All Superinterfaces:

Annotatable, Changeable, Comparable, Feature, FeatureHolder, RankedCrossRefable, RichAnnotatable, RichFeatureRelationshipHolder, StrandedFeature

All Known Implementing Classes:

SimpleRichFeature

public interface RichFeature
extends StrandedFeature, RankedCrossRefable, RichAnnotatable, RichFeatureRelationshipHolder, Comparable 

Since:

1.5

Author:

Richard Holland

• Nested Class Summary

  Nested Classes

  Modifier and Type	Interface and Description
  static class	RichFeature.Template Added-value extension of Feature.Template including bits we're interested in, eg. featureRelationshipSet for relationships with other features, and rankedCrossRefs for lookups into other databases.
  static class	RichFeature.Tools Some useful tools for working with features.

  • 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 ChangeType	CROSSREF
  static ChangeType	LOCATION
  static ChangeType	NAME
  static ChangeType	PARENT
  static ChangeType	RANK
  static ChangeType	RELATION
  static ChangeType	SOURCETERM
  static ChangeType	TYPETERM

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

    NEGATIVE, POSITIVE, STRAND, UNKNOWN

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

    byLocationOrder, 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

• Method Summary

  All Methods

  Modifier and Type	Method and Description
  String	getName () Returns the name of this feature.
  int	getRank () Returns the rank of this feature.
  void	setName (String name) Sets the name of this feature.
  void	setParent (FeatureHolder parent) Sets the parent of this feature.
  void	setRank (int rank) Sets the rank of this feature.

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

    getStrand, 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

  • Methods inherited from interface org.biojavax.RankedCrossRefable

    addRankedCrossRef, getRankedCrossRefs, removeRankedCrossRef, setRankedCrossRefs

  • Methods inherited from interface org.biojavax.RichAnnotatable

    getNoteSet, getRichAnnotation, setNoteSet

  • Methods inherited from interface org.biojavax.bio.seq.RichFeatureRelationshipHolder

    addFeatureRelationship, getFeatureRelationshipSet, removeFeatureRelationship, setFeatureRelationshipSet

  • Methods inherited from interface java.lang.Comparable

    compareTo

• Field Detail

  • NAME

    static final ChangeType NAME 

  • RANK

    static final ChangeType RANK 

  • SOURCETERM

    static final ChangeType SOURCETERM 

  • TYPETERM

    static final ChangeType TYPETERM 

  • LOCATION

    static final ChangeType LOCATION 

  • PARENT

    static final ChangeType PARENT 

  • CROSSREF

    static final ChangeType CROSSREF 

  • RELATION

    static final ChangeType RELATION 

• Method Detail

  • setParent

    void setParent(FeatureHolder parent)
     throws ChangeVetoException 

    Sets the parent of this feature.

    Parameters:

    parent - the parent the feature should identify itself with.

    Throws:

    ChangeVetoException - if the new value is unacceptable.

  • getName

    String getName()

    Returns the name of this feature.

    Returns:

    the name.

  • setName

    void setName(String name)
     throws ChangeVetoException 

    Sets the name of this feature.

    Parameters:

    name - the name the feature should identify itself with.

    Throws:

    ChangeVetoException - if the new value is unacceptable.

  • getRank

    int getRank()

    Returns the rank of this feature.

    Returns:

    the rank.

  • setRank

    void setRank(int rank)
     throws ChangeVetoException 

    Sets the rank of this feature.

    Parameters:

    rank - the rank the feature should identify itself with.

    Throws:

    ChangeVetoException - if the new value is unacceptable.