Package org.biojava.bio.seq.db.emblcd

Class EmblCDROMRandomAccess

java.lang.Object
org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
Direct Known Subclasses:
EntryNamRandomAccess
public abstract class EmblCDROMRandomAccess extends 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

    Fields
    Modifier and Type
    Field
    Description
    protected 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

    Constructors
    Constructor
    Description
    EmblCDROMRandomAccess(File indexFile, int headerLength, int recordLength, long recordCount)
    Creates a new EmblCDROMRandomAccess object.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
    close closes the underlying RandomAccessFile.
    Object[]
    findRecord(String identifier)
    findRecord performs a binary search within the file for a record specified by an identifier String.
    File
    getFile()
    getFile returns the File wrapped.
    protected abstract String
    getRecordKey(Object[] record)
    getRecordKey returns the field from the record on which the records were sorted in the index.
    protected abstract 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 Details

    • raIndexFile

      protected 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 Details

    • EmblCDROMRandomAccess

      public EmblCDROMRandomAccess(File indexFile, int headerLength, int recordLength, long recordCount) throws 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:
      FileNotFoundException - if indexFile cannot be found.

  • Method Details

    • getFile

      public File getFile()
      getFile returns the File wrapped.
      Returns:
      a File.

    • findRecord

      public Object[] findRecord(String identifier) throws 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:
      IOException - if an error occurs.

    • close

      public void close() throws IOException
      close closes the underlying RandomAccessFile.
      Throws:
      IOException - if an error occurs.

    • readRecord

      protected abstract Object[] readRecord() throws 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:
      IOException - if an error occurs.

    • getRecordKey

      protected abstract String getRecordKey(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.