io.repseq.core

Class SequencePartitioning

java.lang.Object

io.repseq.core.SequencePartitioning

Direct Known Subclasses:

AbstractReferencePoints

public abstract class SequencePartitioning
extends java.lang.Object

Object stores information about sequence partitioning (positions of specific anchor points)

Constructor Summary

Constructors

Constructor and Description
SequencePartitioning()

Method Summary

Modifier and Type	Method and Description
static int	floorDiv(int x, int y)
static int	floorMod(int x, int y)
int	getAbsolutePosition(GeneFeature feature, int positionInFeature) Returns absolute position in reference sequence for the specified local position in specified feature or -1 if this position can't be projected.
protected int	getLength(GeneFeature.ReferenceRange refRange)
int	getLength(GeneFeature feature)
abstract int	getPosition(ReferencePoint referencePoint) Return position of specific anchor point
protected com.milaboratory.core.Range	getRange(GeneFeature.ReferenceRange refRange)
com.milaboratory.core.Range	getRange(GeneFeature feature) Return sequence range for non-composite gene features
com.milaboratory.core.Range[]	getRanges(GeneFeature feature)
int	getRelativePosition(GeneFeature feature, ReferencePoint referencePoint) Returns a relative position of specified referencePoint in specified feature or -1 if this position is not available.
com.milaboratory.core.Range	getRelativeRange(GeneFeature feature, GeneFeature subFeature) Returns a relative range of specified subFeature in specified feature or null if this is not available.
com.milaboratory.core.sequence.TranslationParameters	getTranslationParameters(GeneFeature feature) Calculates translation parameters ( ~ translation frame ) for given gene feature using current sequence partitioning.
java.util.List<RangeTranslationParameters>	getTranslationParameters(int length) Returns RangeTranslationParameters for all ranges in current partitioning that can be transcribed
protected boolean	isAvailable(GeneFeature.ReferenceRange refRange)
boolean	isAvailable(GeneFeature feature) Checks if position of gene feature can be obtained using this partitioning
boolean	isAvailable(ReferencePoint referencePoint) Checks if position of anchor point can be obtained using this partitioning
abstract boolean	isReversed() Return true if sequence partitioning is defined on the reverse-complement strand of the sequence, false if on forward strand.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequencePartitioning

public SequencePartitioning()

Method Detail

getPosition

public abstract int getPosition(ReferencePoint referencePoint)

Return position of specific anchor point

Parameters:

referencePoint - anchor point

Returns:

position of anchor point

isReversed

public abstract boolean isReversed()

Return true if sequence partitioning is defined on the reverse-complement strand of the sequence, false if on forward strand.

Returns:

true if partitioning is defined on the reverse-complement strand

isAvailable

public boolean isAvailable(ReferencePoint referencePoint)

Checks if position of anchor point can be obtained using this partitioning

Parameters:

referencePoint - anchor point

Returns:

true if position of anchor point can be obtained using this partitioning

isAvailable

public boolean isAvailable(GeneFeature feature)

Checks if position of gene feature can be obtained using this partitioning

Parameters:

feature - gene feature

Returns:

true if position of gene feature can be obtained using this partitioning

getRange

public com.milaboratory.core.Range getRange(GeneFeature feature)

Return sequence range for non-composite gene features

Parameters:

feature - gene feature

Returns:

range

getRanges

public com.milaboratory.core.Range[] getRanges(GeneFeature feature)

getLength

public int getLength(GeneFeature feature)

getRange

protected com.milaboratory.core.Range getRange(GeneFeature.ReferenceRange refRange)

getLength

protected int getLength(GeneFeature.ReferenceRange refRange)

isAvailable

protected boolean isAvailable(GeneFeature.ReferenceRange refRange)

getRelativeRange

public com.milaboratory.core.Range getRelativeRange(GeneFeature feature,
                                                    GeneFeature subFeature)

Returns a relative range of specified subFeature in specified feature or null if this is not available.

Parameters:

feature - gene feature

subFeature - a part of feature

Returns:

relative range of specified subFeature in specified feature or null if this is not available

getRelativePosition

public int getRelativePosition(GeneFeature feature,
                               ReferencePoint referencePoint)

Returns a relative position of specified referencePoint in specified feature or -1 if this position is not available.

Parameters:

feature - gene feature

referencePoint - reference point

Returns:

a relative position of specified referencePoint in specified feature or -1 if this position is not available

getAbsolutePosition

public int getAbsolutePosition(GeneFeature feature,
                               int positionInFeature)

Returns absolute position in reference sequence for the specified local position in specified feature or -1 if this position can't be projected.

Parameters:

feature - gene feature

positionInFeature - local position in gene feature

Returns:

absolute position in reference sequence for the specified local position in specified feature or -1 if this position can't be projected

getTranslationParameters

public com.milaboratory.core.sequence.TranslationParameters getTranslationParameters(GeneFeature feature)

Calculates translation parameters ( ~ translation frame ) for given gene feature using current sequence partitioning. Return null for untranslatable gene features (like 5'UTR).

Parameters:

feature - target gene feature

Returns:

translation parameters

getTranslationParameters

public java.util.List<RangeTranslationParameters> getTranslationParameters(int length)

Returns RangeTranslationParameters for all ranges in current partitioning that can be transcribed

Parameters:

length - length of original sequence (Integer.MAX_VALUE can be used if value is not known in advance, this value will be set for final range and must be processed accordingly)

floorDiv

public static int floorDiv(int x,
                           int y)

floorMod

public static int floorMod(int x,
                           int y)