Package org.biojava.bio.seq.db
Class SimpleIndex
java.lang.Object
org.biojava.bio.seq.db.SimpleIndex
- All Implemented Interfaces:
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
ConstructorsConstructorDescriptionSimpleIndex
(File file, long start, int length, String id) Build the index using the given file, start and id -
Method Summary
Modifier and TypeMethodDescriptiongetFile()
The file to retrieve from.getID()
The ID of the sequence at this position in this file.int
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 Details
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SimpleIndex
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 Details
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getFile
Description copied from interface:Index
The file to retrieve from. -
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. -
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. -
getID
Description copied from interface:Index
The ID of the sequence at this position in this file.
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