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 -
Constructor Summary
ConstructorsConstructorDescriptionEntryNamRandomAccess(File indexFile, int headerLength, int recordLength, long recordCount) -
Method Summary
Modifier and TypeMethodDescriptionprotected StringgetRecordKey(Object[] record) getRecordKeyreturns the field from the record on which the records were sorted in the index.protected Object[]readRecordcreates 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
readRecordcreates 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:
readRecordin classEmblCDROMRandomAccess- Returns:
- an
Object []array. - Throws:
IOException- if an error occurs.
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getRecordKey
getRecordKeyreturns the field from the record on which the records were sorted in the index. (i.e. sequence ID or accession number).- Specified by:
getRecordKeyin classEmblCDROMRandomAccess- Returns:
- a
String.
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