com.milaboratory.core.sequence

Class SequenceWithQuality<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.sequence.SequenceWithQuality<S>

Type Parameters:

S - type of sequence

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

NSequenceWithQuality

public class SequenceWithQuality<S extends Sequence<S>>
extends Object
implements Serializable

A container of sequence and its quality.

Author:

Dmitry Bolotin, Stanislav Poslavsky

See Also:

Sequence, SequenceQuality, NSequenceWithQuality, Serialized Form

Constructor Summary

Constructors

Constructor and Description
SequenceWithQuality(S sequence, SequenceQuality quality) Creates sequence with quality from specified values.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
SequenceQuality	getQuality() Returns quality.
S	getSequence() Returns sequence.
SequenceWithQuality<S>	getSubSequence(int from, int to) Returns subsequence with its quality starting at from (inclusive) and ending at to (exclusive).
SequenceWithQuality<S>	getSubSequence(Range range) Returns subsequence with its quality with starting (inclusive) and ending (exclusive) points defined by range.
int	hashCode()
int	size() Returns the size of this sequence and quality (sequence and quality has same sizes).
String	toPrettyString() Returns a pretty string representation of this.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceWithQuality

public SequenceWithQuality(S sequence,
                   SequenceQuality quality)

Creates sequence with quality from specified values.

Parameters:

sequence - sequence

quality - sequence quality

Throws:

IllegalArgumentException - if sequence.size() != quality.size()

Method Detail

getSequence

public S getSequence()

Returns sequence.

Returns:

sequence

getQuality

public SequenceQuality getQuality()

Returns quality.

Returns:

quality

getSubSequence

public SequenceWithQuality<S> getSubSequence(int from,
                                    int to)

Returns subsequence with its quality starting at from (inclusive) and ending at to (exclusive).

Parameters:

from - starting point of subsequence (inclusive)

to - ending point of subsequence (exclusive)

Returns:

subsequence with its quality starting at from (inclusively) and ending at to (exclusively

getSubSequence

public SequenceWithQuality<S> getSubSequence(Range range)

Returns subsequence with its quality with starting (inclusive) and ending (exclusive) points defined by range.

Parameters:

range - range that defines starting (inclusive) and ending (exclusive) points of subsequence

Returns:

subsequence with its quality with starting (inclusive) and ending (exclusive) points defined by range.

size

public int size()

Returns the size of this sequence and quality (sequence and quality has same sizes).

Returns:

size of this sequence and quality

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toPrettyString

public String toPrettyString()

Returns a pretty string representation of this.

Returns:

pretty string representation of this

toString

public String toString()

Overrides:

toString in class Object