All Superinterfaces:

Annotatable, Changeable, Feature, FeatureHolder, StrandedFeature

All Known Implementing Classes:

SimpleFramedFeature

public interface FramedFeature
extends StrandedFeature 

Version:

1.0

Author:

Mark Schreiber

• Nested Class Summary

  Nested Classes

  Modifier and Type	Interface and Description
  static class	FramedFeature.ReadingFrame A singleton to hold the frame information
  static class	FramedFeature.Template

  • Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature

    StrandedFeature.Strand

  • Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature

    Feature.ByLocationComparator

  • Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

    FeatureHolder.EmptyFeatureHolder

  • Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

    Annotatable.AnnotationForwarder

• Field Summary

  Fields

  Modifier and Type	Field and Description
  static FramedFeature.ReadingFrame	FRAME_0
  static FramedFeature.ReadingFrame	FRAME_1
  static FramedFeature.ReadingFrame	FRAME_2

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

    NEGATIVE, POSITIVE, STRAND, UNKNOWN

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

    byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM

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

    EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

  • Fields inherited from interface org.biojava.bio.Annotatable

    ANNOTATION

• Method Summary

  All Methods

  Modifier and Type	Method and Description
  FramedFeature.ReadingFrame	getReadingFrame () return the reading frame of the feature.
  StrandedFeature.Strand	getStrand () Retrieve the strand that this feature lies upon.

  • Methods inherited from interface org.biojava.bio.seq.StrandedFeature

    getSymbols, setStrand

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

    features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm

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

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

  • Methods inherited from interface org.biojava.bio.Annotatable

    getAnnotation

  • Methods inherited from interface org.biojava.utils.Changeable

    addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

• Field Detail

  • FRAME_0

    static final FramedFeature.ReadingFrame FRAME_0 

  • FRAME_1

    static final FramedFeature.ReadingFrame FRAME_1 

  • FRAME_2

    static final FramedFeature.ReadingFrame FRAME_2 

• Method Detail

  • getReadingFrame

    FramedFeature.ReadingFrame getReadingFrame()

    return the reading frame of the feature.

  • getStrand

    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:

    the Strand that the feature is found on