org.biojavax.bio.seq

Interface RichFeature

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

Represents a feature that can be given name and rank and be moved from one sequence to another.

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

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.