org.biojava.bio.seq.projection
Class ProjectedStrandedFeature

java.lang.Object
  |
  +--org.biojava.bio.seq.projection.ProjectedFeature
        |
        +--org.biojava.bio.seq.projection.ProjectedStrandedFeature

All Implemented Interfaces:

Annotatable, Changeable, Feature, FeatureHolder, Projection, StrandedFeature

public class ProjectedStrandedFeature

extends ProjectedFeature

implements StrandedFeature

Internal class used by ProjectedFeatureHolder to wrap StrandedFeatures.

Since:

1.1

Author:

Thomas Down, Matthew Pocock

Nested Class Summary

Nested classes inherited from class org.biojava.bio.seq.StrandedFeature

StrandedFeature.Strand, StrandedFeature.Template

Nested classes inherited from class org.biojava.bio.seq.Feature

Feature.ByLocationComparator, Feature.Template

Nested classes inherited from class org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

Nested classes inherited from class org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from interface org.biojava.bio.seq.StrandedFeature

NEGATIVE, POSITIVE, UNKNOWN

Fields inherited from interface org.biojava.bio.seq.Feature

byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, TYPE

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

ProjectedStrandedFeature(StrandedFeature f, ProjectionContext ctx)

Method Summary

StrandedFeature.Strand	getStrand() Retrieve the strand that this feature lies upon.
SymbolList	getSymbols() Return a list of symbols that are contained in this feature.
Feature.Template	makeTemplate() Create a new Template that could be used to generate a feature identical to this one.
java.lang.String	toString()

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

addChangeListener, addChangeListener, containsFeature, countFeatures, createFeature, equals, features, filter, filter, getAnnotation, getLocation, getParent, getProjectedFeatures, getProjectionContext, getSchema, getSequence, getSource, getType, getViewedFeature, hashCode, isUnchanging, removeChangeListener, removeChangeListener, removeFeature, setLocation, setSource, setType

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.bio.seq.Feature

features, getLocation, getParent, getSequence, getSource, getType, setLocation, setSource, setType

Methods inherited from interface org.biojava.bio.seq.FeatureHolder

containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Constructor Detail

ProjectedStrandedFeature

public ProjectedStrandedFeature(StrandedFeature f,
                                ProjectionContext ctx)

Method Detail

getStrand

public StrandedFeature.Strand getStrand()

Description copied from interface: StrandedFeature

Retrieve the strand that this feature lies upon.

This will be one of StrandedFeature.POSITIVE or NEGATIVE.

Specified by:

getStrand in interface StrandedFeature

Returns:

one of the Strand constants

makeTemplate

public Feature.Template makeTemplate()

Description copied from interface: Feature

Create a new Template that could be used to generate a feature identical to this one. The fields of the template can be edited without changing the feature.

Specified by:

makeTemplate in interface Feature

Overrides:

makeTemplate in class ProjectedFeature

Returns:

a new Template that would make a feature like this one

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getSymbols

public SymbolList getSymbols()

Description copied from interface: StrandedFeature

Return a list of symbols that are contained in this feature.

The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.

The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.

If the feature is on the negative strand then the SymbolList will be reverse-complemented as appropriate.

Specified by:

getSymbols in interface StrandedFeature

Overrides:

getSymbols in class ProjectedFeature

Returns:

a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent