Package org.biojava.bio.seq.db.emblcd
Class EmblCDROMRandomAccess
java.lang.Object
org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
- Direct Known Subclasses:
EntryNamRandomAccess
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
FieldsModifier and TypeFieldDescriptionprotected RandomAccessFile
protected byte[]
protected org.biojava.bio.seq.db.emblcd.RecordParser
ArecParser
for implementingreadRecord()
specific to each concrete subclass. -
Constructor Summary
ConstructorsConstructorDescriptionEmblCDROMRandomAccess
(File indexFile, int headerLength, int recordLength, long recordCount) Creates a newEmblCDROMRandomAccess
object. -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
close
closes the underlyingRandomAccessFile
.Object[]
findRecord
(String identifier) findRecord
performs a binary search within the file for a record specified by an identifier String.getFile()
getFile
returns theFile
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
returns an array of objects parsed from a single record.
-
Field Details
-
raIndexFile
-
recParser
ArecParser
for implementingreadRecord()
specific to each concrete subclass. -
recBytes
-
-
Constructor Details
-
EmblCDROMRandomAccess
public EmblCDROMRandomAccess(File indexFile, int headerLength, int recordLength, long recordCount) throws FileNotFoundException Creates a newEmblCDROMRandomAccess
object.- Parameters:
indexFile
- aFile
to wrap.headerLength
- anint
(normally 300 bytes).recordLength
- anint
indicating the length of a single record.recordCount
- anlong
indicating the total number of records.- Throws:
FileNotFoundException
- if indexFile cannot be found.
-
-
Method Details
-
getFile
getFile
returns theFile
wrapped.- Returns:
- a
File
.
-
findRecord
findRecord
performs a binary search within the file for a record specified by an identifier String.- Parameters:
identifier
- aString
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
close
closes the underlyingRandomAccessFile
.- Throws:
IOException
- if an error occurs.
-
readRecord
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
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
.
-