com.milaboratory.core.io.sequence.fasta

Class RandomAccessFastaIndex.IndexRecord

java.lang.Object

com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.IndexRecord

Enclosing class:

RandomAccessFastaIndex

public final class RandomAccessFastaIndex.IndexRecord
extends Object

Constructor Summary

Constructors

Constructor and Description
RandomAccessFastaIndex.IndexRecord(int index, String description, long length, int indexStart)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
String	getDescription() Returns fasta record description line.
List<String>	getIds()
long	getLength() Returns record length in letters.
int	hashCode()
long	queryPosition(long offset) Returns encoded position (positionInFile << 20) | (numberOfLettersToSkip).

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RandomAccessFastaIndex.IndexRecord

public RandomAccessFastaIndex.IndexRecord(int index,
                                  String description,
                                  long length,
                                  int indexStart)

Method Detail

getIds

public List<String> getIds()

getDescription

public String getDescription()

Returns fasta record description line. Line that goes after '>' in record header.

Returns:

fasta record description line; line that goes after '>' in record header

getLength

public long getLength()

Returns record length in letters.

Returns:

record length in letters

queryPosition

public long queryPosition(long offset)

Returns encoded position (positionInFile << 20) | (numberOfLettersToSkip). Operation takes O(1).

Parameters:

offset - sequence offset in letters

Returns:

encoded position (positionInFile << 20) | (numberOfLettersToSkip)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object