org.biojava.bio.seq.projection

Class TranslateFlipContext

java.lang.Object

org.biojava.bio.seq.projection.ReparentContext

org.biojava.bio.seq.projection.TranslateFlipContext

All Implemented Interfaces:

Serializable, ProjectionContext

public class TranslateFlipContext
extends ReparentContext

A ProjectionContext that translates and optionaly flips features.

Use this to 'reverse complement' a feature hierachy, or just to shift it sideways a bit.

If the flipping mode is dissabled, then all translated features are projected as having locations equivalent to feat.getLocation().translate(translation). If the flipping mode is enabled, then all features are flipped arround translation so that translation-i becomes translation+i.

Author:

Matthew Pocock

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
TranslateFlipContext(FeatureHolder parent, FeatureHolder wrapped, int translation) Create a new TranslateFlipContext with translation only.
TranslateFlipContext(FeatureHolder parent, FeatureHolder wrapped, int translate, boolean oppositeStrand) Create a new TranslateFlipContext with explicit translation and flip.
TranslateFlipContext(FeatureHolder parent, FeatureHolder wrapped, int min, int max) Create a new TranslateFlipContext that flips all featurs arround min and max.

Method Summary

Methods

Modifier and Type	Method and Description
protected FilterUtils.FilterTransformer	getReverter()
protected FilterUtils.FilterTransformer	getTransformer()
int	getTranslation()
boolean	isOppositeStrand()
Location	projectLocation(Location oldLoc)
StrandedFeature.Strand	projectStrand(StrandedFeature.Strand strand)
Location	revertLocation(Location oldLoc)
StrandedFeature.Strand	revertStrand(StrandedFeature.Strand strand)

Methods inherited from class org.biojava.bio.seq.projection.ReparentContext

addChangeListener, createFeature, createFeature, getParent, getParent, getSchema, getSequence, getUnprojectedFeatures, projectChildFeatures, projectFeature, projectFeatures, projectFilter, removeChangeListener, removeFeature, removeFeature, revertFeature, revertFilter

Methods inherited from class java.lang.Object

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

Constructor Detail

TranslateFlipContext

public TranslateFlipContext(FeatureHolder parent,
                    FeatureHolder wrapped,
                    int translate,
                    boolean oppositeStrand)

Create a new TranslateFlipContext with explicit translation and flip.

Locations will be mapped according to the rules in @link ProjectionUtils.

Parameters:

parent - the parent to graft all projected features onto

wrapped - the featurs to project

translate - the translation

oppositeStrand - wether or not to flip

TranslateFlipContext

public TranslateFlipContext(FeatureHolder parent,
                    FeatureHolder wrapped,
                    int min,
                    int max)

Create a new TranslateFlipContext that flips all featurs arround min and max.

A Location at exactly min will become one at max, and a Location at exactly max will become one at min.

This is equivalent to TranslateFlipContext(parent, wrapped, min + max, true) and is provided to make client code more readable.

Parameters:

parent - the parent to graft all projected features ont

wrapped - the features to project

min - the lower position

max - the higher position

TranslateFlipContext

public TranslateFlipContext(FeatureHolder parent,
                    FeatureHolder wrapped,
                    int translation)

Create a new TranslateFlipContext with translation only.

This is equivalent to TranslateFlipContext(parent, wrapped, translation, false) and is provided to make client code more readable.

Parameters:

parent - the parent to graft all projected features onto

wrapped - the featurs to project

translation - the translation

Method Detail

getTranslation

public final int getTranslation()

isOppositeStrand

public final boolean isOppositeStrand()

projectLocation

public Location projectLocation(Location oldLoc)

revertLocation

public final Location revertLocation(Location oldLoc)

projectStrand

public final StrandedFeature.Strand projectStrand(StrandedFeature.Strand strand)

revertStrand

public final StrandedFeature.Strand revertStrand(StrandedFeature.Strand strand)

getTransformer

protected FilterUtils.FilterTransformer getTransformer()

Overrides:

getTransformer in class ReparentContext

getReverter

protected FilterUtils.FilterTransformer getReverter()

Overrides:

getReverter in class ReparentContext