Package htsjdk.samtools
Enum SAMFlag
- java.lang.Object
-
- java.lang.Enum<SAMFlag>
-
- htsjdk.samtools.SAMFlag
-
- All Implemented Interfaces:
Serializable
,Comparable<SAMFlag>
public enum SAMFlag extends Enum<SAMFlag>
SAM flags as enum, to be used in GUI, menu, etc...
-
-
Enum Constant Summary
Enum Constants Enum Constant Description DUPLICATE_READ
FIRST_OF_PAIR
MATE_REVERSE_STRAND
MATE_UNMAPPED
NOT_PRIMARY_ALIGNMENT
Deprecated.useSECONDARY_ALIGNMENT
instead.PROPER_PAIR
READ_FAILS_VENDOR_QUALITY_CHECK
READ_PAIRED
READ_REVERSE_STRAND
READ_UNMAPPED
SECOND_OF_PAIR
SECONDARY_ALIGNMENT
SUPPLEMENTARY_ALIGNMENT
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static SAMFlag
findByName(String flag)
String
getDescription()
static Set<SAMFlag>
getFlags(int flag)
String
getLabel()
int
intValue()
boolean
isSet(int flag)
boolean
isUnset(int flag)
static SAMFlag
valueOf(int flag)
Returns the enum constant of this type with the specified name.static SAMFlag
valueOf(String name)
Returns the enum constant of this type with the specified name.static SAMFlag[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
-
-
-
Enum Constant Detail
-
READ_PAIRED
public static final SAMFlag READ_PAIRED
-
PROPER_PAIR
public static final SAMFlag PROPER_PAIR
-
READ_UNMAPPED
public static final SAMFlag READ_UNMAPPED
-
MATE_UNMAPPED
public static final SAMFlag MATE_UNMAPPED
-
READ_REVERSE_STRAND
public static final SAMFlag READ_REVERSE_STRAND
-
MATE_REVERSE_STRAND
public static final SAMFlag MATE_REVERSE_STRAND
-
FIRST_OF_PAIR
public static final SAMFlag FIRST_OF_PAIR
-
SECOND_OF_PAIR
public static final SAMFlag SECOND_OF_PAIR
-
SECONDARY_ALIGNMENT
public static final SAMFlag SECONDARY_ALIGNMENT
-
NOT_PRIMARY_ALIGNMENT
@Deprecated public static final SAMFlag NOT_PRIMARY_ALIGNMENT
Deprecated.useSECONDARY_ALIGNMENT
instead.
-
READ_FAILS_VENDOR_QUALITY_CHECK
public static final SAMFlag READ_FAILS_VENDOR_QUALITY_CHECK
-
DUPLICATE_READ
public static final SAMFlag DUPLICATE_READ
-
SUPPLEMENTARY_ALIGNMENT
public static final SAMFlag SUPPLEMENTARY_ALIGNMENT
-
-
Method Detail
-
values
public static SAMFlag[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:for (SAMFlag c : SAMFlag.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
-
valueOf
public static SAMFlag valueOf(String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
-
intValue
public int intValue()
- Returns:
- this flag as an int
-
getLabel
public String getLabel()
- Returns:
- a human label for this SAMFlag
-
getDescription
public String getDescription()
- Returns:
- a human description for this SAMFlag
-
valueOf
public static SAMFlag valueOf(int flag)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)- Parameters:
flag
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
-
findByName
public static SAMFlag findByName(String flag)
- Returns:
- find SAMFlag the flag by name, or null if it was not found
-
isSet
public boolean isSet(int flag)
-
isUnset
public boolean isUnset(int flag)
-
-