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