org.biojava.nbio.core.sequence.transcription

Enum Frame

java.lang.Object

java.lang.Enum<Frame>

org.biojava.nbio.core.sequence.transcription.Frame

All Implemented Interfaces:

Serializable, Comparable<Frame>

public enum Frame
extends Enum<Frame>

Indicates a way of translating a sequence.

Author:

ayates

Enum Constant Summary

Enum Constants

Enum Constant and Description
ONE
REVERSED_ONE
REVERSED_THREE
REVERSED_TWO
THREE
TWO

Method Summary

Methods

Modifier and Type	Method and Description
static Frame[]	getAllFrames() Delegates to values()
static Frame	getDefaultFrame()
static Frame[]	getForwardFrames() Returns all frames in the forward orientation
static Frame[]	getReverseFrames() Returns all frames which are in the reverse orientation
static Frame	valueOf(String name) Returns the enum constant of this type with the specified name.
static Frame[]	values() Returns an array containing the constants of this enum type, in the order they are declared.
<C extends NucleotideCompound> Sequence<C>	wrap(Sequence<C> incoming) Optionally wraps a Sequence in a reverse complementing view (if the frame is on the reverse strand) and creates a sub sequence view if it is required.

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

ONE

public static final Frame ONE

TWO

public static final Frame TWO

THREE

public static final Frame THREE

REVERSED_ONE

public static final Frame REVERSED_ONE

REVERSED_TWO

public static final Frame REVERSED_TWO

REVERSED_THREE

public static final Frame REVERSED_THREE

Method Detail

values

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

Returns:

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

valueOf

public static Frame 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 name

NullPointerException - if the argument is null

getDefaultFrame

public static Frame getDefaultFrame()

getForwardFrames

public static Frame[] getForwardFrames()

Returns all frames in the forward orientation

getReverseFrames

public static Frame[] getReverseFrames()

Returns all frames which are in the reverse orientation

getAllFrames

public static Frame[] getAllFrames()

Delegates to values()

wrap

public <C extends NucleotideCompound> Sequence<C> wrap(Sequence<C> incoming)

Optionally wraps a Sequence in a reverse complementing view (if the frame is on the reverse strand) and creates a sub sequence view if it is required. If you pass in ONE in you will get the same Sequence returned.