public class FastaSequenceIndexEntry extends Object
Constructor | Description |
---|---|
FastaSequenceIndexEntry(String contig,
long location,
long size,
int basesPerLine,
int bytesPerLine,
int sequenceIndex) |
Create a new entry with the given parameters.
|
Modifier and Type | Method | Description |
---|---|---|
boolean |
equals(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?
|
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(String contig) |
Sometimes contigs need to be adjusted on-the-fly to
match sequence dictionary entries.
|
String |
toString() |
For debugging.
|
public FastaSequenceIndexEntry(String contig, long location, long size, int basesPerLine, int bytesPerLine, int sequenceIndex)
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).public String getContig()
protected void setContig(String contig)
contig
- New value for the contig.public long getLocation()
public long getSize()
public int getBasesPerLine()
public int getBytesPerLine()
public int getSequenceIndex()
public String toString()
public boolean equals(Object other)