org.biojava.bio.seq

Class CircularView

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.impl.ViewSequence

org.biojava.bio.seq.CircularView

All Implemented Interfaces:

Serializable, Annotatable, FeatureHolder, RealizingFeatureHolder, Sequence, SymbolList, Changeable

public class CircularView
extends ViewSequence

A circular view onto another Sequence object. The class allows for reinterpretation of locations and indices onto the sequence to allow for overlapping of the origin. The origin is assumed to be the first symbol. Future versions may support changing the origin.

In biojavax RichSequences intrinsicly know about circularity. No view is required. We strongly recommend using RichSequence if possible.

Since:

1.1

Version:

1.2

Author:

Mark Schreiber

See Also:

RichSequence, Serialized Form

Nested Class Summary

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

EDIT, EMPTY_LIST

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

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

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Constructor Summary

Constructors

Constructor and Description
CircularView(Sequence seq)
CircularView(Sequence seq, FeatureRealizer fr)

Method Summary

Methods

Modifier and Type	Method and Description
Feature	createFeature(Feature.Template template) Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
SymbolList	subList(int start, int end) Over rides ViewSequence.
String	subStr(int start, int end) Over rides ViewSequence.
Symbol	symbolAt(int index) Over rides ViewSequence.

Methods inherited from class org.biojava.bio.seq.impl.ViewSequence

containsFeature, countFeatures, edit, features, filter, filter, getAddedFeatures, getAlphabet, getAnnotation, getName, getSchema, getURN, iterator, length, realizeFeature, removeFeature, seqString, toList

Methods inherited from class org.biojava.utils.Unchangeable

addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

CircularView

public CircularView(Sequence seq,
            FeatureRealizer fr)

CircularView

public CircularView(Sequence seq)

Method Detail

symbolAt

public Symbol symbolAt(int index)

Over rides ViewSequence. Allows any integer index, positive or negative to return a symbol via the equation val = (val % length); Note that base zero is the base immediately before base 1 which is of course the last base of the sequence.

Specified by:

symbolAt in interface SymbolList

Overrides:

symbolAt in class ViewSequence

Parameters:

index - the index of the Symbol requested.

Returns:

the Symbol specified by the index.

subStr

public String subStr(int start,
            int end)

Over rides ViewSequence. Allows any integer index, positive or negative to return a symbol via the equation val = (val % length);

Will return a linear String which can, if nescessary, span the origin.

Specified by:

subStr in interface SymbolList

Overrides:

subStr in class ViewSequence

Parameters:

start - the index of the fist base

end - the index of the last base

Returns:

a String representation of the tokenized Symbols

createFeature

public Feature createFeature(Feature.Template template)
                      throws ChangeVetoException,
                             BioException

Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).

Specified by:

createFeature in interface FeatureHolder

Overrides:

createFeature in class ViewSequence

Parameters:

template - the template of the feature to be created.

Returns:

the feature created you can use the template of the returned feature to create another of the same type.

Throws:

BioException - if a non circular location is added that exceeds the 'boundaries' of the sequence.

ChangeVetoException - if the sequence is locked.

Since:

1.2

subList

public SymbolList subList(int start,
                 int end)

Over rides ViewSequence. Allows any integer index, positive or negative to return a symbol via the equation index = ((index -1) % length)+1

Will return a linear SymbolList which can ,if nescessary, span the origin.

Specified by:

subList in interface SymbolList

Overrides:

subList in class ViewSequence

Parameters:

start - the first base of the sublist

end - the last base of the sublist

Returns:

a SymbolList containing the Symbols from start to end inclusive