org.biojava.bio.seq

Class SimpleAssembly

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.SimpleAssembly

All Implemented Interfaces:

Annotatable, FeatureHolder, RealizingFeatureHolder, Sequence, SymbolList, Changeable

public class SimpleAssembly
extends AbstractChangeable
implements Sequence, RealizingFeatureHolder

A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.

There is still some potential for optimising SymbolList operations on this class.

Since:

1.1

Author:

Thomas Down, Matthew Pocock

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

Modifier and Type	Field and Description
protected ChangeForwarder	annotationForwarder

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
SimpleAssembly(int length, String name, String uri) Construct a new SimpleAssembly using the DNA alphabet.
SimpleAssembly(String name, String uri) Construct a new SimpleAssembly using the DNA alphabet.

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 temp) Create a new Feature, and add it to this FeatureHolder.
void	edit(Edit e) 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 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.
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
Annotation	getAnnotation() Should return the associated annotation object.
protected ChangeSupport	getChangeSupport(ChangeType ct) Called to retrieve the ChangeSupport for this 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 fh, Feature.Template temp) Realize a feature template.
void	removeFeature(Feature f) Remove a feature from this FeatureHolder.
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 pos) Return the symbol at index, counting from 1.
List	toList() Returns a List of symbols.

Methods inherited from class org.biojava.utils.AbstractChangeable

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

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

Field Detail

annotationForwarder

protected transient ChangeForwarder annotationForwarder

Constructor Detail

SimpleAssembly

public SimpleAssembly(int length,
              String name,
              String uri)

Construct a new SimpleAssembly using the DNA alphabet. Initially, the sequence will just contain a list of `N's. Sequence data can be added by adding one or more ComponentFeatures.

Parameters:

length - The length of the sequence

name - The name of the sequence (returned by getName())

uri - The identifier of the sequence (returned by getURN());

SimpleAssembly

public SimpleAssembly(String name,
              String uri)

Construct a new SimpleAssembly using the DNA alphabet. Initially, the sequence will just contain a list of `N's. Sequence data can be added by adding one or more ComponentFeatures.

Parameters:

name - The name of the sequence (returned by getName())

uri - The identifier of the sequence (returned by getURN());

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

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

symbolAt

public Symbol symbolAt(int pos)

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

pos - the offset into this SymbolList

Returns:

the Symbol at that index

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

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

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

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

edit

public void edit(Edit e)
          throws IllegalAlphabetException,
                 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:

e - the Edit to perform

Throws:

IllegalAlphabetException - if the SymbolList to insert has an incompatible alphabet

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

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

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

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

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

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.

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.

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

createFeature

public Feature createFeature(Feature.Template temp)
                      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

removeFeature

public void removeFeature(Feature f)
                   throws ChangeVetoException

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

realizeFeature

public Feature realizeFeature(FeatureHolder fh,
                     Feature.Template temp)
                       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

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable

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