Package org.biojava.bio.seq.db
Class SimpleIndex
- java.lang.Object
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- org.biojava.bio.seq.db.SimpleIndex
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- 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
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Constructor Summary
Constructors Constructor Description SimpleIndex(File file, long start, int length, String id)
Build the index using the given file, start and id
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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.
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Constructor Detail
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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 instart
- how many bytes to skip to reach the first byte of the sequencelength
- how many bytes can be pulled out of the file to grab the recordid
- the ID of the sequence
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Method Detail
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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.
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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.
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