Package org.biojava.bio.seq.db
Class BioIndex
java.lang.Object
org.biojava.bio.seq.db.BioIndex
- All Implemented Interfaces:
IndexStore
The original object for indexing sequence files.
This class may not be thread-safe.
- Author:
- Matthew Pocock, Thomas Down
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
commit()
Commit the stored indices to permanent storage.Fetch an Index based upon an ID.getFiles()
Retrieve the Set of files that are currently indexed.Retrieve the format of the index file.getIDs()
Retrieve the set of all current IDs.getName()
Retrieve the name of this store.Retrieve the SequenceBuilderFactory used to build Sequence instances.Retrieve the symbol parser used to turn the sequence characters into Symobl objects.int
guessRecLen
(RandomAccessFile file) void
rollback()
Discard all uncommited changes.void
Add the Index to the store.
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Constructor Details
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BioIndex
public BioIndex(File indexDirectory, String namespace, int idLength) throws IOException, BioException - Throws:
IOException
BioException
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BioIndex
Load an existing index file. If indexDirectory does not exist, or is not a bioindex stoore, this will barf.- Throws:
IOException
BioException
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Method Details
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getName
Description copied from interface:IndexStore
Retrieve the name of this store. This will be reflected as the name of the IndexedSequenceDB.- Specified by:
getName
in interfaceIndexStore
- Returns:
- the String name of the index
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guessRecLen
- Throws:
IOException
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fetch
Description copied from interface:IndexStore
Fetch an Index based upon an ID.- Specified by:
fetch
in interfaceIndexStore
- Parameters:
id
- The ID of the sequence Index to retrieve- Throws:
IllegalIDException
- if the ID couldn't be foundBioException
- if the fetch fails in the underlying storage mechanism
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store
Description copied from interface:IndexStore
Add the Index to the store.This method should be transactional. If the store fails, the IndexStore should be left in its original state.
If the file of the Index is not known yet, it is the responsibility of the IndexStore to add it to the set returned by getFiles.
- Specified by:
store
in interfaceIndexStore
- Parameters:
indx
- the Index to add
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commit
Description copied from interface:IndexStore
Commit the stored indices to permanent storage.- Specified by:
commit
in interfaceIndexStore
- Throws:
BioException
- if for any reason the commit fails
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rollback
Description copied from interface:IndexStore
Discard all uncommited changes.- Specified by:
rollback
in interfaceIndexStore
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getIDs
Description copied from interface:IndexStore
Retrieve the set of all current IDs.This set should either be immutable, or modifiable totally separately from the IndexStore.
- Specified by:
getIDs
in interfaceIndexStore
- Returns:
- a Set of all legal IDs
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getFiles
Description copied from interface:IndexStore
Retrieve the Set of files that are currently indexed.- Specified by:
getFiles
in interfaceIndexStore
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getFormat
Description copied from interface:IndexStore
Retrieve the format of the index file.This set should either be immutable, or modifiable totally separately from the IndexStore.
- Specified by:
getFormat
in interfaceIndexStore
- Returns:
- a Set of all indexed files
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getSBFactory
Description copied from interface:IndexStore
Retrieve the SequenceBuilderFactory used to build Sequence instances.- Specified by:
getSBFactory
in interfaceIndexStore
- Returns:
- the associated SequenceBuilderFactory
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getSymbolParser
Description copied from interface:IndexStore
Retrieve the symbol parser used to turn the sequence characters into Symobl objects.- Specified by:
getSymbolParser
in interfaceIndexStore
- Returns:
- the associated SymbolParser
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