org.biojava.bio.seq.impl
Class RevCompSequence

java.lang.Object
  org.biojava.utils.AbstractChangeable
      org.biojava.bio.seq.impl.SimpleSequence
          org.biojava.bio.seq.impl.RevCompSequence

All Implemented Interfaces:

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

public class RevCompSequence
extends SimpleSequence

A reverse complement view onto Sequence interface.

All features of the underlying sequence are reflected onto the RevCompSequence using a ProjectedFeatureHolder

calling createFeature() on a RevCompSequence creates a feature on the underlying sequence. Non-Stranded features will return the reverse compemented view of the sequence when getSymbols() is called that is to say if you get what you expect as if your RevCompSequence was a regular Sequence.

Author:

David Waring, Thomas Down

See Also:

Serialized Form

Nested Class Summary

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

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

FeatureHolder.EmptyFeatureHolder

Field Summary

protected Sequence

origSeq

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

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

RevCompSequence(Sequence seq)
URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these.

RevCompSequence(Sequence seq, String urn, String name, Annotation annotation)

Method Summary

Object	clone() clone() should make a complete copy of the Sequence with all features (and children) and return a SimpleSequence that is unconnected from the original sequence.
boolean	containsFeature(Feature f) containsFeature() will return true if this seq contains the feature in question, or if if the original (non reverse complement) sequence contains the feature;
int	countFeatures() Count how many features are contained.
Feature	createFeature(Feature.Template ft) createFeature() will call createFeature() on the underlying Sequence.
void	edit(Edit e) edit() will try to edit the underlying Sequence.
Iterator	features() Iterate over the features in no well defined order.
FeatureHolder	filter(FeatureFilter ff) Query this set of features using a supplied FeatureFilter.
FeatureHolder	filter(FeatureFilter ff, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
Feature	getFeatureFromOriginal(Feature f) getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence.
void	removeFeature(Feature f) Remove a feature attached to this sequence.

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

createFeature, featureHolderAllocated, getAlphabet, getAnnotation, getChangeSupport, getFeatureHolder, getName, getSchema, getURN, iterator, length, realizeFeature, seqString, setName, setURN, subList, subStr, symbolAt, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

origSeq

protected Sequence origSeq

Constructor Detail

RevCompSequence

public RevCompSequence(Sequence seq)
                throws IllegalAlphabetException

URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these.

Throws:

IllegalAlphabetException

RevCompSequence

public RevCompSequence(Sequence seq,
                       String urn,
                       String name,
                       Annotation annotation)
                throws IllegalAlphabetException

Throws:

IllegalAlphabetException

Method Detail

edit

public void edit(Edit e)
          throws ChangeVetoException,
                 IndexOutOfBoundsException

edit() will try to edit the underlying Sequence. So if it is editable this will be too

Since I have not seen and editable Sequence I have not tested this

Specified by:

edit in interface SymbolList

Overrides:

edit in class SimpleSequence

Parameters:

e - the Edit to perform

Throws:

ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed

IndexOutOfBoundsException - if the edit does not lie within the SymbolList

features

public Iterator features()

Description copied from interface: FeatureHolder

Iterate over the features in no well defined order.

Specified by:

features in interface FeatureHolder

Overrides:

features in class SimpleSequence

Returns:

an Iterator

countFeatures

public int countFeatures()

Description copied from interface: FeatureHolder

Count how many features are contained.

Specified by:

countFeatures in interface FeatureHolder

Overrides:

countFeatures in class SimpleSequence

Returns:

a positive integer or zero, equal to the number of features contained

filter

public FeatureHolder filter(FeatureFilter ff)

Description copied from interface: FeatureHolder

Query this set of features using a supplied FeatureFilter.

Specified by:

filter in interface FeatureHolder

Overrides:

filter in class SimpleSequence

Parameters:

ff - the FeatureFilter to apply.

Returns:

all features in this container which match filter.

filter

public FeatureHolder filter(FeatureFilter ff,
                            boolean recurse)

Description copied from interface: FeatureHolder

Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.

Specified by:

filter in interface FeatureHolder

Overrides:

filter in class SimpleSequence

Parameters:

ff - the FeatureFilter to apply

recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.

containsFeature

public boolean containsFeature(Feature f)

containsFeature() will return true if this seq contains the feature in question, or if if the original (non reverse complement) sequence contains the feature;

Specified by:

containsFeature in interface FeatureHolder

Overrides:

containsFeature in class SimpleSequence

Parameters:

f - the Feature to check

Returns:

true if f is in this set

removeFeature

public void removeFeature(Feature f)
                   throws ChangeVetoException,
                          BioException

Description copied from class: SimpleSequence

Remove a feature attached to this sequence.

Specified by:

removeFeature in interface FeatureHolder

Overrides:

removeFeature in class SimpleSequence

Throws:

ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed

BioException - if there was an error removing the feature

createFeature

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

createFeature() will call createFeature() on the underlying Sequence. returns the feature as it will be projected onto the reverse complement sequence not the actual feature that was created.

Specified by:

createFeature in interface FeatureHolder

Overrides:

createFeature in class SimpleSequence

Throws:

ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed

BioException - if something went wrong during creating the feature

getFeatureFromOriginal

public Feature getFeatureFromOriginal(Feature f)

getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence. (which is not projected) and do something with that such as createFeature().

clone

public Object clone()

clone() should make a complete copy of the Sequence with all features (and children) and return a SimpleSequence that is unconnected from the original sequence.

Overrides:

clone in class Object