htsjdk.samtools.reference

Class FastaSequenceIndexEntry

java.lang.Object

htsjdk.samtools.reference.FastaSequenceIndexEntry

public class FastaSequenceIndexEntry
extends java.lang.Object

Hold an individual entry in a fasta sequence index file.

Constructor Summary

Constructors

Constructor and Description
FastaSequenceIndexEntry(java.lang.String contig, long location, long size, int basesPerLine, int bytesPerLine, int sequenceIndex) Create a new entry with the given parameters.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object other) Compare this index entry to another index entry.
int	getBasesPerLine() Gets the number of bases in a given line.
int	getBytesPerLine() How many bytes (bases + whitespace) are consumed by the given line?
java.lang.String	getContig() Gets the contig associated with this entry.
long	getLocation() Gets the location of this contig within the fasta.
int	getSequenceIndex()
long	getSize() Gets the size, in bytes, of the data in the contig.
int	hashCode() In general, we expect one entry per contig, so compute the hash based only on the contig.
protected void	setContig(java.lang.String contig) Sometimes contigs need to be adjusted on-the-fly to match sequence dictionary entries.
java.lang.String	toString() For debugging.

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaSequenceIndexEntry

public FastaSequenceIndexEntry(java.lang.String contig,
                               long location,
                               long size,
                               int basesPerLine,
                               int bytesPerLine,
                               int sequenceIndex)

Create a new entry with the given parameters.

Parameters:

contig - Contig this entry represents.

location - Location (byte coordinate) in the fasta file.

size - The number of bases in the contig.

basesPerLine - How many bases are on each line.

bytesPerLine - How many bytes are on each line (includes newline characters).

Method Detail

getContig

public java.lang.String getContig()

Gets the contig associated with this entry.

Returns:

String representation of the contig.

setContig

protected void setContig(java.lang.String contig)

Sometimes contigs need to be adjusted on-the-fly to match sequence dictionary entries. Provide that capability to other classes w/i the package.

Parameters:

contig - New value for the contig.

getLocation

public long getLocation()

Gets the location of this contig within the fasta.

Returns:

seek position within the fasta.

getSize

public long getSize()

Gets the size, in bytes, of the data in the contig.

Returns:

size of the contig bases in bytes.

getBasesPerLine

public int getBasesPerLine()

Gets the number of bases in a given line.

Returns:

Number of bases in the fasta line.

getBytesPerLine

public int getBytesPerLine()

How many bytes (bases + whitespace) are consumed by the given line?

Returns:

Number of bytes in a line.

getSequenceIndex

public int getSequenceIndex()

toString

public java.lang.String toString()

For debugging. Emit the contents of each contig line.

Overrides:

toString in class java.lang.Object

Returns:

A string representation of the contig line.

equals

public boolean equals(java.lang.Object other)

Compare this index entry to another index entry.

Overrides:

equals in class java.lang.Object

Parameters:

other - another FastaSequenceIndexEntry

Returns:

True if each has the same name, location, size, basesPerLine and bytesPerLine

hashCode

public int hashCode()

In general, we expect one entry per contig, so compute the hash based only on the contig.

Overrides:

hashCode in class java.lang.Object

Returns:

A unique hash code representing this object.