org.biojava.bio.seq.impl

Class ViewSequence

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.impl.ViewSequence

All Implemented Interfaces:

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

Direct Known Subclasses:

CircularView

public class ViewSequence
extends Unchangeable
implements Sequence, RealizingFeatureHolder, Serializable

A view onto another Sequence object. This class allows new features and annotations to be overlaid onto an existing Sequence without modifying it. You will almost certainly want to be calling SequenceTools.view(Sequence seq) instead of instantiating this class directly.

Author:

Thomas Down, Matthew Pocock

See Also:

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
ViewSequence(Sequence seq) Construct a view onto an existing sequence which takes on that sequence's name.
ViewSequence(Sequence seq, FeatureRealizer fr) Construct a view onto a sequence, using a specific FeatureRealizer.
ViewSequence(Sequence seq, String name) Construct a view onto an existing sequence and give it a new name.

Method Summary

Methods

Modifier and Type	Method and 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 template) Create a new Feature, and add it to this FeatureHolder.
void	edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
Iterator	features() Iterate over the features in no well defined order.
FeatureHolder	filter(FeatureFilter fc) Query this set of features using a supplied FeatureFilter.
FeatureHolder	filter(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
FeatureHolder	getAddedFeatures()
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
Annotation	getAnnotation() Should return the associated annotation object.
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.
Iterator	iterator() An Iterator over all Symbols in this SymbolList.
int	length() The number of symbols in this SymbolList.
Feature	realizeFeature(FeatureHolder parent, Feature.Template template) Realize a feature template.
void	removeFeature(Feature f) Remove a feature from this sequence.
String	seqString() Stringify this symbol list.
SymbolList	subList(int start, int end) Return a new SymbolList for the symbols start to end inclusive.
String	subStr(int start, int end) Return a region of this symbol list as a String.
Symbol	symbolAt(int indx) Return the symbol at index, counting from 1.
List	toList() Returns a List of symbols.

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

ViewSequence

public ViewSequence(Sequence seq,
            String name)

Construct a view onto an existing sequence and give it a new name.

The prefered method is SequenceTools.view(Sequence seq, String name)

ViewSequence

public ViewSequence(Sequence seq)

Construct a view onto an existing sequence which takes on that sequence's name.

The prefered method is SequenceTools.view(Sequence seq)

ViewSequence

public ViewSequence(Sequence seq,
            FeatureRealizer fr)

Construct a view onto a sequence, using a specific FeatureRealizer.

The prefered method is SequenceTools.view(Sequence seq, FeatureRealizer fr)

Method Detail

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: SymbolList

The alphabet that this SymbolList is over.

Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

Specified by:

getAlphabet in interface SymbolList

Returns:

the alphabet

iterator

public Iterator iterator()

Description copied from interface: SymbolList

An Iterator over all Symbols in this SymbolList.

This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.

Specified by:

iterator in interface SymbolList

Returns:

an iterator

length

public int length()

Description copied from interface: SymbolList

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

seqString

public String seqString()

Description copied from interface: SymbolList

Stringify this symbol list.

It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.

Specified by:

seqString in interface SymbolList

Returns:

a string representation of the symbol list

subStr

public String subStr(int start,
            int end)

Description copied from interface: SymbolList

Return a region of this symbol list as a String.

This should use the same rules as seqString.

Specified by:

subStr in interface SymbolList

Parameters:

start - the first symbol to include

end - the last symbol to include

Returns:

the string representation

subList

public SymbolList subList(int start,
                 int end)

Description copied from interface: SymbolList

Return a new SymbolList for the symbols start to end inclusive.

The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.

Specified by:

subList in interface SymbolList

Parameters:

start - the first symbol of the new SymbolList

end - the last symbol (inclusive) of the new SymbolList

symbolAt

public Symbol symbolAt(int indx)

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

indx - the offset into this SymbolList

Returns:

the Symbol at that index

toList

public List toList()

Description copied from interface: SymbolList

Returns a List of symbols.

This is an immutable list of symbols. Do not edit it.

Specified by:

toList in interface SymbolList

Returns:

a List of Symbols

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

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

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

features

public Iterator 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 fc,
                   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:

fc - 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.

filter

public FeatureHolder filter(FeatureFilter fc)

Description copied from interface: FeatureHolder

Query this set of features using a supplied FeatureFilter.

Specified by:

filter in interface FeatureHolder

Parameters:

fc - the FeatureFilter to apply.

Returns:

all features in this container which match filter.

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

Remove a feature from this sequence. NOTE: This method will only succeed for features which were added to this ViewSequence. Trying to remove a Feature from the underlying sequence will cause an IllegalArgumentException. I think this is the correct behaviour.

Specified by:

removeFeature in interface FeatureHolder

Throws:

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

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

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

realizeFeature

public Feature realizeFeature(FeatureHolder parent,
                     Feature.Template template)
                       throws BioException

Description copied from interface: RealizingFeatureHolder

Realize a feature template. This will be a template which has been passed to the createFeature method of either this FeatureHolder or one of our child Features.

Specified by:

realizeFeature in interface RealizingFeatureHolder

Throws:

BioException

createFeature

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

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:

BioException - if something went wrong during creating the feature

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

getAddedFeatures

public FeatureHolder getAddedFeatures()

edit

public void edit(Edit edit)
          throws ChangeVetoException

Description copied from interface: SymbolList

Apply an edit to the SymbolList as specified by the edit object.

Description

All edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.

When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).

The pos and pos+length should always be valid positions on the SymbolList to:

• be edited (between 0 and symL.length()+1).
• To append to a sequence, pos=symL.length()+1, pos=0.
• To insert something at the beginning of the sequence, set pos=1 and length=0.

Examples

 SymbolList seq = DNATools.createDNA("atcaaaaacgctagc");
 System.out.println(seq.seqString());

 // delete 5 bases from position 4
 Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
 seq.edit(ed);
 System.out.println(seq.seqString());

 // delete one base from the start
 ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
 seq.edit(ed);

 // delete one base from the end
 ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
 seq.edit(ed);
 System.out.println(seq.seqString());

 // overwrite 2 bases from position 3 with "tt"
 ed = new Edit(3, 2, DNATools.createDNA("tt"));
 seq.edit(ed);
 System.out.println(seq.seqString());

 // add 6 bases to the start
 ed = new Edit(1, 0, DNATools.createDNA("aattgg");
 seq.edit(ed);
 System.out.println(seq.seqString());

 // add 4 bases to the end
 ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
 seq.edit(ed);
 System.out.println(seq.seqString());

 // full edit
 ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
 seq.edit(ed);
 System.out.println(seq.seqString());
 

Specified by:

edit in interface SymbolList

Parameters:

edit - the Edit to perform

Throws:

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