public class Cigar
extends java.lang.Object
implements java.io.Serializable
Modifier and Type | Field and Description |
---|---|
static long |
serialVersionUID |
Constructor and Description |
---|
Cigar() |
Cigar(java.util.List<CigarElement> cigarElements) |
Modifier and Type | Method and Description |
---|---|
void |
add(CigarElement cigarElement) |
boolean |
equals(java.lang.Object o) |
CigarElement |
getCigarElement(int i) |
java.util.List<CigarElement> |
getCigarElements() |
int |
getPaddedReferenceLength() |
int |
getReadLength() |
static int |
getReadLength(java.util.List<CigarElement> cigarElements) |
int |
getReferenceLength() |
int |
hashCode() |
boolean |
isEmpty() |
java.util.List<SAMValidationError> |
isValid(java.lang.String readName,
long recordNumber)
Exhaustive validation of CIGAR.
|
int |
numCigarElements() |
java.lang.String |
toString() |
public static final long serialVersionUID
public Cigar()
public Cigar(java.util.List<CigarElement> cigarElements)
public java.util.List<CigarElement> getCigarElements()
public CigarElement getCigarElement(int i)
public void add(CigarElement cigarElement)
public int numCigarElements()
public boolean isEmpty()
public int getReferenceLength()
public int getPaddedReferenceLength()
public int getReadLength()
public static int getReadLength(java.util.List<CigarElement> cigarElements)
public java.util.List<SAMValidationError> isValid(java.lang.String readName, long recordNumber)
readName
- For error reporting only. May be null if not known.recordNumber
- For error reporting only. May be -1 if not known.public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
public java.lang.String toString()
toString
in class java.lang.Object