com.milaboratory.core.merger

Class PairedReadMergingResult

java.lang.Object

com.milaboratory.core.merger.PairedReadMergingResult

All Implemented Interfaces:

Serializable

public class PairedReadMergingResult
extends Object
implements Serializable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	MATCH_SCORE
static int	MISMATCH_SCORE

Constructor Summary

Constructors

Constructor and Description
PairedReadMergingResult(PairedRead originalRead) Constructor for failed merging result.
PairedReadMergingResult(PairedRead originalRead, NSequenceWithQuality overlappedSequence, int overlap, int errors, boolean reversed, int offset, MergerParameters.IdentityType identityType, double identity) Constructor for successful merging result.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
int	getErrors()
double	getIdentity()
MergerParameters.IdentityType	getIdentityType()
int	getOffset()
PairedRead	getOriginalRead()
int	getOverlap()
NSequenceWithQuality	getOverlappedSequence()
int	hashCode()
boolean	isReversed()
boolean	isSuccessful()
int	score()
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

MATCH_SCORE

public static final int MATCH_SCORE

See Also:

Constant Field Values

MISMATCH_SCORE

public static final int MISMATCH_SCORE

See Also:

Constant Field Values

Constructor Detail

PairedReadMergingResult

public PairedReadMergingResult(PairedRead originalRead)

Constructor for failed merging result.

Parameters:

originalRead - original read

PairedReadMergingResult

public PairedReadMergingResult(PairedRead originalRead,
                       NSequenceWithQuality overlappedSequence,
                       int overlap,
                       int errors,
                       boolean reversed,
                       int offset,
                       MergerParameters.IdentityType identityType,
                       double identity)

Constructor for successful merging result.

Parameters:

originalRead - original read

overlappedSequence - reconstructed (overlapped) sequence from paired-end reads

overlap - number of overlapped nucleotides

errors - number of mismatches/insertions/deletions found in overlapping region

Method Detail

isSuccessful

public boolean isSuccessful()

getOriginalRead

public PairedRead getOriginalRead()

getOverlappedSequence

public NSequenceWithQuality getOverlappedSequence()

getOverlap

public int getOverlap()

getOffset

public int getOffset()

getErrors

public int getErrors()

getIdentity

public double getIdentity()

getIdentityType

public MergerParameters.IdentityType getIdentityType()

score

public int score()

isReversed

public boolean isReversed()

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object