Package org.biojava.bio.seq.impl

Class SimpleGappedSequence

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.symbol.SimpleGappedSymbolList

org.biojava.bio.seq.impl.SimpleGappedSequence

All Implemented Interfaces:

Serializable, Annotatable, FeatureHolder, GappedSequence, Sequence, GappedSymbolList, SymbolList, Changeable

public class SimpleGappedSequence
extends SimpleGappedSymbolList
implements GappedSequence

Simple implementation of GappedSequence. Please note that this is a view onto another Sequence. Gaps created and removed are only in the view not the underlying original. This means that any gaps present in the original cannot be manipulated in this view. To manipulate the original you would need to use Edit objects.

Since:

1.3

Author:

Thomas Down, Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	SimpleGappedSequence.GappedContext

Nested classes/interfaces inherited from class org.biojava.bio.symbol.SimpleGappedSymbolList

SimpleGappedSymbolList.Block

Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList

AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater

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.Annotatable

ANNOTATION

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

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

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

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor	Description
SimpleGappedSequence(GappedSequence seq)
SimpleGappedSequence(Sequence seq)
SimpleGappedSequence(Alphabet alpha)

Method Summary

Modifier and Type	Method	Description
boolean	containsFeature(Feature f)	Check if the feature is present in this holder.
int	countFeatures()	Count how many features are contained.
Feature	createFeature(Feature.Template templ)	Create a new Feature, and add it to this FeatureHolder.
Iterator<Feature>	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.
Annotation	getAnnotation()	Should return the associated annotation object.
boolean	getCreateOnUnderlyingSequence()
String	getName()	The name of this sequence.
FeatureFilter	getSchema()	Return a schema-filter for this FeatureHolder.
String	getURN()	A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
void	removeFeature(Feature f)	Remove a feature from this FeatureHolder.
void	setCreateOnUnderlyingSequence(boolean underlying)

Methods inherited from class org.biojava.bio.symbol.SimpleGappedSymbolList

addGapInSource, addGapInView, addGapsInSource, addGapsInView, BlockIterator, dumpBlocks, findSourceBlock, findSourceGap, findViewBlock, findViewGap, firstNonGap, gappedToLocation, getAlphabet, getSourceSymbolList, getUngappedLocation, isSane, lastNonGap, length, locationToGapped, removeGap, removeGaps, renumber, sourceToView, sourceToView, symbolAt, viewToSource, viewToSource

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList

edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

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

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

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

addGapInSource, addGapInView, addGapsInSource, addGapsInView, firstNonGap, getSourceSymbolList, getUngappedLocation, lastNonGap, removeGap, removeGaps, sourceToView, viewToSource

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

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

Constructor Detail

SimpleGappedSequence

public SimpleGappedSequence(Alphabet alpha)

SimpleGappedSequence

public SimpleGappedSequence(Sequence seq)

SimpleGappedSequence

public SimpleGappedSequence(GappedSequence seq)

Method Detail

getCreateOnUnderlyingSequence

public boolean getCreateOnUnderlyingSequence()

setCreateOnUnderlyingSequence

public void setCreateOnUnderlyingSequence(boolean underlying)

getAnnotation

public Annotation getAnnotation()

Description copied from interface: Annotatable

Should return the associated annotation object.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

getName

public String getName()

Description copied from interface: Sequence

The name of this sequence.

The name may contain spaces or odd characters.

Specified by:

getName in interface Sequence

Returns:

the name as a String

getURN

public String getURN()

Description copied from interface: Sequence

A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. For sequences in well-known database, this may be a URN, e.g.

 urn:sequence/embl:AL121903
 

It may also be a URL identifying a specific resource, either locally or over the network

 file:///home/thomas/myseq.fa|seq22
 http://www.mysequences.net/chr22.seq
 

Specified by:

getURN in interface Sequence

Returns:

the URI as a String

features

public Iterator<Feature> features()

Description copied from interface: FeatureHolder

Iterate over the features in no well defined order.

Specified by:

features in interface FeatureHolder

Returns:

an Iterator

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

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

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.

countFeatures

public int countFeatures()

Description copied from interface: FeatureHolder

Count how many features are contained.

Specified by:

countFeatures in interface FeatureHolder

Returns:

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

containsFeature

public boolean containsFeature(Feature f)

Description copied from interface: FeatureHolder

Check if the feature is present in this holder.

Specified by:

containsFeature in interface FeatureHolder

Parameters:

f - the Feature to check

Returns:

true if f is in this set

getSchema

public FeatureFilter getSchema()

Description copied from interface: FeatureHolder

Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

Specified by:

getSchema in interface FeatureHolder

Returns:

the schema filter

removeFeature

public void removeFeature(Feature f)
                   throws ChangeVetoException,
                          BioException

Description copied from interface: FeatureHolder

Remove a feature from this FeatureHolder.

Specified by:

removeFeature in interface FeatureHolder

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 templ)
                      throws ChangeVetoException,
                             BioException

Description copied from interface: FeatureHolder

Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.

Specified by:

createFeature in interface FeatureHolder

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