byte[] buffer, java.lang.Object item)
java.lang.Object	get(int indx)
abstract java.util.Comparator	getComparator()
java.util.Iterator	iterator()
protected abstract java.lang.Object	parseRecord(byte[] buffer)
byte[]	rawGet(int indx) rawGet reads the record at the specified index as a raw byte array.
void	rollback() rollback reverses pending changes to restore initial (or prior commit) state.
java.lang.Object	set(int indx, java.lang.Object o) This always returns null, not the previous object.
int	size()

Methods inherited from class java.util.AbstractList

add, addAll, equals, hashCode, indexOf, lastIndexOf, listIterator, listIterator, remove, removeRange, subList

Methods inherited from class java.util.AbstractCollection

addAll, contains, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

addAll, contains, containsAll, isEmpty, remove, removeAll, replaceAll, retainAll, sort, spliterator, toArray, toArray

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Constructor Detail

FileAsList

public FileAsList(java.io.File mappedFile,
                  int recordLength)
           throws java.io.IOException

Creates a new FileAsList and corresponding backing file.

Parameters:

mappedFile - a File used to back the list. This file must not already exist.

recordLength - an int byte record length.

Throws:

java.io.IOException - if an error occurs.

FileAsList

public FileAsList(java.io.File mappedFile,
                  boolean mutable)
           throws java.io.IOException

Creates a new FileAsList instance from an existing backing file.

Parameters:

mappedFile - a File used to back the list. This file must already exist.

mutable - true if this list should support edits, false otherwise

Throws:

java.io.IOException - if an error occurs.

Method Detail

rawGet

public byte[] rawGet(int indx)

rawGet reads the record at the specified index as a raw byte array.

Parameters:

indx - an int list index.

Returns:

a byte [] array containing the raw record data.

get

public java.lang.Object get(int indx)

Specified by:

get in interface java.util.List

Specified by:

get in class java.util.AbstractList

size

public int size()

Specified by:

size in interface java.util.Collection

Specified by:

size in interface java.util.List

Specified by:

size in class java.util.AbstractCollection

add

public boolean add(java.lang.Object o)

Specified by:

add in interface java.util.Collection

Specified by:

add in interface java.util.List

Overrides:

add in class java.util.AbstractList

set

public java.lang.Object set(int indx,
                            java.lang.Object o)

This always returns null, not the previous object.

Specified by:

set in interface java.util.List

Overrides:

set in class java.util.AbstractList

clear

public void clear()

Specified by:

clear in interface java.util.Collection

Specified by:

clear in interface java.util.List

Overrides:

clear in class java.util.AbstractList

commit

public void commit()

Description copied from interface: Commitable

commit commits pending changes.

Specified by:

commit in interface Commitable

rollback

public void rollback()

Description copied from interface: Commitable

rollback reverses pending changes to restore initial (or prior commit) state. This always succededs or raises an unchecked exception. If the rollback fails, you must raise an AssertionFailure.

Specified by:

rollback in interface Commitable

parseRecord

protected abstract java.lang.Object parseRecord(byte[] buffer)

generateRecord

protected abstract void generateRecord(byte[] buffer,
                                       java.lang.Object item)
                                throws java.io.IOException

Throws:

java.io.IOException

getComparator

public abstract java.util.Comparator getComparator()

iterator

public java.util.Iterator iterator()

Specified by:

iterator in interface java.lang.Iterable

Specified by:

iterator in interface java.util.Collection

Specified by:

iterator in interface java.util.List

Overrides:

iterator in class java.util.AbstractList