htsjdk.variant.bcf2

Enum BCF2Type

java.lang.Object

java.lang.Enum<BCF2Type>

htsjdk.variant.bcf2.BCF2Type

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<BCF2Type>

public enum BCF2Type
extends java.lang.Enum<BCF2Type>

BCF2 types and associated information

Since:

05/12

Enum Constant Summary

Enum Constants

Enum Constant and Description
CHAR
FLOAT
INT16
INT32
INT8
MISSING

Method Summary

Methods

Modifier and Type	Method and Description
int	getID() The ID according to the BCF2 specification
int	getMissingBytes() The bytes (encoded as an int) that are used to represent a missing value for this type in BCF2
java.lang.Object	getMissingJavaValue() Return the java object (aka null) that is used to represent a missing value for this type in Java
int	getSizeInBytes() How many bytes are used to represent this type on disk?
boolean	isIntegerType()
boolean	isMissingType()
int	read(java.io.InputStream in) Read a value from in stream of this BCF2 type as an int [32 bit] collection of bits For intX and char values this is just the int / byte value of the underlying data represented as a 32 bit int For a char the result must be converted to a char by (char)(byte)(0x0F & value) For doubles it's necessary to convert subsequently this value to a double via Double.bitsToDouble()
static BCF2Type	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static BCF2Type[]	values() Returns an array containing the constants of this enum type, in the order they are declared.
boolean	withinRange(long v) Can we encode value v in this type, according to its declared range.
void	write(int value, java.io.OutputStream out)

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

MISSING

public static final BCF2Type MISSING

INT8

public static final BCF2Type INT8

INT16

public static final BCF2Type INT16

INT32

public static final BCF2Type INT32

FLOAT

public static final BCF2Type FLOAT

CHAR

public static final BCF2Type CHAR

Method Detail

values

public static BCF2Type[] 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 (BCF2Type c : BCF2Type.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static BCF2Type valueOf(java.lang.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:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null

getSizeInBytes

public int getSizeInBytes()

How many bytes are used to represent this type on disk?

Returns:

getID

public int getID()

The ID according to the BCF2 specification

Returns:

withinRange

public final boolean withinRange(long v)

Can we encode value v in this type, according to its declared range. Only makes sense for integer values

Parameters:

v -

Returns:

getMissingJavaValue

public java.lang.Object getMissingJavaValue()

Return the java object (aka null) that is used to represent a missing value for this type in Java

Returns:

getMissingBytes

public int getMissingBytes()

The bytes (encoded as an int) that are used to represent a missing value for this type in BCF2

Returns:

isMissingType

public boolean isMissingType()

Returns:

true if this BCF2Type corresponds to the magic "MISSING" type (0x00)

isIntegerType

public boolean isIntegerType()

read

public int read(java.io.InputStream in)
         throws java.io.IOException

Read a value from in stream of this BCF2 type as an int [32 bit] collection of bits For intX and char values this is just the int / byte value of the underlying data represented as a 32 bit int For a char the result must be converted to a char by (char)(byte)(0x0F & value) For doubles it's necessary to convert subsequently this value to a double via Double.bitsToDouble()

Parameters:

in -

Returns:

Throws:

java.io.IOException

write

public void write(int value,
         java.io.OutputStream out)
           throws java.io.IOException

Throws:

java.io.IOException