Serializable
, Comparable<CigarOperator>
public enum CigarOperator extends Enum<CigarOperator>
Enum Constant | Description |
---|---|
D |
Deletion vs.
|
EQ |
Matches the reference.
|
H |
Hard clip.
|
I |
Insertion vs.
|
M |
Match or mismatch
|
N |
Skipped region from the reference.
|
P |
Padding.
|
S |
Soft clip.
|
X |
Mismatches the reference.
|
Modifier and Type | Field | Description |
---|---|---|
static CigarOperator |
DELETION |
|
static CigarOperator |
HARD_CLIP |
|
static CigarOperator |
INSERTION |
|
static CigarOperator |
MATCH_OR_MISMATCH |
|
static CigarOperator |
PADDING |
|
static CigarOperator |
SKIPPED_REGION |
|
static CigarOperator |
SOFT_CLIP |
Modifier and Type | Method | Description |
---|---|---|
static CigarOperator |
binaryToEnum(int i) |
|
static CigarOperator |
characterToEnum(int b) |
|
boolean |
consumesReadBases() |
If true, represents that this cigar operator "consumes" bases from the read bases.
|
boolean |
consumesReferenceBases() |
If true, represents that this cigar operator "consumes" bases from the reference sequence.
|
static int |
enumToBinary(CigarOperator e) |
|
static byte |
enumToCharacter(CigarOperator e) |
Returns the character that should be used within a SAM file.
|
boolean |
isAlignment() |
Returns true if the operator is a M, a X or a EQ
|
boolean |
isClipping() |
Returns true if the operator is a clipped (hard or soft) operator
|
boolean |
isIndel() |
Returns true if the operator is a Insertion or Deletion operator
|
boolean |
isIndelOrSkippedRegion() |
Returns true if the operator is a Skipped Region Insertion or Deletion operator
|
boolean |
isPadding() |
Returns true if the operator is a Padding operator
|
String |
toString() |
Returns the cigar operator as it would be seen in a SAM file.
|
static CigarOperator |
valueOf(String name) |
Returns the enum constant of this type with the specified name.
|
static CigarOperator[] |
values() |
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static final CigarOperator M
public static final CigarOperator I
public static final CigarOperator D
public static final CigarOperator N
public static final CigarOperator S
public static final CigarOperator H
public static final CigarOperator P
public static final CigarOperator EQ
public static final CigarOperator X
public static final CigarOperator MATCH_OR_MISMATCH
public static final CigarOperator INSERTION
public static final CigarOperator DELETION
public static final CigarOperator SKIPPED_REGION
public static final CigarOperator SOFT_CLIP
public static final CigarOperator HARD_CLIP
public static final CigarOperator PADDING
public static CigarOperator[] values()
for (CigarOperator c : CigarOperator.values()) System.out.println(c);
public static CigarOperator valueOf(String name)
name
- the name of the enum constant to be returned.IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is nullpublic boolean consumesReadBases()
public boolean consumesReferenceBases()
public static CigarOperator characterToEnum(int b)
b
- CIGAR operator in character form as appears in a text CIGAR stringpublic static CigarOperator binaryToEnum(int i)
i
- CIGAR operator in binary form as appears in a BAMRecord.public static int enumToBinary(CigarOperator e)
e
- CigarOperator enum value.public static byte enumToCharacter(CigarOperator e)
public boolean isClipping()
public boolean isIndel()
public boolean isIndelOrSkippedRegion()
public boolean isAlignment()
public boolean isPadding()
public String toString()
toString
in class Enum<CigarOperator>