com.milaboratory.core.sequence

Class SequenceQuality

java.lang.Object

com.milaboratory.core.sequence.AbstractSeq<SequenceQuality>

com.milaboratory.core.sequence.SequenceQuality

All Implemented Interfaces:

Seq<SequenceQuality>, Serializable

public final class SequenceQuality
extends AbstractSeq<SequenceQuality>
implements Serializable

Representation of nucleotide sequence quality based on phred quality scores.

Author:

Dmitry Bolotin, Stanislav Poslavsky

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static byte	BAD_QUALITY_VALUE Default value of bad quality
static SequenceQuality	EMPTY
static byte	GOOD_QUALITY_VALUE Default value of good quality
static byte	MAX_QUALITY_VALUE This value encoded with Phred+33 will giv 'z'.

Constructor Summary

Constructors

Constructor and Description
SequenceQuality(byte[] data) Creates quality object from raw quality score values.
SequenceQuality(String string) Creates a phred sequence quality from a Sanger formatted quality string (33 based).
SequenceQuality(String string, int offset) Creates a phred sequence quality from a string formatted with corresponding offset.
SequenceQuality(String string, QualityFormat format) Creates a phred sequence quality from a string formatted with corresponding offset.

Method Summary

Methods

Modifier and Type	Method and Description
byte[]	asArray() Returns an underlying array of bytes.
SequenceQuality	concatenate(SequenceQuality... other)
static SequenceQuality	create(QualityFormat format, byte[] data, boolean check) Factory method for the SequenceQualityPhred object.
static SequenceQuality	create(QualityFormat format, byte[] data, int from, int length, boolean check) Factory method for the SequenceQualityPhred object.
byte[]	encode(int offset) Encodes current quality line with given offset.
byte[]	encode(QualityFormat format) Encodes current quality line with given format.
void	encodeTo(QualityFormat format, byte[] buffer, int offset) Encodes current quality line with given offset.
String	encodeToString(int offset) Encodes current quality line with given offset.
boolean	equals(Object o)
SequenceQualityBuilder	getBuilder() Returns a builder for corresponding seq type.
SequenceQuality	getRange(int from, int to) Returns substring of current quality scores line.
SequenceQuality	getRange(Range range) Returns substring of current quality scores line.
static SequenceQuality	getUniformQuality(byte qualityValue, int length) Creates a phred sequence quality containing only given values of quality.
int	hashCode()
float	log10ProbabilityOfErrorAt(int position) Get the log10 of probability of error (e.g.
byte	meanValue() Returns average sequence quality value
byte	minValue() Returns the worst sequence quality value
float	probabilityOfErrorAt(int position) Get probability of error (e.g.
SequenceQuality	reverse() Gets quality values in reverse order
int	size() Returns size of quality array
String	toString()
byte	value(int position) Get the raw sequence quality value (in binary format) at given sequence point

Methods inherited from class com.milaboratory.core.sequence.AbstractSeq

concatenate

Methods inherited from class java.lang.Object

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

Field Detail

EMPTY

public static final SequenceQuality EMPTY

GOOD_QUALITY_VALUE

public static final byte GOOD_QUALITY_VALUE

Default value of good quality

See Also:

Constant Field Values

MAX_QUALITY_VALUE

public static final byte MAX_QUALITY_VALUE

This value encoded with Phred+33 will giv 'z'. 59 would produce '{' which is a special character, and may spoil formatting in some cases.

See Also:

Constant Field Values

BAD_QUALITY_VALUE

public static final byte BAD_QUALITY_VALUE

Default value of bad quality

See Also:

Constant Field Values

Constructor Detail

SequenceQuality

public SequenceQuality(String string)

Creates a phred sequence quality from a Sanger formatted quality string (33 based).

Parameters:

string -

SequenceQuality

public SequenceQuality(String string,
               int offset)

Creates a phred sequence quality from a string formatted with corresponding offset.

Parameters:

string - string

SequenceQuality

public SequenceQuality(String string,
               QualityFormat format)

Creates a phred sequence quality from a string formatted with corresponding offset.

Parameters:

string - string

SequenceQuality

public SequenceQuality(byte[] data)

Creates quality object from raw quality score values.

Parameters:

data - raw quality score values

Method Detail

asArray

public byte[] asArray()

Returns an underlying array of bytes.

Returns:

underlying array of bytes

log10ProbabilityOfErrorAt

public float log10ProbabilityOfErrorAt(int position)

Get the log10 of probability of error (e.g. nucleotide substitution) at given sequence point

Parameters:

position - positioninate in sequence

Returns:

log10 of probability of error

probabilityOfErrorAt

public float probabilityOfErrorAt(int position)

Get probability of error (e.g. nucleotide substitution) at given sequence point

Parameters:

position - positioninate in sequence

Returns:

probability of error

value

public byte value(int position)

Get the raw sequence quality value (in binary format) at given sequence point

Parameters:

position - positioninate in sequence

Returns:

raw sequence quality value

minValue

public byte minValue()

Returns the worst sequence quality value

Returns:

worst sequence quality value

meanValue

public byte meanValue()

Returns average sequence quality value

Returns:

average sequence quality value

reverse

public SequenceQuality reverse()

Gets quality values in reverse order

Returns:

quality values in reverse order

getRange

public SequenceQuality getRange(int from,
                       int to)

Returns substring of current quality scores line.

Specified by:

getRange in interface Seq<SequenceQuality>

Parameters:

from - inclusive

to - exclusive

Returns:

substring of current quality scores line

getRange

public SequenceQuality getRange(Range range)

Returns substring of current quality scores line.

Specified by:

getRange in interface Seq<SequenceQuality>

Overrides:

getRange in class AbstractSeq<SequenceQuality>

Parameters:

range - range

Returns:

substring of current quality scores line

size

public int size()

Returns size of quality array

Specified by:

size in interface Seq<SequenceQuality>

Returns:

size of quality array

getBuilder

public SequenceQualityBuilder getBuilder()

Description copied from interface: Seq

Returns a builder for corresponding seq type.

Specified by:

getBuilder in interface Seq<SequenceQuality>

Returns:

builder for corresponding seq type

concatenate

public SequenceQuality concatenate(SequenceQuality... other)

encodeTo

public void encodeTo(QualityFormat format,
            byte[] buffer,
            int offset)

Encodes current quality line with given offset. Common values for offset are 33 and 64.

Parameters:

offset - offset

encode

public byte[] encode(int offset)

Encodes current quality line with given offset. Common values for offset are 33 and 64.

Parameters:

offset - offset

Returns:

bytes encoded quality values

encode

public byte[] encode(QualityFormat format)

Encodes current quality line with given format. Common values for offset are 33 and 64.

Parameters:

format - quality format with offset

Returns:

bytes encoded quality values

encodeToString

public String encodeToString(int offset)

Encodes current quality line with given offset. Common values for offset are 33 and 64.

Parameters:

offset - offset

Returns:

encoded quality values

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

getUniformQuality

public static SequenceQuality getUniformQuality(byte qualityValue,
                                int length)

Creates a phred sequence quality containing only given values of quality.

Parameters:

qualityValue - value to fill the quality values with

length - size of quality string

create

public static SequenceQuality create(QualityFormat format,
                     byte[] data,
                     int from,
                     int length,
                     boolean check)

Factory method for the SequenceQualityPhred object. It performs all necessary range checks if required.

Parameters:

format - format of encoded quality values

data - byte with encoded quality values

from - starting position in data

length - number of bytes to parse

check - determines whether range check is required

Returns:

quality line object

Throws:

WrongQualityFormat - if encoded value are out of range and checking is enabled

create

public static SequenceQuality create(QualityFormat format,
                     byte[] data,
                     boolean check)

Factory method for the SequenceQualityPhred object. It performs all necessary range checks if required.

Parameters:

format - format of encoded quality values

data - byte with encoded quality values

check - determines whether range check is required

Returns:

quality line object

Throws:

WrongQualityFormat - if encoded value are out of range and checking is enabled