Package org.biojava.bio.seq.db.emblcd
Class EntryNamRandomAccess
java.lang.Object
org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
EntryNamRandomAccess
objects provide random access to
records within the "entrynam.idx" file of an EMBL CD-ROM format
binary index. Records are retrieved by their sequence ID.- Since:
- 1.2
- Author:
- Keith James
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Field Summary
Fields inherited from class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
raIndexFile, recBytes, recParser
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Constructor Summary
ConstructorsConstructorDescriptionEntryNamRandomAccess
(File indexFile, int headerLength, int recordLength, long recordCount) -
Method Summary
Modifier and TypeMethodDescriptionprotected String
getRecordKey
(Object[] record) getRecordKey
returns the field from the record on which the records were sorted in the index.protected Object[]
readRecord
creates an array of Objects from the raw byte array of a single record.Methods inherited from class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
close, findRecord, getFile
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Constructor Details
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EntryNamRandomAccess
public EntryNamRandomAccess(File indexFile, int headerLength, int recordLength, long recordCount) throws FileNotFoundException - Throws:
FileNotFoundException
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Method Details
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readRecord
readRecord
creates an array of Objects from the raw byte array of a single record. For this file type the array containsString seqID, Long rPosition, Long sPosition, Integer fileNumber
. See EMBOSS documentation for a full description.- Specified by:
readRecord
in classEmblCDROMRandomAccess
- Returns:
- an
Object []
array. - Throws:
IOException
- if an error occurs.
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getRecordKey
getRecordKey
returns the field from the record on which the records were sorted in the index. (i.e. sequence ID or accession number).- Specified by:
getRecordKey
in classEmblCDROMRandomAccess
- Returns:
- a
String
.
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