org.biojavax.bio.seq

Interface RichSequence

All Superinterfaces:

Annotatable, BioEntry, Changeable, Comparable, FeatureHolder, RankedCrossRefable, RichAnnotatable, Sequence, SymbolList

All Known Implementing Classes:

SimpleRichSequence, ThinRichSequence

public interface RichSequence
extends BioEntry, Sequence

A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence. It inherits and merges the methods of both. The RichSequence is based on the BioSQL model and provides a richer array of methods to access information than Sequence does. Whenever possible RichSequence should be used in preference to Sequence.

Since:

1.5

Author:

Mark Schreiber, Richard Holland, George Waldon

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	RichSequence.IOTools A set of convenience methods for handling common file formats.
static class	RichSequence.Terms Stores a number of useful terms used across many sequence formats for consistency's sake.
static class	RichSequence.Tools Some useful tools for working with RichSequence objects.

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

Annotatable.AnnotationForwarder

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

FeatureHolder.EmptyFeatureHolder

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	CIRCULAR
static ChangeType	SYMLISTVERSION

Fields inherited from interface org.biojavax.bio.BioEntry

COMMENT, DESCRIPTION, DIVISION, IDENTIFIER, RANKEDCROSSREF, RANKEDDOCREF, RELATIONS, SEQVERSION, TAXON

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

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

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Method Summary

Modifier and Type	Method and Description
boolean	getCircular() Is the sequence circular?
Set<Feature>	getFeatureSet() The features for this sequence.
SymbolList	getInternalSymbolList() A special function that returns the SymbolList that this RichSequence is based around.
Double	getSeqVersion() The version of the associated symbol list.
void	setCircular(boolean circular) Circularises the Sequence.
void	setFeatureSet(Set<Feature> features) Sets the features of this sequence.
void	setSeqVersion(Double seqVersion) Sets the version of the associated symbol list.

Methods inherited from interface org.biojavax.bio.BioEntry

addComment, addRankedDocRef, addRelationship, getAccession, getComments, getDescription, getDivision, getIdentifier, getName, getNamespace, getRankedDocRefs, getRelationships, getTaxon, getVersion, removeComment, removeRankedDocRef, removeRelationship, setDescription, setDivision, setIdentifier, setTaxon

Methods inherited from interface org.biojavax.RichAnnotatable

getNoteSet, getRichAnnotation, setNoteSet

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 java.lang.Comparable

compareTo

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

getName, getURN

Methods inherited from interface org.biojava.bio.symbol.SymbolList

edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList

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

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

Field Detail

SYMLISTVERSION

static final ChangeType SYMLISTVERSION

CIRCULAR

static final ChangeType CIRCULAR

Method Detail

getSeqVersion

Double getSeqVersion()

The version of the associated symbol list. Note the use of an object for the value means that it can be nulled.

Returns:

the version

setSeqVersion

void setSeqVersion(Double seqVersion)
            throws ChangeVetoException

Sets the version of the associated symbol list. Note the use of an object for the value means that it can be nulled.

Parameters:

seqVersion - the version to set.

Throws:

ChangeVetoException - if it doesn't want to change.

getFeatureSet

Set<Feature> getFeatureSet()

The features for this sequence.

Returns:

a set of RichFeature objects.

setFeatureSet

void setFeatureSet(Set<Feature> features)
            throws ChangeVetoException

Sets the features of this sequence. Note that it is not checked to see if the features actually belong to this sequence, you'd best check that yourself and make changes using feature.setParent() if necessary.

Parameters:

features - the features to assign to this sequence, replacing all others. Must be a set of RichFeature objects.

Throws:

ChangeVetoException - if they could not be assigned.

setCircular

void setCircular(boolean circular)
          throws ChangeVetoException

Circularises the Sequence. The circular length can then be said to be the length of the sequence itself.

Parameters:

circular - set to true if you want it to be circular

Throws:

ChangeVetoException - if the change is blocked. Some implementations may choose not to support circularisation and should throw an exception here. Some implementations may only support this method for certain Alphabets.

getCircular

boolean getCircular()

Is the sequence circular? Circularity has implications for work with locations and any coordinate work eg symbolAt(int i). Classes that allow it should test this method when working with coordinates or locations / features.

Returns:

true if the this is circular else false.

getInternalSymbolList

SymbolList getInternalSymbolList()

A special function that returns the SymbolList that this RichSequence is based around. This should _not_ be the RichSequence object itself, as this function is used to perform actions on the symbol list without referring to the RichSequence object directly.

Returns:

the internal SymbolList of the RichSequence, NOT the RichSequence object itself.