Package org.biojava.bio.seq.db.emblcd
Class EntryNamRandomAccess
- java.lang.Object
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- org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
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- org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
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public class EntryNamRandomAccess extends EmblCDROMRandomAccess
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
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Fields inherited from class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
raIndexFile, recBytes, recParser
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Constructor Summary
Constructors Constructor Description EntryNamRandomAccess(java.io.File indexFile, int headerLength, int recordLength, long recordCount)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected 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 java.lang.Object[]
readRecord()
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 Detail
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EntryNamRandomAccess
public EntryNamRandomAccess(java.io.File indexFile, int headerLength, int recordLength, long recordCount) throws java.io.FileNotFoundException
- Throws:
java.io.FileNotFoundException
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Method Detail
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readRecord
protected java.lang.Object[] readRecord() throws java.io.IOException
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:
java.io.IOException
- if an error occurs.
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getRecordKey
protected 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).- Specified by:
getRecordKey
in classEmblCDROMRandomAccess
- Returns:
- a
String
.
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