public class Cigar extends java.lang.Object implements java.io.Serializable, java.lang.Iterable<CigarElement>
Modifier and Type | Field and Description |
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static long |
serialVersionUID |
Constructor and Description |
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Cigar() |
Cigar(java.util.List<CigarElement> cigarElements) |
Modifier and Type | Method and Description |
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void |
add(CigarElement cigarElement) |
boolean |
containsOperator(CigarOperator operator)
returns true if the cigar string contains the given operator
|
boolean |
equals(java.lang.Object o) |
static Cigar |
fromCigarOperators(java.util.List<CigarOperator> cigarOperators)
build a new Cigar object from a list of cigar operators.
|
CigarElement |
getCigarElement(int i) |
java.util.List<CigarElement> |
getCigarElements() |
CigarElement |
getFirstCigarElement()
returns the first cigar element
|
CigarElement |
getLastCigarElement()
returns the last cigar element
|
int |
getPaddedReferenceLength() |
int |
getReadLength() |
static int |
getReadLength(java.util.List<CigarElement> cigarElements) |
int |
getReferenceLength() |
int |
hashCode() |
boolean |
isClipped()
returns true if the cigar is clipped
|
boolean |
isEmpty() |
boolean |
isLeftClipped()
returns true if the cigar string starts With a clipping operator
|
boolean |
isRightClipped()
returns true if the cigar string ends With a clipping operator
|
java.util.List<SAMValidationError> |
isValid(java.lang.String readName,
long recordNumber)
Exhaustive validation of CIGAR.
|
java.util.Iterator<CigarElement> |
iterator()
shortcut to
getCigarElements().iterator() |
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 static Cigar fromCigarOperators(java.util.List<CigarOperator> cigarOperators)
[M,M,M,M,M,M,M,M,M,M]
, here
fromCigarOperators would generate the cigar '10M'
later the user resolved the 'M' to '=' or 'X', the array is now
[=,=,=,=,=,X,X,=,=,=]
fromCigarOperators would generate the cigar '5M2X3M'public java.util.Iterator<CigarElement> iterator()
getCigarElements().iterator()
iterator
in interface java.lang.Iterable<CigarElement>
public boolean containsOperator(CigarOperator operator)
public CigarElement getFirstCigarElement()
public CigarElement getLastCigarElement()
public boolean isLeftClipped()
public boolean isRightClipped()
public boolean isClipped()
public int hashCode()
hashCode
in class java.lang.Object
public java.lang.String toString()
toString
in class java.lang.Object