EmblCDROMIndexStore (biojava-legacy 1.9.4 API)

java.lang.Object
- org.biojava.bio.seq.db.EmblCDROMIndexStore

All Implemented Interfaces:

IndexStore
```
public class EmblCDROMIndexStore
extends Object
implements IndexStore
```
EmblCDROMIndexStores implement a read-only IndexStore backed by EMBL CD-ROM format binary indices. The required index files are typically named "division.lkp" and "entrynam.idx". As an IndexStore performs lookups by sequence ID, the index files "acnum.trg" and "acnum.hit" (which store additional accession number data) are not used.

The sequence IDs are found using a binary search via a pointer into the index file. The whole file is not read unless a request for all the IDs is made using the getIDs() method. The set of IDs is then cached after the first pass. This class also has a close() method to free resources associated with the underlying RandomAccessFile.

The binary index files may be created using the EMBOSS programs dbifasta, dbiblast, dbiflat or dbigcg. The least useful from the BioJava perspective is dbigcg because we do not have a SequenceFormat implementation for GCG format files.

The Index instances returned by this class do not have the record length set because this information is not available in the binary index. The value -1 is used instead, as described in the Index interface.

Since:

1.2

Author:

Keith James

Constructor Summary

Constructors
Constructor and Description
`EmblCDROMIndexStore(File pathPrefix, File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)` Creates a new `EmblCDROMIndexStore` backed by a random access binary index.
`EmblCDROMIndexStore(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)` Creates a new `EmblCDROMIndexStore` backed by a random access binary index.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()` `close` closes the underlying `EntryNamRandomAccess` which in turn closes the lower level `RandomAccessFile`.
`void`	`commit()` `commit` commits changes.
`Index`	`fetch(String id)` Fetch an Index based upon an ID.
`Set`	`getFiles()` Retrieve the Set of files that are currently indexed.
`SequenceFormat`	`getFormat()` Retrieve the format of the index file.
`Set`	`getIDs()` Retrieve the set of all current IDs.
`String`	`getName()` `getName` returns the database name as defined within the EMBL CD-ROM index.
`File`	`getPathPrefix()` `getPathPrefix` returns the abstract path currently being appended to the raw sequence database filenames extracted from the binary index.
`SequenceBuilderFactory`	`getSBFactory()` Retrieve the SequenceBuilderFactory used to build Sequence instances.
`SymbolTokenization`	`getSymbolParser()` Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
`void`	`rollback()` `rollback` rolls back changes made since the last `commit`.
`void`	`setPathPrefix(File pathPrefix)` `setPathPrefix` sets the abstract path to be appended to sequence database filenames retrieved from the binary index.
`void`	`store(Index index)` `store` adds an `Index` to the store.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - EmblCDROMIndexStore
```
public EmblCDROMIndexStore(File divisionLkp,
                           File entryNamIdx,
                           SequenceFormat format,
                           SequenceBuilderFactory factory,
                           SymbolTokenization parser)
                    throws IOException
```
    Creates a new EmblCDROMIndexStore backed by a random access binary index.
    
    Parameters:
    
    divisionLkp - a File containing the master index.
    
    entryNamIdx - a File containing the sequence IDs and offsets.
    
    format - a SequenceFormat.
    
    factory - a SequenceBuilderFactory.
    
    parser - a SymbolTokenization.
    
    Throws:
    
    IOException - if an error occurs.
  - EmblCDROMIndexStore
```
public EmblCDROMIndexStore(File pathPrefix,
                           File divisionLkp,
                           File entryNamIdx,
                           SequenceFormat format,
                           SequenceBuilderFactory factory,
                           SymbolTokenization parser)
                    throws IOException
```
    Creates a new EmblCDROMIndexStore backed by a random access binary index.
    
    Parameters:
    
    pathPrefix - a File containing the abstract path to be appended to sequence database filenames retrieved from the binary index.
    
    divisionLkp - a File containing the master index.
    
    entryNamIdx - a File containing the sequence IDs and offsets.
    
    format - a SequenceFormat.
    
    factory - a SequenceBuilderFactory.
    
    parser - a SymbolTokenization.
    
    Throws:
    
    IOException - if an error occurs.
- Method Detail
  - getPathPrefix
```
public File getPathPrefix()
```
    getPathPrefix returns the abstract path currently being appended to the raw sequence database filenames extracted from the binary index. This value defaults to the empty abstract path.
    
    Returns:
    
    a File.
  - setPathPrefix
```
public void setPathPrefix(File pathPrefix)
```
    setPathPrefix sets the abstract path to be appended to sequence database filenames retrieved from the binary index. E.g. if the binary index refers to the database as 'SWALL' and the pathPrefix is set to "/usr/local/share/data/seq/", then the IndexStore will know the database path as "/usr/local/share/data/seq/swall" and any Index instances produced by the store will return the latter path when their getFile() method is called. This value defaults to the empty abstract path.
    
    Parameters:
    
    pathPrefix - a File prefix specifying the abstract path to append.
  - getName
```
public String getName()
```
    getName returns the database name as defined within the EMBL CD-ROM index.
    
    Specified by:
    
    getName in interface IndexStore
    
    Returns:
    
    a String value.
  - store
```
public void store(Index index)
           throws IllegalIDException,
                  BioException
```
    store adds an Index to the store. As EMBL CD-ROM indices are read-only, this implementation throws a BioException.
    
    Specified by:
    
    store in interface IndexStore
    
    Parameters:
    
    index - an Index.
    
    Throws:
    
    IllegalIDException - if an error occurs.
    
    BioException - if an error occurs.
  - commit
```
public void commit()
            throws BioException
```
    commit commits changes. As EMBL CD-ROM indices are read-only, this implementation throws a BioException.
    
    Specified by:
    
    commit in interface IndexStore
    
    Throws:
    
    BioException - if an error occurs.
  - rollback
```
public void rollback()
```
    rollback rolls back changes made since the last commit. As EMBL CD-ROM indices are read-only, this implementation does nothing.
    
    Specified by:
    
    rollback in interface IndexStore
  - fetch
```
public Index fetch(String id)
            throws IllegalIDException,
                   BioException
```
    Description copied from interface: IndexStore
    
    Fetch an Index based upon an ID.
    
    Specified by:
    
    fetch in interface IndexStore
    
    Parameters:
    
    id - The ID of the sequence Index to retrieve
    
    Throws:
    
    IllegalIDException - if the ID couldn't be found
    
    BioException - if the fetch fails in the underlying storage mechanism
  - getIDs
```
public Set 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 interface IndexStore
    
    Returns:
    
    a Set of all legal IDs
  - getFiles
```
public Set getFiles()
```
    Description copied from interface: IndexStore
    
    Retrieve the Set of files that are currently indexed.
    
    Specified by:
    
    getFiles in interface IndexStore
  - getFormat
```
public SequenceFormat 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 interface IndexStore
    
    Returns:
    
    a Set of all indexed files
  - getSBFactory
```
public SequenceBuilderFactory getSBFactory()
```
    Description copied from interface: IndexStore
    
    Retrieve the SequenceBuilderFactory used to build Sequence instances.
    
    Specified by:
    
    getSBFactory in interface IndexStore
    
    Returns:
    
    the associated SequenceBuilderFactory
  - getSymbolParser
```
public SymbolTokenization getSymbolParser()
```
    Description copied from interface: IndexStore
    
    Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
    
    Specified by:
    
    getSymbolParser in interface IndexStore
    
    Returns:
    
    the associated SymbolParser
  - close
```
public void close()
           throws IOException
```
    close closes the underlying EntryNamRandomAccess which in turn closes the lower level RandomAccessFile. This frees the resources associated with the file.
    
    Throws:
    
    IOException - if an error occurs.

Class EmblCDROMIndexStore

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

EmblCDROMIndexStore

EmblCDROMIndexStore

Method Detail

getPathPrefix

setPathPrefix

getName

store

commit

rollback

fetch

getIDs

getFiles

getFormat

getSBFactory

getSymbolParser

close