com.milaboratory.core

Enum PairedEndReadsLayout

java.lang.Object

java.lang.Enum<PairedEndReadsLayout>

com.milaboratory.core.PairedEndReadsLayout

All Implemented Interfaces:

Serializable, Comparable<PairedEndReadsLayout>

public enum PairedEndReadsLayout
extends Enum<PairedEndReadsLayout>
implements Serializable

Enum Constant Summary

Enum Constants

Enum Constant and Description
Collinear R1 R2 ---> ---> + R2 R1 <--- <---
CollinearDirect R1 R2 ---> --->
DirectOnly R1 R2 ---> <---
Opposite R1 R2 ---> <--- + R2 R1 ---> <---
ReverseOnly R2 R1 ---> <---
Unknown R1 R2 ---> <--- + R2 R1 ---> <--- + R1 R2 ---> ---> + R2 R1 <--- <---

Method Summary

Methods

Modifier and Type	Method and Description
Target[]	createTargets(PairedRead read)
Target[]	createTargets(SequenceRead read)
Target[]	createTargets(SingleRead read)
boolean[]	getPossibleRelativeStrands() Determines possible relative (R1 relative to R2) strands.
static PairedEndReadsLayout	valueOf(String name) Returns the enum constant of this type with the specified name.
static PairedEndReadsLayout[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

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

DirectOnly

public static final PairedEndReadsLayout DirectOnly

R1 R2 ---> <---

ReverseOnly

public static final PairedEndReadsLayout ReverseOnly

R2 R1 ---> <---

Opposite

public static final PairedEndReadsLayout Opposite

R1 R2 ---> <--- + R2 R1 ---> <---

Collinear

public static final PairedEndReadsLayout Collinear

R1 R2 ---> ---> + R2 R1 <--- <---

CollinearDirect

public static final PairedEndReadsLayout CollinearDirect

R1 R2 ---> --->

Unknown

public static final PairedEndReadsLayout Unknown

R1 R2 ---> <--- + R2 R1 ---> <--- + R1 R2 ---> ---> + R2 R1 <--- <---

Method Detail

values

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

Returns:

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

valueOf

public static PairedEndReadsLayout 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

createTargets

public Target[] createTargets(PairedRead read)

createTargets

public Target[] createTargets(SingleRead read)

createTargets

public Target[] createTargets(SequenceRead read)

getPossibleRelativeStrands

public boolean[] getPossibleRelativeStrands()

Determines possible relative (R1 relative to R2) strands. (true for RC; false for same strand) Used only in paired-end reads merger.