Class TabIndexStore
- All Implemented Interfaces:
Serializable
,IndexStore
Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets.
Use the constructor to create a new index store. Use the static factory method open() to load an existing store.
The tab-delimited file looks like:fileNumber \t offset \t id \n
- Author:
- Matthew Pocock, Thomas Down, Keith James, David Huen
- See Also:
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Constructor Summary
ConstructorsConstructorDescriptionTabIndexStore
(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser) Create a new TabIndexStore. -
Method Summary
Modifier and TypeMethodDescriptionprotected void
void
commit()
Commit the stored indices to permanent storage.protected void
Fetch an Index based upon an ID.protected int
getFileIndex
(File file) 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.protected void
static TabIndexStore
Open an existing index store.void
rollback()
Discard all uncommited changes.void
Add the Index to the store.
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Constructor Details
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TabIndexStore
public TabIndexStore(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser) throws IOException, BioException Create a new TabIndexStore.The store file and index file must not exist. This is to prevent you from accidentally destroying an existing index.
- Parameters:
storeFile
- the file that will be used to persist this index storeindexFile
- the file that will hold the actual indeciesname
- the name that will be used by the database backed by this indexformat
- the SequenceFormat for files being indexedsbFactory
- the SequenceBuilderFactory used in building sequencessymbolParser
- the SymbolTokenization to use- Throws:
IOException
- if there was a problem writing the filesBioException
- if any of the parameters were not acceptable
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Method Details
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open
Open an existing index store.- Parameters:
storeFile
- the File encapsulating the store- Returns:
- a new TabIndexStore for that file
- Throws:
IOException
- if the storeFile could not be processed
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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- Throws:
IllegalIDException
- if the index has an invalid ID fieldBioException
- if the store failed
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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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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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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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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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commitStore
- Throws:
IOException
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addFile
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getFileIndex
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initialize
- Throws:
IOException
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