org.biojava.bio.seq.db.emblcd
Class EmblCDROMRandomAccess

java.lang.Object
  extended by org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
Direct Known Subclasses:
EntryNamRandomAccess

public abstract class EmblCDROMRandomAccess
extends java.lang.Object

EmblCDROMRandomAccess is an abstract class whose concrete subclasses can perform fast lookups in EMBL CD-ROM format index files. As the format of the records varies between file types, subclasses should implement two methods; readRecord(), which should parse the record into an array of objects and getRecordKey() which should retrieve the the field from the parsed record on which the records were sorted in the index. This is used during the binary search in the findRecord() method.

Implementing readRecord() is easy because it simply means delegating to the supplied RecordParser and calling the appropriate method on it.

Since:
1.2
Author:
Keith James

Field Summary
protected  java.io.RandomAccessFile raIndexFile
           
protected  byte[] recBytes
           
protected  org.biojava.bio.seq.db.emblcd.RecordParser recParser
          A recParser for implementing readRecord() specific to each concrete subclass.
 
Constructor Summary
EmblCDROMRandomAccess(java.io.File indexFile, int headerLength, int recordLength, long recordCount)
          Creates a new EmblCDROMRandomAccess object.
 
Method Summary
 void close()
          close closes the underlying RandomAccessFile.
 java.lang.Object[] findRecord(java.lang.String identifier)
          findRecord performs a binary search within the file for a record specified by an identifier String.
 java.io.File getFile()
          getFile returns the File wrapped.
protected abstract  java.lang.String getRecordKey(java.lang.Object[] record)
          getRecordKey returns the field from the record on which the records were sorted in the index.
protected abstract  java.lang.Object[] readRecord()
          readRecord returns an array of objects parsed from a single record.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

raIndexFile

protected java.io.RandomAccessFile raIndexFile

recParser

protected org.biojava.bio.seq.db.emblcd.RecordParser recParser
A recParser for implementing readRecord() specific to each concrete subclass.


recBytes

protected byte[] recBytes
Constructor Detail

EmblCDROMRandomAccess

public EmblCDROMRandomAccess(java.io.File indexFile,
                             int headerLength,
                             int recordLength,
                             long recordCount)
                      throws java.io.FileNotFoundException
Creates a new EmblCDROMRandomAccess object.

Parameters:
indexFile - a File to wrap.
headerLength - an int (normally 300 bytes).
recordLength - an int indicating the length of a single record.
recordCount - an long indicating the total number of records.
Throws:
java.io.FileNotFoundException - if indexFile cannot be found.
Method Detail

getFile

public java.io.File getFile()
getFile returns the File wrapped.

Returns:
a File.

findRecord

public java.lang.Object[] findRecord(java.lang.String identifier)
                              throws java.io.IOException
findRecord performs a binary search within the file for a record specified by an identifier String.

Parameters:
identifier - a String identifier (sequence ID or accession number).
Returns:
an Object [] array containing the record. If there is no such record an empty array is returned.
Throws:
java.io.IOException - if an error occurs.

close

public void close()
           throws java.io.IOException
close closes the underlying RandomAccessFile.

Throws:
java.io.IOException - if an error occurs.

readRecord

protected abstract java.lang.Object[] readRecord()
                                          throws java.io.IOException
readRecord returns an array of objects parsed from a single record. Its content will depend on the type of index file. Concrete subclasses must provide an implementation of this method.

Returns:
an Object [] array.
Throws:
java.io.IOException - if an error occurs.

getRecordKey

protected abstract java.lang.String getRecordKey(java.lang.Object[] record)
getRecordKey returns the field from the record on which the records were sorted in the index. (i.e. sequence ID or accession number).

Returns:
a String.