public class CRAIEntry extends Object implements Comparable<CRAIEntry>, Cloneable
Modifier and Type | Field and Description |
---|---|
int |
alignmentSpan |
int |
alignmentStart |
static Comparator<CRAIEntry> |
byEnd |
static Comparator<CRAIEntry> |
byStart |
static Comparator<CRAIEntry> |
byStartDesc |
long |
containerStartOffset |
int |
sequenceId |
int |
sliceIndex |
int |
sliceOffset |
int |
sliceSize |
Constructor and Description |
---|
CRAIEntry() |
CRAIEntry(String line)
Create a CRAI Entry from a serialized CRAI index line.
|
Modifier and Type | Method and Description |
---|---|
CRAIEntry |
clone() |
int |
compareTo(CRAIEntry o) |
static List<CRAIEntry> |
fromContainer(Container container) |
static boolean |
intersect(CRAIEntry e0,
CRAIEntry e1) |
String |
toString() |
void |
writeToStream(OutputStream os)
Serialize the entry to a CRAI index stream.
|
public int sequenceId
public int alignmentStart
public int alignmentSpan
public long containerStartOffset
public int sliceOffset
public int sliceSize
public int sliceIndex
public static Comparator<CRAIEntry> byEnd
public static final Comparator<CRAIEntry> byStart
public static Comparator<CRAIEntry> byStartDesc
public CRAIEntry()
public CRAIEntry(String line) throws CRAIIndex.CRAIIndexException
line
- string formatted as a CRAI index entryCRAIIndex.CRAIIndexException
public void writeToStream(OutputStream os)
os
- stream to write topublic int compareTo(CRAIEntry o)
compareTo
in interface Comparable<CRAIEntry>
public CRAIEntry clone() throws CloneNotSupportedException
clone
in class Object
CloneNotSupportedException