org.biojava.bio.seq.db

Class SimpleIndex

java.lang.Object

org.biojava.bio.seq.db.SimpleIndex

All Implemented Interfaces:

Index

public class SimpleIndex
extends Object
implements Index

This is a no-frills implementation of the Index interface.

The file, start and ID are explicitly maintained as immutable properties of the index. This implementation should be appropriate for many indexing schemes. However, some schemes may wish to implement this interface as a wrapper around a simple file offset, or an array index.

Author:

Matthew Pocock

Constructor Summary

Constructors

Constructor and Description
SimpleIndex(File file, long start, int length, String id) Build the index using the given file, start and id

Method Summary

Methods

Modifier and Type	Method and Description
File	getFile() The file to retrieve from.
String	getID() The ID of the sequence at this position in this file.
int	getLength() The entry can be slurped out of the file by grabbing length bytes from start.
long	getStart() Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence.

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleIndex

public SimpleIndex(File file,
           long start,
           int length,
           String id)

Build the index using the given file, start and id

Parameters:

file - the File this sequence is in

start - how many bytes to skip to reach the first byte of the sequence

length - how many bytes can be pulled out of the file to grab the record

id - the ID of the sequence

Method Detail

getFile

public File getFile()

Description copied from interface: Index

The file to retrieve from.

Specified by:

getFile in interface Index

Returns:

the File containing this Sequence

getStart

public long getStart()

Description copied from interface: Index

Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence.

Specified by:

getStart in interface Index

Returns:

the offset within the file

getLength

public int getLength()

Description copied from interface: Index

The entry can be slurped out of the file by grabbing length bytes from start. If the length can't be read from a store then this method should return -1.

Specified by:

getLength in interface Index

Returns:

the length in bytes of this indexed entry

getID

public String getID()

Description copied from interface: Index

The ID of the sequence at this position in this file.

Specified by:

getID in interface Index

Returns:

the ID of the indexed Sequence